From 55536fbb30024b7037049913a36577d85e9d3cf2 Mon Sep 17 00:00:00 2001
From: donkirkby <donkirkby@gmail.com>
Date: Fri, 23 Jul 2021 17:16:32 -0700
Subject: [PATCH 01/47] Add HIVIntact analysis, for #10.

---
 Singularity                         | 19 +++++++++++++++
 gene_splicer/primer_finder.py       | 37 +++++++++++++++++++++++++----
 gene_splicer/primer_finder_class.py |  2 +-
 gene_splicer/sample.py              | 18 +++++++++++---
 gene_splicer/study_summary.py       | 13 +++++++---
 5 files changed, 78 insertions(+), 11 deletions(-)

diff --git a/Singularity b/Singularity
index d938b8e..5f18945 100644
--- a/Singularity
+++ b/Singularity
@@ -28,6 +28,9 @@ From: ubuntu:22.04
         fontconfig libbz2-dev liblzma-dev libssl-dev \
         libffi-dev libsqlite3-dev
 
+    echo ===== Installing MAFFT ===== >/dev/null
+    apt-get install -y mafft
+
     echo ===== Installing Python ===== >/dev/null
     apt-get install -y python3 python3-pip
 
@@ -35,6 +38,8 @@ From: ubuntu:22.04
     apt-get install -y ncbi-blast+
 
     echo ===== Installing Python packages ===== >/dev/null
+    pip3 install git+https://github.com/cfe-lab/HIVIntact@cfe-1.2
+
     cd /opt/primer_finder
     pip3 install .
 
@@ -55,3 +60,17 @@ From: ubuntu:22.04
 
 %runscript
     gene_splicer_sample --hivseqinr /opt/hivseqinr "$@"
+
+%apprun hivintact
+    gene_splicer_sample --hivintact "$@"
+
+%apphelp hivintact
+    Search proviral consensus sequences for primers, then use HIVIntact to
+    decide if the genomes are complete.
+
+%applabels hivintact
+    KIVE_INPUTS sample_info_csv contigs_csv conseqs_csv cascade_csv
+    KIVE_OUTPUTS outcome_summary_csv conseqs_primers_csv contigs_primers_csv \
+        table_precursor_csv hivseqinr_results_tar
+    KIVE_THREADS 1
+    KIVE_MEMORY 200
diff --git a/gene_splicer/primer_finder.py b/gene_splicer/primer_finder.py
index dbb741e..62dbdcc 100644
--- a/gene_splicer/primer_finder.py
+++ b/gene_splicer/primer_finder.py
@@ -1,4 +1,5 @@
 import re
+import subprocess
 from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter, FileType
 from csv import DictReader, DictWriter
 from itertools import groupby
@@ -77,6 +78,9 @@ def parse_args():
                         help="Path to HIVSeqinR source code, or download "
                              "destination. HIVSeqinR will be skipped if this "
                              "isn't given.")
+    parser.add_argument('--hivintact',
+                        action='store_true',
+                        help="Launch the HIVIntact analysis.")
     parser.add_argument(
         '--nodups',
         action='store_false',
@@ -386,8 +390,8 @@ def add_primers(row):
 def remove_primers(row):
     # Strip the primers out, convert index values from floats.
     newseq = row.sequence[
-             int(row.fwd_sample_primer_size + row.fwd_sample_primer_start)
-             :-int(row.rev_sample_primer_size + row.rev_sample_primer_start)]
+             int(row.fwd_sample_primer_size + row.fwd_sample_primer_start):
+             -int(row.rev_sample_primer_size + row.rev_sample_primer_start)]
     row.sequence = newseq
     return row
 
@@ -422,6 +426,13 @@ def archive_hivseqinr_results(working_path: Path,
         archive.add(result_path, result_path.name)
 
 
+def archive_hivintact_results(working_path: Path,
+                              hivintact_results_tar: typing.IO):
+    archive = TarFile(fileobj=hivintact_results_tar, mode='w')
+    for result_path in working_path.iterdir():
+        archive.add(result_path, result_path.name)
+
+
 def run(contigs_csv,
         conseqs_csv,
         cascade_csv,
@@ -433,7 +444,9 @@ def run(contigs_csv,
         sample_size=50,
         force_all_proviral=False,
         default_sample_name: str = None,
-        hivseqinr_results_tar: typing.IO = None):
+        hivseqinr_results_tar: typing.IO = None,
+        run_hivintact: bool = False,
+        hivintact_results_tar: typing.IO = None):
     all_samples = utils.get_samples_from_cascade(cascade_csv,
                                                  default_sample_name)
 
@@ -517,6 +530,21 @@ def run(contigs_csv,
                 if hivseqinr_results_tar is not None:
                     archive_hivseqinr_results(working_path,
                                               hivseqinr_results_tar)
+            if run_hivintact:
+                working_path: Path = outpath / f'hivintact_{i}'
+                working_path.mkdir(exist_ok=True)
+                with (working_path / 'hiv-intact.log').open('w') as log_file:
+                    subprocess.run(['proviral',
+                                    'intact',
+                                    '--subtype=B',
+                                    str(no_primers_fasta)],
+                                   check=True,
+                                   stdout=log_file,
+                                   stderr=subprocess.STDOUT,
+                                   cwd=working_path)
+                if hivintact_results_tar is not None:
+                    archive_hivintact_results(working_path,
+                                              hivintact_results_tar)
             files.append(no_primers_fasta)
     return files
 
@@ -531,7 +559,8 @@ def main():
                       hivseqinr=args.hivseqinr,
                       nodups=args.nodups,
                       split=args.split,
-                      sample_size=args.sample_size)
+                      sample_size=args.sample_size,
+                      run_hivintact=args.hivintact)
     return {'fasta_files': fasta_files, 'args': args}
 
 
diff --git a/gene_splicer/primer_finder_class.py b/gene_splicer/primer_finder_class.py
index d5f8cd5..a4f5cf9 100644
--- a/gene_splicer/primer_finder_class.py
+++ b/gene_splicer/primer_finder_class.py
@@ -144,7 +144,7 @@ def get_slices(self):
             hxb2_slice = utils.hxb2[self.hxb2_start -
                                     self.validation_size:self.hxb2_end]
         if len(sample_slice) == 0:
-            logger.debug(\
+            logger.debug(
                 'Sample slice size is 0! \n'
                 f'start: {self.start} \n'
                 f'end: {self.end} \n'
diff --git a/gene_splicer/sample.py b/gene_splicer/sample.py
index 5e49fb9..858782b 100644
--- a/gene_splicer/sample.py
+++ b/gene_splicer/sample.py
@@ -44,7 +44,8 @@ def parse_args():
                         help='Data for proviral landscape plot',
                         type=FileType('w'))
     parser.add_argument('hivseqinr_results_tar',
-                        help="Archive file with HIVSeqinR's final results folder.",
+                        help="Archive file with HIVSeqinR's final results "
+                             "folder, or HIVIntact's results.",
                         type=FileType('wb'))
     parser.add_argument(
         '-p',
@@ -57,6 +58,9 @@ def parse_args():
                         help="Path to HIVSeqinR source code, or download "
                              "destination. HIVSeqinR will be skipped if this "
                              "isn't given.")
+    parser.add_argument('--hivintact',
+                        action='store_true',
+                        help="Launch the HIVIntact analysis.")
     parser.add_argument(
         '--nodups',
         action='store_false',
@@ -88,10 +92,16 @@ def main():
         info_reader = DictReader(args.sample_info_csv)
         sample_info: dict = next(info_reader)
     run_name = sample_info.get('run_name', 'kive_run')
+    if args.hivintact:
+        hivseqinr_results_tar = None
+        hivintact_results_tar = args.hivseqinr_results_tar
+    else:
+        hivseqinr_results_tar = args.hivseqinr_results_tar
+        hivintact_results_tar = None
     fasta_files = primer_finder.run(contigs_csv=args.contigs_csv,
                                     conseqs_csv=args.conseqs_csv,
                                     cascade_csv=args.cascade_csv,
-                                    hivseqinr_results_tar=args.hivseqinr_results_tar,
+                                    hivseqinr_results_tar=hivseqinr_results_tar,
                                     name=run_name,
                                     outpath=outpath,
                                     hivseqinr=args.hivseqinr,
@@ -99,7 +109,9 @@ def main():
                                     split=args.split,
                                     sample_size=args.sample_size,
                                     force_all_proviral=True,
-                                    default_sample_name=sample_info['sample'])
+                                    default_sample_name=sample_info['sample'],
+                                    run_hivintact=args.hivintact,
+                                    hivintact_results_tar=hivintact_results_tar)
     for file in fasta_files:
         gene_splicer.run(file, outdir=outpath)
     utils.generate_table_precursor(name=run_name, outpath=outpath)
diff --git a/gene_splicer/study_summary.py b/gene_splicer/study_summary.py
index 74a5652..45efe1f 100644
--- a/gene_splicer/study_summary.py
+++ b/gene_splicer/study_summary.py
@@ -43,6 +43,10 @@ def parse_args():
                              'the runs in samples_csv. Any samples not found '
                              'in samples.csv will guess the participant id '
                              'from the first part of the sample name.')
+    parser.add_argument('--hivintact',
+                        action='store_true',
+                        help="Launch the HIVIntact analysis instead of "
+                             "HIVSeqinR.")
     return parser.parse_args()
 
 
@@ -197,7 +201,7 @@ def write_warnings(self, report_file: typing.TextIO, limit: int = None):
                   file=report_file)
 
 
-def run_gene_splicer(run_path: Path, outcome_folder: Path):
+def run_gene_splicer(run_path: Path, outcome_folder: Path, run_hivintact: bool):
     version_results_path = run_path / 'Results' / 'version_7.14'
     assert version_results_path.exists(), version_results_path
     denovo_path = version_results_path / 'denovo'
@@ -214,11 +218,14 @@ def run_gene_splicer(run_path: Path, outcome_folder: Path):
     pipeline_args = [python_path,
                      '-m', 'gene_splicer.pipeline',
                      '--outpath', str(outcome_folder),
-                     '--hivseqinr', str(hivseqinr_path),
                      contigs_path,
                      conseq_path,
                      cascade_path,
                      short_run_name]
+    if run_hivintact:
+        pipeline_args.append('--hivintact')
+    else:
+        pipeline_args.append(f'--hivseqinr={hivseqinr_path}')
     try:
         with log_path.open('w') as log_file:
             run(pipeline_args,
@@ -259,7 +266,7 @@ def main():
                 print('Missing denovo results:', run_path)
                 continue
             else:
-                run_gene_splicer(run_path, outcome_path.parent)
+                run_gene_splicer(run_path, outcome_path.parent, args.hivintact)
                 assert outcome_path.exists(), outcome_path
                 print('.', end='', flush=True)
                 dots_printed = True

From 1d549872a50e211d86d098f1cce747c61f4e603d Mon Sep 17 00:00:00 2001
From: donkirkby <donkirkby@gmail.com>
Date: Mon, 26 Jul 2021 11:45:00 -0700
Subject: [PATCH 02/47] Install mafft and blast in GitHub Actions, for #10.

---
 .github/workflows/python-app.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index a4e8adf..8a9e0d6 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -24,6 +24,7 @@ jobs:
         echo /opt/minimap2-2.17_x64-linux >> $GITHUB_PATH
     - name: Install dependencies
       run: |
+        sudo apt install -qq mafft ncbi-blast+
         python -m pip install --upgrade pip pipenv
         pipenv install --dev
     - name: Test with pytest

From 6b77caceeac9446d6ea464528bf06a8ae92049f8 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 19 May 2023 15:48:19 -0700
Subject: [PATCH 03/47] Enable more checks in HIVIntact

---
 gene_splicer/primer_finder.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/gene_splicer/primer_finder.py b/gene_splicer/primer_finder.py
index 62dbdcc..8027440 100644
--- a/gene_splicer/primer_finder.py
+++ b/gene_splicer/primer_finder.py
@@ -537,6 +537,12 @@ def run(contigs_csv,
                     subprocess.run(['proviral',
                                     'intact',
                                     '--subtype=B',
+                                    '--run-hypermut',
+                                    '--check-long-deletion',
+                                    '--check-nonhiv',
+                                    '--check-scramble',
+                                    '--check-internal-inversion',
+                                    '--include-small-orfs',
                                     str(no_primers_fasta)],
                                    check=True,
                                    stdout=log_file,

From 28ae510236da3918130090da3ea21046cacf6db2 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 14 Jul 2023 13:54:52 -0700
Subject: [PATCH 04/47] Specify writable workdir for hivintact

---
 gene_splicer/primer_finder.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gene_splicer/primer_finder.py b/gene_splicer/primer_finder.py
index 8027440..6a631cb 100644
--- a/gene_splicer/primer_finder.py
+++ b/gene_splicer/primer_finder.py
@@ -536,6 +536,7 @@ def run(contigs_csv,
                 with (working_path / 'hiv-intact.log').open('w') as log_file:
                     subprocess.run(['proviral',
                                     'intact',
+                                    '--working-folder', working_path,
                                     '--subtype=B',
                                     '--run-hypermut',
                                     '--check-long-deletion',

From 9aadb156b992bf58e1b4e3b5a5af916e4f264f4f Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 5 Jun 2023 11:32:27 -0700
Subject: [PATCH 05/47] Update dependencies in the README file

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index fa27f8d..718ae86 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,7 @@
 1. minimap2 (https://github.com/lh3/minimap2) (must be available via commandline)
 2. blast tools (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
 3. R and RSCRIPT (https://www.r-project.org/)
+4. mafft (https://mafft.cbrc.jp/alignment/software/)
 
 ### Singularity builds
 * Build all singularity images inside of the `simages` folder

From 7cfd902c61efde1d4f4704fae23bac21768fb562 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 5 Jun 2023 12:58:56 -0700
Subject: [PATCH 06/47] Add HIVIntact to our python dependencies

---
 Pipfile      |   1 +
 Pipfile.lock | 188 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 setup.py     |   1 +
 3 files changed, 187 insertions(+), 3 deletions(-)

diff --git a/Pipfile b/Pipfile
index a039031..a9d403d 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,6 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
+intactness-pipeline = {ref = "cfe-1.2", git = "https://github.com/cfe-lab/HIVIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index 5bc34d3..aed6c1c 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "73432848a2ff11546bd4d06f2cabd2c46876a987e2d0a9e8c0d379cdfd9eb4f5"
+            "sha256": "100f2cea5bdbda87105a66b042daed34e24cc3e092e8382794b6f03c5553b02d"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -16,6 +16,43 @@
         ]
     },
     "default": {
+        "appdirs": {
+            "hashes": [
+                "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41",
+                "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"
+            ],
+            "version": "==1.4.4"
+        },
+        "biopython": {
+            "hashes": [
+                "sha256:11d673698b3d0d6589292ea951fb62cb24ea27d273eca0d08dbbd956690f97f5",
+                "sha256:2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0",
+                "sha256:2f9cfaf16d55ab80d514e7aebe5710dabe4e4ff47ede851031202e33b3249da3",
+                "sha256:35506e39822c52d11cf09a3951e82375ca1bb9303960b4286acf02c9a6f6c4cc",
+                "sha256:3b36ba1bf6395c09a365c53530c9d71f3617763fa2c1d452b3d8948368c0f1de",
+                "sha256:655df416936662c0c8a06a549cb25e1560e1fea5067d850f34fb714b8a3fae6c",
+                "sha256:65b93b513ce9dd7b2ce058720eadf42cd03f312db3409356efeb93123d1320aa",
+                "sha256:6ebfbce0d91796c7aef422ee9dffe8827e07e5abaa94545e006f1f20e965c80b",
+                "sha256:762c6c43a8486b5fcd07f136a3217b87d24755618b9ea9da1f17124ff44c2ad6",
+                "sha256:793c42a376cd63f62f8a088ce39b7dc6b5c55e4e9031d887c434de1595bfa4b8",
+                "sha256:7a168709694e10b338718c18d967edd5b56c237dc88642c22275796007a70000",
+                "sha256:7c5c07123ff5f44c9e6b5369df854a38afd3c0c50ef58498a0ae8f7eb799f3e8",
+                "sha256:811796f8d222aa3869a50e31e54ce62b69106b47cd8bb06934867c0d843297b5",
+                "sha256:8bb0c690c7368f255ed45236bf0f5464b476b8c083c8f634533921af78278261",
+                "sha256:919a2c583cabf9c96d2ae4e1245a6b0376932fb342aca302a0fc198b71ab3275",
+                "sha256:97cbdbed01b2512471f36c74b91658d1dfbdcbf39bc038f6ce5a41c3e60a8fc6",
+                "sha256:9ba33244f0eff830beaa7240065bdb5095d96fded6599b76bbb9ddab45cd2bbd",
+                "sha256:a51d9c1d1b4b634447535da74a644fae59bc234fbbf9001e2dc6b6fbabb98019",
+                "sha256:b09efcb4733c8770f25eab5fe555a96a08f5ab9e1bc36939e08ebf2ffbf3e0f1",
+                "sha256:b37c0d24191e5c96ca02415a5188551980c83a0d518bbc4ffe3c9a5d1fe0ee81",
+                "sha256:ccd729249fd5f586dd4c2a3507c2ea2456825d7e615e97c07c409c850eaf4594",
+                "sha256:e41b55edcfd448630e77bf4de66a7235324a8a149621499891da6bd1d5085b9a",
+                "sha256:ee51bb1cd7decffd24da6b76d5e01b7e2fd818ab85cf0c180226cbb5793a3abd",
+                "sha256:ef7c79b65b0b3f3c7dc59e20a7f8ae5758d8e852cb8b9cace590dc5617e348ba"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==1.81"
+        },
         "certifi": {
             "hashes": [
                 "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7",
@@ -105,6 +142,14 @@
             "markers": "python_full_version >= '3.7.0'",
             "version": "==3.2.0"
         },
+        "click": {
+            "hashes": [
+                "sha256:48ee849951919527a045bfe3bf7baa8a959c423134e1a5b98c05c20ba75a1cbd",
+                "sha256:fa244bb30b3b5ee2cae3da8f55c9e5e0c0e86093306301fb418eb9dc40fbded5"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==8.1.6"
+        },
         "gotoh": {
             "git": "https://github.com/cfe-lab/MiCall.git",
             "ref": "f1687e7b7c7f1f3a6f3cb63107f1cf9b2b210f26",
@@ -118,6 +163,118 @@
             "markers": "python_version >= '3.5'",
             "version": "==3.4"
         },
+        "intactness-pipeline": {
+            "git": "https://github.com/cfe-lab/HIVIntact",
+            "ref": "14f571d873131d2521a6bddcefbf795914ac78c7"
+        },
+        "jarowinkler": {
+            "hashes": [
+                "sha256:07df473a812772794181885fc8e9950b629809297c8a1c00e06d0376cb6f5611",
+                "sha256:0dd61e79babfbca37f6f4d2b81bfbc92979e5e22f02d04ba5e762d84901a95bf",
+                "sha256:1097b349e09c6ae2d92520ef0ab79580b6b136f6f1c1d62ad783595011f0f260",
+                "sha256:18da76d3a6d7a0898f36525a1ce8303fcb5413d1bcbc30c3f3634344aeecf397",
+                "sha256:18e3af57ac066a617bd688d62b9d0da11da32dca977d9fe5c1726040be26ad2e",
+                "sha256:1b243a43ef1740bdec3101243347ceb59f698f28df0c514935f4cf856af22795",
+                "sha256:21869871774ea4a34222538c33704234ee8e1b4c1a82fe95471215994575e631",
+                "sha256:21ae65449c52b14578fd28f51c2efdd976a632979054cf12e714cc86fdc1d1aa",
+                "sha256:28654c3cfd1f917900a44650cee3a6827210c1f1783ef5aca3399ee31ee2cd17",
+                "sha256:288c615134ec2d5d122fb834eb0e134f5ccd0080ce1091e2f8170d861de4c24d",
+                "sha256:298c708bd8609b0563846cd770891f4fc6492ea1c09ef7ac24a68731f4ede37a",
+                "sha256:2daa79de5856d34ee6a813d9b049d55aad7014a92ce1d90fb3e487338ec362ef",
+                "sha256:3af4e4aab7c6ba14f75bd74a21ee00befed67cd2221e626c5741545b4a57c60c",
+                "sha256:439d66dd82a452535293c2503a0930c2aacc4ebf9542f0ca52b351084e9f3e32",
+                "sha256:447c9b1323e7b16ff21da9121164b54c4a806f352f716b2a6e1f937acabc6e73",
+                "sha256:46e042d75ee91e1fe678ad0bdb6eea4d6d052f6e6ee35adac8bf5d01942e1f6a",
+                "sha256:49796215bd66bb87d2d88da7131b785330b3b2e50cbd7a7be75b4964512f5aa9",
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+                "sha256:91ccb6b51cff6158a7f699e0912ab243b7f0026d63919a7696214303e709a21e",
+                "sha256:93cb99fc11b44db61631eea23294f6ae66e944d27129b2856e52f66f11eb8082",
+                "sha256:967a10aed9fca73b826ab41d859ac6a35021ac39efeea5991070964db10a9b13",
+                "sha256:97175ef8bf47e796280c899c8d72788313e277a30cd5c4a549bbab60ce70e5f5",
+                "sha256:9b2c89b9893c2c0fb1c7369160e2a08258415df5345019dd61c3e15c2ca74b65",
+                "sha256:9bd54d4635bc9d01510fff1545b4ec1e26bddafde0aff6af1af4e46b80407e9e",
+                "sha256:9f968112e0b8be55b259e041be1f9f294931c8790f014c5c04f7c1ffe7928b78",
+                "sha256:a03972d2878e6954852ffce67a843de8a30c515eaa257313b609151e16036bab",
+                "sha256:a3f03c8178b94380e103c9368e84b88bfca437e59e484dc71d8b059d43c6e8dc",
+                "sha256:a71063e01863f561d86459929ad7c5f6c389922aada4170b67ab7c266e6cf96c",
+                "sha256:aa12fa8a788804fca8fde0f24c14015f3adf18b2336adb66526e326c15b59c72",
+                "sha256:ae3b951ff925a5c1fc7746845d796ce34891313813f6c3bc2d057759c8090c47",
+                "sha256:aea994d5673e9c3b49d548b58f961448bd8a2ba40d3244c1809c891ed29daa02",
+                "sha256:af28ea284cfbd1b21b29ff94b759f20e94e4f7c06f424b0b4702e701c2a21668",
+                "sha256:b24b58bd62de20cc773b0b55352d0a43d6cf2beb9b0a21bbaf5ca1f6f50d3d44",
+                "sha256:b29a7adb25bf02f1e007fec412a67a5c3c8de1ba062454de539e623eb638fcaf",
+                "sha256:b39b7cdb985f6c040830f047cd98a0563bbfa909944130223c23667432b39c73",
+                "sha256:b56248ab6e734b40309b6337b0de5cb37e7f0e71d64c7f5f0d58bcb46c05699d",
+                "sha256:b59b4e82ade4b9b147646189b500f2085e06c8c7746dd6311e03bc4d4ad126e8",
+                "sha256:b696f0f80df13e8e86958a9d0eaa9218a6a311b5c566f6a081ef17d7d594713b",
+                "sha256:b73bba435e9cd7618130907d753c708c84baddec5ee6e2637f9630f02496b189",
+                "sha256:b91d6fe7fd12c5d3bb82b644500df13ee0f7ae949f067e6d967be896aa340732",
+                "sha256:b959d3fcf4ffe865ee518328d77d137ea7b6ad0c8f1f8b96b7a08cd97d3a9c87",
+                "sha256:bbb94c0d894cde960b264f3f797c99cbe316e0280ea1b81e240d6ee4ec19fa0c",
+                "sha256:bc0dcc31ce493aa70067e1f7ed2cb1528b8bd86bb276f25b6c09fabf746b3df7",
+                "sha256:bc8182ba6561a19eddbbd88106b986b93ae11205919cea36385a260d2146c638",
+                "sha256:c0eac3a71193575002e2c374ff7be5ef4005e9370c29dad83e2537f57d09e07e",
+                "sha256:c1f3e5d5137419a608a878b76ec277c1618119259134ef94e323d5e7fdc2acfd",
+                "sha256:c834dd86fc4f372c0cd6ec7a33432e49e644de7b5d37f520b96500cab7e9d992",
+                "sha256:cba8a789610e97d29c850370c6c8f68c0481355446a356bfa0b2703d8afb8436",
+                "sha256:d2cf546b18f9d49d25f33dd564c06fbe29c0e3090d062bad84ba04e77fc7d168",
+                "sha256:d2debc08e15e6c16999c27c1afc4c2493c0d3f140206d24970872f4619ea840a",
+                "sha256:d4638b6b4569e418365aa12d8175025b93336bb074288ec8b9b259734da9990e",
+                "sha256:d5399e513b58496483eeda61ff180676fc6ff9c3b6ef53af3c53be0777e71247",
+                "sha256:d6648d9c68bcc79f80092fa00e9f897df12b9826f05b7211260b494742ae3e12",
+                "sha256:d8da4660934bbf3958e6bd0165ab088d6e65ef6cee0c52d82e86d424ca1be96f",
+                "sha256:da09cbcbb917d99fb341730dbb7892b7a642ef0ca371c7f3a647b4dae6770190",
+                "sha256:db49e56139da097b5d85f323b1ed906a5d9d6d3a4336ce694910852d0a4cd607",
+                "sha256:dd1cd8a99f7f3347d3b30941460531a0ee8b855f199a3b56ac6d49aa98266600",
+                "sha256:e2d2c6341b021b146db418c77ee71d4318013074761681aba42c1d332a723f7d",
+                "sha256:e36a5af0db07010e3cc70000edebc2cdb92c39beb2d10d721604a7a52c48100d",
+                "sha256:e3edd98b7fa078b06b1bd0e12d7e244c875e7030ad242eb31719f2f87e343862",
+                "sha256:e40905895ddbce8cbdc5f079299371630e771db3c0e7820b2d262c4bb6a8bea0",
+                "sha256:e480e39ed2420a881ac445f6fea8064c36f535970deb4ee94677afe06985b917",
+                "sha256:e68cb387d79871b45d20a670bdd33b0f9edb08ed85aa7a5eb19dafdecfa1c091",
+                "sha256:e8c6dba59166803347c96f48e1af608f8bbc8efe9d545e1a3f9bfb526e76fd62",
+                "sha256:eaa520f9b4e6e955269a117d7481332b06aff3fb04981fd218294793ba4ae5fc",
+                "sha256:ef39035486ce07745a0fee9dd80bd9a0b692811111da4ef9aedbc0ddd23ff9cd",
+                "sha256:f2afe56a6cb3e84cc77af6e4a1e8eb6f4f6211a8dd0468237aeee27e16501752",
+                "sha256:f8dd58576c81e8115ca29dc757feb413fd689d194789670a533384997306385e",
+                "sha256:fa1db18ba0a0fe383e9396e2db91d31fcabfc0ff03fa599b5a10edc57416084a",
+                "sha256:fa2d76d3572229ad282dd7ed0005387e9085bdfd954a7636a6f920530e3b670d",
+                "sha256:fa55d91bcf097b464df6efa92762434aa3026a9774ab2509895a1948bf64b121",
+                "sha256:fbcb4aafadf3ac758de12deb3c90c4e4b6497a104d00ecc8cb6585757af3ab90",
+                "sha256:fd4b9111a2092eaaaabd7dd33aa8703d734075a2f75ec87976eab0a2b60273ac"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==1.2.3"
+        },
         "numpy": {
             "hashes": [
                 "sha256:012097b5b0d00a11070e8f2e261128c44157a8689f7dedcf35576e525893f4fe",
@@ -185,7 +342,7 @@
                 "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86",
                 "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==2.8.2"
         },
         "python-levenshtein": {
@@ -256,6 +413,31 @@
             "index": "pypi",
             "version": "==2.31.0"
         },
+        "scipy": {
+            "hashes": [
+                "sha256:08d957ca82d3535b3b9ba6c8ff355d78fe975271874e2af267cb5add5bd78625",
+                "sha256:249cfa465c379c9bb2c20123001e151ff5e29b351cbb7f9c91587260602c58d0",
+                "sha256:366a6a937110d80dca4f63b3f5b00cc89d36f678b2d124a01067b154e692bab1",
+                "sha256:39154437654260a52871dfde852adf1b93b1d1bc5dc0ffa70068f16ec0be2624",
+                "sha256:396fae3f8c12ad14c5f3eb40499fd06a6fef8393a6baa352a652ecd51e74e029",
+                "sha256:3b9963798df1d8a52db41a6fc0e6fa65b1c60e85d73da27ae8bb754de4792481",
+                "sha256:3e8eb42db36526b130dfbc417609498a6192381abc1975b91e3eb238e0b41c1a",
+                "sha256:512fdc18c65f76dadaca139348e525646d440220d8d05f6d21965b8d4466bccd",
+                "sha256:aec8c62fbe52914f9cf28d846cf0401dd80ab80788bbab909434eb336ed07c04",
+                "sha256:b41a0f322b4eb51b078cb3441e950ad661ede490c3aca66edef66f4b37ab1877",
+                "sha256:b4bb943010203465ac81efa392e4645265077b4d9e99b66cf3ed33ae12254173",
+                "sha256:b588311875c58d1acd4ef17c983b9f1ab5391755a47c3d70b6bd503a45bfaf71",
+                "sha256:ba94eeef3c9caa4cea7b402a35bb02a5714ee1ee77eb98aca1eed4543beb0f4c",
+                "sha256:be8c962a821957fdde8c4044efdab7a140c13294997a407eaee777acf63cbf0c",
+                "sha256:cce154372f0ebe88556ed06d7b196e9c2e0c13080ecb58d0f35062dc7cc28b47",
+                "sha256:d51565560565a0307ed06fa0ec4c6f21ff094947d4844d6068ed04400c72d0c3",
+                "sha256:e866514bc2d660608447b6ba95c8900d591f2865c07cca0aa4f7ff3c4ca70f30",
+                "sha256:fb5b492fa035334fd249f0973cc79ecad8b09c604b42a127a677b45a9a3d4289",
+                "sha256:ffb28e3fa31b9c376d0fb1f74c1f13911c8c154a760312fbee87a21eb21efe31"
+            ],
+            "markers": "python_version < '3.13' and python_version >= '3.9'",
+            "version": "==1.11.1"
+        },
         "setuptools": {
             "hashes": [
                 "sha256:11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f",
@@ -269,7 +451,7 @@
                 "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926",
                 "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==1.16.0"
         },
         "tzdata": {
diff --git a/setup.py b/setup.py
index 069adcc..8fc0cd8 100644
--- a/setup.py
+++ b/setup.py
@@ -10,6 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
+        'intactness-pipeline @ git+https://github.com/cfe-lab/HIVIntact.git@cfe-1.2',
         'pyyaml'
     ],
     package_data={

From 7f4eba1267a313ee602ae51548006b8eaaea964e Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 9 Jun 2023 09:13:19 -0700
Subject: [PATCH 07/47] Generate table_precursor table from hivintact output

---
 gene_splicer/utils.py | 78 ++++++++++++++++++++++++++++++++++++-------
 1 file changed, 66 insertions(+), 12 deletions(-)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index b01b5bd..c11ab20 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -5,6 +5,7 @@
 import typing
 
 import yaml
+import json
 import shutil
 import subprocess as sp
 import pandas as pd
@@ -391,14 +392,54 @@ def align(target_seq,
         return alignment_path
 
 
-def generate_table_precursor(name, outpath, add_columns=None):
-    # Output csv
-    precursor_path: Path = outpath / 'table_precursor.csv'
+HIVINTACT_TRANSLATION_TABLE = {
+    'APOBECHypermutationDetected': 'Hypermut',
+    'LongDeletion': 'LargeDeletion',
+    'PackagingSignalDeletion': '5DEFECT',
+    'WrongORFNumber': 'PrematureStop_OR_AAtooLong_OR_AAtooShort',
+    }
 
-    # Load filtered sequences
-    filtered_path = outpath / (name + '_filtered.csv')
-    filtered = pd.read_csv(filtered_path)
-    # Load hivseqinr data
+def translate_hivintact_error(error):
+    return HIVINTACT_TRANSLATION_TABLE.get(error, error)
+
+HIVINTACT_ERRORS_TABLE = [
+    'NonHIV',
+    'LongDeletion',
+    'Scramble',
+    'InternalInversion',
+    'APOBECHypermutationDetected',
+    'MisplacedORF',
+    'WrongORFNumber',
+    'DeletionInOrf',
+    'FrameshiftInOrf',
+    'MajorSpliceDonorSiteMutated',
+    'PackagingSignalDeletion',
+    'PackagingSignalNotComplete',
+    'RevResponseElementDeletion',
+    ]
+
+def iterate_hivintact_data(name, outpath):
+    for d in glob.glob(str(outpath / 'hivintact*')):
+        for (SEQID, sequence) in read_fasta(os.path.join(d, 'intact.fasta')):
+            row = [SEQID, 'Intact']
+            yield row
+
+        with open(os.path.join(d, 'errors.json'), 'r') as f:
+            js = json.load(f)
+            for SEQID in js:
+                all_errors = [obj.get('error') for obj in js[SEQID] if 'error' in obj]
+                if all_errors:
+                    ordered = sorted(all_errors, key=HIVINTACT_ERRORS_TABLE.index)
+                    verdict = translate_hivintact_error(ordered[0])
+                    row = [SEQID, verdict]
+                    yield row
+
+def get_hivintact_data(name, outpath):
+    column_names = ['SEQID', 'MyVerdict']
+    data = iterate_hivintact_data(name, outpath)
+    return pd.DataFrame(data, columns=column_names)
+
+def get_hivseqinr_data(name, outpath):
     seqinr_paths = glob.glob(
         str(outpath / 'hivseqinr*' / 'Results_Final' /
             'Output_MyBigSummary_DF_FINAL.csv'))
@@ -409,13 +450,26 @@ def generate_table_precursor(name, outpath, add_columns=None):
         part = pd.read_csv(path)
         parts.append(part)
     # seqinr = pd.read_csv(seqinr_path)
+    return pd.concat(parts)
+
+def generate_table_precursor(name, outpath, add_columns=None):
+    # Output csv
+    precursor_path: Path = outpath / 'table_precursor.csv'
+
+    # Load filtered sequences
+    filtered_path = outpath / (name + '_filtered.csv')
+    filtered = pd.read_csv(filtered_path)
+    # Load hivseqinr data or HIVIntact results
+    results = get_hivintact_data(name, outpath)
+    if results.empty:
+        results = get_hivseqinr_data(name, outpath)
+
     try:
-        seqinr = pd.concat(parts)
         # Assign new columns based on split
-        seqinr[['name', 'sample', 'reference',
-                'seqtype']] = seqinr['SEQID'].str.split('::', expand=True)
+        results[['name', 'sample', 'reference',
+                'seqtype']] = results['SEQID'].str.split('::', expand=True)
         # Merge
-        merged = seqinr.merge(filtered, on='sample')
+        merged = results.merge(filtered, on='sample')
     except ValueError:
         with precursor_path.open('w') as output_file:
             writer = DictWriter(output_file,
@@ -448,7 +502,7 @@ def generate_table_precursor(name, outpath, add_columns=None):
     if add_columns:
         for key, val in add_columns.items():
             merged[key] = val
-    if parts:
+    if not results.empty:
         merged[['sample', 'sequence', 'MyVerdict'] + genes_of_interest].to_csv(
             precursor_path, index=False)
     else:

From 891b4a88a980baab635196020eda6ad838be139f Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 9 Jun 2023 10:17:38 -0700
Subject: [PATCH 08/47] Remember intact sequences

---
 gene_splicer/utils.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index c11ab20..d92a4e0 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -419,14 +419,17 @@ def translate_hivintact_error(error):
     ]
 
 def iterate_hivintact_data(name, outpath):
+    intact = {}
     for d in glob.glob(str(outpath / 'hivintact*')):
         for (SEQID, sequence) in read_fasta(os.path.join(d, 'intact.fasta')):
             row = [SEQID, 'Intact']
+            intact[SEQID] = True
             yield row
 
         with open(os.path.join(d, 'errors.json'), 'r') as f:
             js = json.load(f)
             for SEQID in js:
+                if SEQID in intact: continue
                 all_errors = [obj.get('error') for obj in js[SEQID] if 'error' in obj]
                 if all_errors:
                     ordered = sorted(all_errors, key=HIVINTACT_ERRORS_TABLE.index)

From b88c4e40f501021f92169b67d7bc471ff14bd67a Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 23 Jun 2023 17:32:42 -0700
Subject: [PATCH 09/47] Update hivintact errors list

---
 gene_splicer/utils.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index d92a4e0..f576034 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -411,6 +411,8 @@ def translate_hivintact_error(error):
     'MisplacedORF',
     'WrongORFNumber',
     'DeletionInOrf',
+    'InsertionInOrf',
+    'InternalStopInOrf',
     'FrameshiftInOrf',
     'MajorSpliceDonorSiteMutated',
     'PackagingSignalDeletion',

From 0bca5bebf7f7c1f2be0b051bb0736280f378eebd Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 30 Jun 2023 12:11:30 -0700
Subject: [PATCH 10/47] Improve hivintact errors priority and translation

---
 gene_splicer/utils.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index f576034..b5f65b6 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -396,6 +396,8 @@ def align(target_seq,
     'APOBECHypermutationDetected': 'Hypermut',
     'LongDeletion': 'LargeDeletion',
     'PackagingSignalDeletion': '5DEFECT',
+    'PackagingSignalNotComplete': '5DEFECT',
+    'MajorSpliceDonorSiteMutated': '5DEFECT',
     'WrongORFNumber': 'PrematureStop_OR_AAtooLong_OR_AAtooShort',
     }
 
@@ -405,19 +407,19 @@ def translate_hivintact_error(error):
 HIVINTACT_ERRORS_TABLE = [
     'NonHIV',
     'LongDeletion',
-    'Scramble',
     'InternalInversion',
+    'Scramble',
     'APOBECHypermutationDetected',
+    'MajorSpliceDonorSiteMutated',
+    'PackagingSignalDeletion',
+    'PackagingSignalNotComplete',
+    'RevResponseElementDeletion',
     'MisplacedORF',
     'WrongORFNumber',
     'DeletionInOrf',
     'InsertionInOrf',
     'InternalStopInOrf',
     'FrameshiftInOrf',
-    'MajorSpliceDonorSiteMutated',
-    'PackagingSignalDeletion',
-    'PackagingSignalNotComplete',
-    'RevResponseElementDeletion',
     ]
 
 def iterate_hivintact_data(name, outpath):

From 6ad62bd35d5cd738aa95ca173162acd75cbb8655 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 21 Jul 2023 14:26:37 -0700
Subject: [PATCH 11/47] Bump HIVIntact from cfe-1.2 to cfe-1.3

---
 Pipfile      | 2 +-
 Pipfile.lock | 8 ++++----
 Singularity  | 2 +-
 setup.py     | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/Pipfile b/Pipfile
index a9d403d..80785b2 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-intactness-pipeline = {ref = "cfe-1.2", git = "https://github.com/cfe-lab/HIVIntact"}
+intactness-pipeline = {ref = "cfe-1.3", git = "https://github.com/cfe-lab/HIVIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index aed6c1c..840919c 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "100f2cea5bdbda87105a66b042daed34e24cc3e092e8382794b6f03c5553b02d"
+            "sha256": "c5e8c3f18599c2490183a8f39736737ebf0b47821cc0908a613f2e95e8ee8684"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -165,7 +165,7 @@
         },
         "intactness-pipeline": {
             "git": "https://github.com/cfe-lab/HIVIntact",
-            "ref": "14f571d873131d2521a6bddcefbf795914ac78c7"
+            "ref": "2bb83a07b42e78a08c0f40a971d06f9393795717"
         },
         "jarowinkler": {
             "hashes": [
@@ -342,7 +342,7 @@
                 "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86",
                 "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
             "version": "==2.8.2"
         },
         "python-levenshtein": {
@@ -451,7 +451,7 @@
                 "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926",
                 "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
             "version": "==1.16.0"
         },
         "tzdata": {
diff --git a/Singularity b/Singularity
index 5f18945..83379d4 100644
--- a/Singularity
+++ b/Singularity
@@ -38,7 +38,7 @@ From: ubuntu:22.04
     apt-get install -y ncbi-blast+
 
     echo ===== Installing Python packages ===== >/dev/null
-    pip3 install git+https://github.com/cfe-lab/HIVIntact@cfe-1.2
+    pip3 install git+https://github.com/cfe-lab/HIVIntact@cfe-1.3
 
     cd /opt/primer_finder
     pip3 install .
diff --git a/setup.py b/setup.py
index 8fc0cd8..42a0f7d 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'intactness-pipeline @ git+https://github.com/cfe-lab/HIVIntact.git@cfe-1.2',
+        'intactness-pipeline @ git+https://github.com/cfe-lab/HIVIntact.git@cfe-1.3',
         'pyyaml'
     ],
     package_data={

From 7e15cf09e22e31f8b265ef09a8018f1dda7ec83e Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 21 Jul 2023 14:31:36 -0700
Subject: [PATCH 12/47] Generate proviral_landscape for HIVIntact runs too

---
 gene_splicer/sample.py | 2 +-
 gene_splicer/utils.py  | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/gene_splicer/sample.py b/gene_splicer/sample.py
index 858782b..8048830 100644
--- a/gene_splicer/sample.py
+++ b/gene_splicer/sample.py
@@ -115,7 +115,7 @@ def main():
     for file in fasta_files:
         gene_splicer.run(file, outdir=outpath)
     utils.generate_table_precursor(name=run_name, outpath=outpath)
-    utils.generate_proviral_landscape_csv(outpath)
+    utils.generate_proviral_landscape_csv(outpath, is_hivintact=args.hivintact)
     copy_output(outpath / 'outcome_summary.csv', args.outcome_summary_csv)
     copy_output(outpath / (run_name + '_conseqs_primer_analysis.csv'),
                 args.conseqs_primers_csv)
diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index b5f65b6..3f0ff15 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -558,12 +558,14 @@ def generate_table_precursor_2(hivseqinr_resultsfile, filtered_file,
     return table_precursorfile
 
 
-def generate_proviral_landscape_csv(outpath):
+def generate_proviral_landscape_csv(outpath, is_hivintact):
     proviral_landscape_csv = os.path.join(outpath, 'proviral_landscape.csv')
     landscape_rows = []
 
     table_precursor_csv = os.path.join(outpath, 'table_precursor.csv')
     blastn_csv = glob.glob(
+        os.path.join(outpath, 'hivintact*', 'blast.tsv') \
+        if is_hivintact else \
         os.path.join(
             outpath,
             'hivseqinr*',

From 719a14bc86c60819f54a605d5efc4a8d12763dfb Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 21 Jul 2023 14:01:52 -0700
Subject: [PATCH 13/47] Singularity: make HIVIntact the default and the only
 app

---
 Singularity | 22 +---------------------
 1 file changed, 1 insertion(+), 21 deletions(-)

diff --git a/Singularity b/Singularity
index 83379d4..b1bbae6 100644
--- a/Singularity
+++ b/Singularity
@@ -3,7 +3,7 @@ Bootstrap: docker
 From: ubuntu:22.04
 
 %help
-    Search proviral consensus sequences for primers, then use HIVSeqinR to
+    Search proviral consensus sequences for primers, then use HIVIntact to
     decide if the genomes are complete.
 
     This Singularity container can be run on Kive: http://cfe-lab.github.io/Kive
@@ -46,12 +46,6 @@ From: ubuntu:22.04
     echo ===== Installing minimap2 ===== >/dev/null
     apt-get install -y minimap2
 
-    echo ===== Installing hivseqinr ===== >/dev/null
-    apt-get install -y libz-dev libcurl4-openssl-dev libxml2-dev
-    DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y r-base
-    Rscript /opt/primer_finder/gene_splicer/configure_r.sh
-    python3 -m gene_splicer.hivseqinr /opt/hivseqinr
-
     # Clean up
     apt-get remove -y wget git build-essential
 
@@ -59,18 +53,4 @@ From: ubuntu:22.04
     export LANG=en_US.UTF-8
 
 %runscript
-    gene_splicer_sample --hivseqinr /opt/hivseqinr "$@"
-
-%apprun hivintact
     gene_splicer_sample --hivintact "$@"
-
-%apphelp hivintact
-    Search proviral consensus sequences for primers, then use HIVIntact to
-    decide if the genomes are complete.
-
-%applabels hivintact
-    KIVE_INPUTS sample_info_csv contigs_csv conseqs_csv cascade_csv
-    KIVE_OUTPUTS outcome_summary_csv conseqs_primers_csv contigs_primers_csv \
-        table_precursor_csv hivseqinr_results_tar
-    KIVE_THREADS 1
-    KIVE_MEMORY 200

From a1294dfa65823c91d1c414e38d75c45b432f95f4 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 21 Jul 2023 15:16:07 -0700
Subject: [PATCH 14/47] Switch to csv outputs in HIVIntact

---
 gene_splicer/primer_finder.py |  1 +
 gene_splicer/utils.py         | 36 +++++++++++++++++++++++++----------
 2 files changed, 27 insertions(+), 10 deletions(-)

diff --git a/gene_splicer/primer_finder.py b/gene_splicer/primer_finder.py
index 6a631cb..40a15f4 100644
--- a/gene_splicer/primer_finder.py
+++ b/gene_splicer/primer_finder.py
@@ -544,6 +544,7 @@ def run(contigs_csv,
                                     '--check-scramble',
                                     '--check-internal-inversion',
                                     '--include-small-orfs',
+                                    '--output-csv',
                                     str(no_primers_fasta)],
                                    check=True,
                                    stdout=log_file,
diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index 3f0ff15..d4fee4f 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -424,22 +424,38 @@ def translate_hivintact_error(error):
 
 def iterate_hivintact_data(name, outpath):
     intact = {}
+
+    def get_verdict(SEQID, all_errors):
+        ordered = sorted(all_errors, key=HIVINTACT_ERRORS_TABLE.index)
+        verdict = translate_hivintact_error(ordered[0])
+        return [SEQID, verdict]
+
     for d in glob.glob(str(outpath / 'hivintact*')):
         for (SEQID, sequence) in read_fasta(os.path.join(d, 'intact.fasta')):
             row = [SEQID, 'Intact']
             intact[SEQID] = True
             yield row
 
-        with open(os.path.join(d, 'errors.json'), 'r') as f:
-            js = json.load(f)
-            for SEQID in js:
-                if SEQID in intact: continue
-                all_errors = [obj.get('error') for obj in js[SEQID] if 'error' in obj]
-                if all_errors:
-                    ordered = sorted(all_errors, key=HIVINTACT_ERRORS_TABLE.index)
-                    verdict = translate_hivintact_error(ordered[0])
-                    row = [SEQID, verdict]
-                    yield row
+        sequence_name = None
+        with open(os.path.join(d, 'errors.csv'), 'r') as f:
+            reader = csv.DictReader(f)
+
+            last_name = None
+            all_errors = []
+            for row in reader:
+                sequence_name = row['sequence_name']
+                if sequence_name in intact: continue
+
+                if last_name != sequence_name and last_name is not None:
+                    if all_errors:
+                        yield get_verdict(sequence_name, all_errors)
+                        all_errors = []
+
+                all_errors.append(row['error'])
+                last_name = sequence_name
+
+        if all_errors:
+            yield get_verdict(sequence_name, all_errors)
 
 def get_hivintact_data(name, outpath):
     column_names = ['SEQID', 'MyVerdict']

From 5c378e9e06c08e55867daadd0118292dcca0d02d Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 21 Jul 2023 15:33:31 -0700
Subject: [PATCH 15/47] Rename "hivseqinr_results_tar" argument to
 "detailed_results_tar"

---
 Singularity            | 2 +-
 gene_splicer/sample.py | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Singularity b/Singularity
index b1bbae6..66611f3 100644
--- a/Singularity
+++ b/Singularity
@@ -13,7 +13,7 @@ From: ubuntu:22.04
     MAINTAINER BC CfE in HIV/AIDS https://github.com/cfe-lab/
     KIVE_INPUTS sample_info_csv contigs_csv conseqs_csv cascade_csv
     KIVE_OUTPUTS outcome_summary_csv conseqs_primers_csv contigs_primers_csv \
-        table_precursor_csv proviral_landscape_csv hivseqinr_results_tar
+        table_precursor_csv proviral_landscape_csv detailed_results_tar
     KIVE_THREADS 1
     KIVE_MEMORY 6000
 
diff --git a/gene_splicer/sample.py b/gene_splicer/sample.py
index 8048830..076ce3c 100644
--- a/gene_splicer/sample.py
+++ b/gene_splicer/sample.py
@@ -43,7 +43,7 @@ def parse_args():
     parser.add_argument('proviral_landscape_csv',
                         help='Data for proviral landscape plot',
                         type=FileType('w'))
-    parser.add_argument('hivseqinr_results_tar',
+    parser.add_argument('detailed_results_tar',
                         help="Archive file with HIVSeqinR's final results "
                              "folder, or HIVIntact's results.",
                         type=FileType('wb'))
@@ -73,7 +73,7 @@ def parse_args():
         help='To avoid memory issues in hivseqinr, split the resulting '
              'qc-passed sequences into this number of fastas, each will be '
              'processed sequentially and then all will be merged into the '
-             'final result')
+             'final result. Obsolete for HIVIntact.')
     return parser.parse_args()
 
 
@@ -94,9 +94,9 @@ def main():
     run_name = sample_info.get('run_name', 'kive_run')
     if args.hivintact:
         hivseqinr_results_tar = None
-        hivintact_results_tar = args.hivseqinr_results_tar
+        hivintact_results_tar = args.detailed_results_tar
     else:
-        hivseqinr_results_tar = args.hivseqinr_results_tar
+        hivseqinr_results_tar = args.detailed_results_tar
         hivintact_results_tar = None
     fasta_files = primer_finder.run(contigs_csv=args.contigs_csv,
                                     conseqs_csv=args.conseqs_csv,

From 56d06d90e8590789ea718446ff11835dafc3d8f6 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 19 Sep 2023 14:40:05 -0700
Subject: [PATCH 16/47] Bump HIVIntact from 1.3 to 1.4

---
 Pipfile               |   2 +-
 Pipfile.lock          | 224 ++++++++++++++++++++++--------------------
 Singularity           |   2 +-
 gene_splicer/utils.py |  42 ++++----
 setup.py              |   2 +-
 5 files changed, 142 insertions(+), 130 deletions(-)

diff --git a/Pipfile b/Pipfile
index 80785b2..bd1ed10 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-intactness-pipeline = {ref = "cfe-1.3", git = "https://github.com/cfe-lab/HIVIntact"}
+intactness-pipeline = {ref = "cfe-1.4", git = "https://github.com/cfe-lab/HIVIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index 840919c..05f6d7c 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "c5e8c3f18599c2490183a8f39736737ebf0b47821cc0908a613f2e95e8ee8684"
+            "sha256": "089fff873ef627ba4da8943f369d35baf072b48b4421d4d025abb17d951ffce8"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -55,11 +55,11 @@
         },
         "certifi": {
             "hashes": [
-                "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7",
-                "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"
+                "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082",
+                "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==2023.5.7"
+            "version": "==2023.7.22"
         },
         "charset-normalizer": {
             "hashes": [
@@ -144,11 +144,11 @@
         },
         "click": {
             "hashes": [
-                "sha256:48ee849951919527a045bfe3bf7baa8a959c423134e1a5b98c05c20ba75a1cbd",
-                "sha256:fa244bb30b3b5ee2cae3da8f55c9e5e0c0e86093306301fb418eb9dc40fbded5"
+                "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28",
+                "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==8.1.6"
+            "version": "==8.1.7"
         },
         "gotoh": {
             "git": "https://github.com/cfe-lab/MiCall.git",
@@ -165,7 +165,7 @@
         },
         "intactness-pipeline": {
             "git": "https://github.com/cfe-lab/HIVIntact",
-            "ref": "2bb83a07b42e78a08c0f40a971d06f9393795717"
+            "ref": "739478485deef5fecae47e89d2baaaa16b763aef"
         },
         "jarowinkler": {
             "hashes": [
@@ -342,7 +342,7 @@
                 "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86",
                 "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==2.8.2"
         },
         "python-levenshtein": {
@@ -354,14 +354,16 @@
         },
         "pytz": {
             "hashes": [
-                "sha256:1d8ce29db189191fb55338ee6d0387d82ab59f3d00eac103412d64e0ebd0c588",
-                "sha256:a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb"
+                "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b",
+                "sha256:ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7"
             ],
-            "version": "==2023.3"
+            "version": "==2023.3.post1"
         },
         "pyyaml": {
             "hashes": [
+                "sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5",
                 "sha256:062582fca9fabdd2c8b54a3ef1c978d786e0f6b3a1510e0ac93ef59e0ddae2bc",
+                "sha256:0d3304d8c0adc42be59c5f8a4d9e3d7379e6955ad754aa9d6ab7a398b59dd1df",
                 "sha256:1635fd110e8d85d55237ab316b5b011de701ea0f29d07611174a1b42f1444741",
                 "sha256:184c5108a2aca3c5b3d3bf9395d50893a7ab82a38004c8f61c258d4428e80206",
                 "sha256:18aeb1bf9a78867dc38b259769503436b7c72f7a1f1f4c93ff9a17de54319b27",
@@ -369,7 +371,10 @@
                 "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62",
                 "sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98",
                 "sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696",
+                "sha256:326c013efe8048858a6d312ddd31d56e468118ad4cdeda36c719bf5bb6192290",
+                "sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9",
                 "sha256:42f8152b8dbc4fe7d96729ec2b99c7097d656dc1213a3229ca5383f973a5ed6d",
+                "sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6",
                 "sha256:4fb147e7a67ef577a588a0e2c17b6db51dda102c71de36f8549b6816a96e1867",
                 "sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47",
                 "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486",
@@ -377,9 +382,12 @@
                 "sha256:596106435fa6ad000c2991a98fa58eeb8656ef2325d7e158344fb33864ed87e3",
                 "sha256:6965a7bc3cf88e5a1c3bd2e0b5c22f8d677dc88a455344035f03399034eb3007",
                 "sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938",
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                 "sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c",
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                 "sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d",
+                "sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28",
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                 "sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5",
@@ -394,7 +402,9 @@
                 "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43",
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                 "sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673",
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                 "sha256:d858aa552c999bc8a8d57426ed01e40bef403cd8ccdd0fc5f6f04a00414cac2a",
+                "sha256:e7d73685e87afe9f3b36c799222440d6cf362062f78be1013661b00c5c6f678b",
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                 "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c",
@@ -415,43 +425,49 @@
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             "markers": "python_version < '3.13' and python_version >= '3.9'",
-            "version": "==1.11.1"
+            "version": "==1.11.2"
         },
         "setuptools": {
             "hashes": [
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-            "markers": "python_version >= '3.7'",
-            "version": "==68.0.0"
+            "markers": "python_version >= '3.8'",
+            "version": "==68.2.2"
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         "six": {
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-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==1.16.0"
         },
         "tzdata": {
@@ -474,77 +490,69 @@
     "develop": {
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+                "sha256:ac3c5b7e75acac31e490b7851595212ed951889918d398b7afa12736c85e13ce",
+                "sha256:ac9ad38204887349853d7c313f53a7b1c210ce138c73859e925bc4e5d8fc18e7",
+                "sha256:b9c0c19f70d30219113b18fe07e372b244fb2a773d4afde29d5a2f7930765136",
+                "sha256:c397c70cd20f6df7d2a52283857af622d5f23300c4ca8e5bd8c7a543825baa5a",
+                "sha256:c6601a60318f9c3945be6ea0f2a80571f4299b6801716f8a6e4846892737ebe4",
+                "sha256:c6f55d38818ca9596dc9019eae19a47410d5322408140d9a0076001a3dcb938c",
+                "sha256:ca70466ca3a17460e8fc9cea7123c8cbef5ada4be3140a1ef8f7b63f2f37108f",
+                "sha256:ca833941ec701fda15414be400c3259479bfde7ae6d806b69e63b3dc423b1832",
+                "sha256:cd0f7429ecfd1ff597389907045ff209c8fdb5b013d38cfa7c60728cb484b6e3",
+                "sha256:cd694e19c031733e446c8024dedd12a00cda87e1c10bd7b8539a87963685e969",
+                "sha256:cdd088c00c39a27cfa5329349cc763a48761fdc785879220d54eb785c8a38520",
+                "sha256:de30c1aa80f30af0f6b2058a91505ea6e36d6535d437520067f525f7df123887",
+                "sha256:defbbb51121189722420a208957e26e49809feafca6afeef325df66c39c4fdb3",
+                "sha256:f09195dda68d94a53123883de75bb97b0e35f5f6f9f3aa5bf6e496da718f0cb6",
+                "sha256:f12d8b11a54f32688b165fd1a788c408f927b0960984b899be7e4c190ae758f1",
+                "sha256:f1a317fdf5c122ad642db8a97964733ab7c3cf6009e1a8ae8821089993f175ff",
+                "sha256:f2781fd3cabc28278dc982a352f50c81c09a1a500cc2086dc4249853ea96b981",
+                "sha256:f4f456590eefb6e1b3c9ea6328c1e9fa0f1006e7481179d749b3376fc793478e"
             ],
             "index": "pypi",
-            "version": "==7.2.7"
+            "version": "==7.3.1"
         },
         "exceptiongroup": {
             "hashes": [
-                "sha256:12c3e887d6485d16943a309616de20ae5582633e0a2eda17f4e10fd61c1e8af5",
-                "sha256:e346e69d186172ca7cf029c8c1d16235aa0e04035e5750b4b95039e65204328f"
+                "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9",
+                "sha256:343280667a4585d195ca1cf9cef84a4e178c4b6cf2274caef9859782b567d5e3"
             ],
             "markers": "python_version < '3.11'",
-            "version": "==1.1.2"
+            "version": "==1.1.3"
         },
         "iniconfig": {
             "hashes": [
@@ -564,19 +572,19 @@
         },
         "pluggy": {
             "hashes": [
-                "sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849",
-                "sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3"
+                "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12",
+                "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"
             ],
-            "markers": "python_version >= '3.7'",
-            "version": "==1.2.0"
+            "markers": "python_version >= '3.8'",
+            "version": "==1.3.0"
         },
         "pytest": {
             "hashes": [
-                "sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32",
-                "sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a"
+                "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002",
+                "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"
             ],
             "index": "pypi",
-            "version": "==7.4.0"
+            "version": "==7.4.2"
         },
         "tomli": {
             "hashes": [
diff --git a/Singularity b/Singularity
index 66611f3..018d4df 100644
--- a/Singularity
+++ b/Singularity
@@ -38,7 +38,7 @@ From: ubuntu:22.04
     apt-get install -y ncbi-blast+
 
     echo ===== Installing Python packages ===== >/dev/null
-    pip3 install git+https://github.com/cfe-lab/HIVIntact@cfe-1.3
+    pip3 install git+https://github.com/cfe-lab/HIVIntact@cfe-1.4
 
     cd /opt/primer_finder
     pip3 install .
diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index d4fee4f..e088a31 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -580,7 +580,7 @@ def generate_proviral_landscape_csv(outpath, is_hivintact):
 
     table_precursor_csv = os.path.join(outpath, 'table_precursor.csv')
     blastn_csv = glob.glob(
-        os.path.join(outpath, 'hivintact*', 'blast.tsv') \
+        os.path.join(outpath, 'hivintact*', 'blast.csv') \
         if is_hivintact else \
         os.path.join(
             outpath,
@@ -590,25 +590,29 @@ def generate_proviral_landscape_csv(outpath, is_hivintact):
         )
     )[0]
 
-    blastn_columns = ['qseqid',
-                      'qlen',
-                      'sseqid',
-                      'sgi',
-                      'slen',
-                      'qstart',
-                      'qend',
-                      'sstart',
-                      'send',
-                      'evalue',
-                      'bitscore',
-                      'length',
-                      'pident',
-                      'nident',
-                      'btop',
-                      'stitle',
-                      'sstrand']
     with open(blastn_csv, 'r') as blastn_file:
-        blastn_reader = DictReader(blastn_file, fieldnames=blastn_columns, delimiter='\t')
+        if is_hivintact:
+            blastn_reader = DictReader(blastn_file)
+        else:
+            blastn_columns = ['qseqid',
+                              'qlen',
+                              'sseqid',
+                              'sgi',
+                              'slen',
+                              'qstart',
+                              'qend',
+                              'sstart',
+                              'send',
+                              'evalue',
+                              'bitscore',
+                              'length',
+                              'pident',
+                              'nident',
+                              'btop',
+                              'stitle',
+                              'sstrand']
+            blastn_reader = DictReader(blastn_file, fieldnames=blastn_columns, delimiter='\t')
+
         for row in blastn_reader:
             if row['qseqid'] in ['8E5LAV', 'HXB2']:
                 # skip the positive control rows
diff --git a/setup.py b/setup.py
index 42a0f7d..299c967 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'intactness-pipeline @ git+https://github.com/cfe-lab/HIVIntact.git@cfe-1.3',
+        'intactness-pipeline @ git+https://github.com/cfe-lab/HIVIntact.git@cfe-1.4',
         'pyyaml'
     ],
     package_data={

From eae7b0f32dd789d7becf721dad7c0754f183d3b1 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 19 Sep 2023 16:43:22 -0700
Subject: [PATCH 17/47] Do not translate HIVIntact errors to HIVSeqinR ones

---
 gene_splicer/utils.py | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index e088a31..19cfa0f 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -391,19 +391,6 @@ def align(target_seq,
     else:
         return alignment_path
 
-
-HIVINTACT_TRANSLATION_TABLE = {
-    'APOBECHypermutationDetected': 'Hypermut',
-    'LongDeletion': 'LargeDeletion',
-    'PackagingSignalDeletion': '5DEFECT',
-    'PackagingSignalNotComplete': '5DEFECT',
-    'MajorSpliceDonorSiteMutated': '5DEFECT',
-    'WrongORFNumber': 'PrematureStop_OR_AAtooLong_OR_AAtooShort',
-    }
-
-def translate_hivintact_error(error):
-    return HIVINTACT_TRANSLATION_TABLE.get(error, error)
-
 HIVINTACT_ERRORS_TABLE = [
     'NonHIV',
     'LongDeletion',
@@ -427,7 +414,7 @@ def iterate_hivintact_data(name, outpath):
 
     def get_verdict(SEQID, all_errors):
         ordered = sorted(all_errors, key=HIVINTACT_ERRORS_TABLE.index)
-        verdict = translate_hivintact_error(ordered[0])
+        verdict = ordered[0]
         return [SEQID, verdict]
 
     for d in glob.glob(str(outpath / 'hivintact*')):

From 775f10078018ee54254092b4b939a8f59ab432aa Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 19 Sep 2023 17:12:30 -0700
Subject: [PATCH 18/47] Fix table precursor construction

---
 gene_splicer/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index 19cfa0f..8a4df3e 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -435,7 +435,7 @@ def get_verdict(SEQID, all_errors):
 
                 if last_name != sequence_name and last_name is not None:
                     if all_errors:
-                        yield get_verdict(sequence_name, all_errors)
+                        yield get_verdict(last_name, all_errors)
                         all_errors = []
 
                 all_errors.append(row['error'])

From 120fe49aaef16ee63bf2622a5e556dec62ecba7f Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 19 Sep 2023 17:13:24 -0700
Subject: [PATCH 19/47] Add missing codes to the HIVINACT_ERRORS_TABLE

---
 gene_splicer/utils.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index 8a4df3e..5ec660e 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -392,6 +392,8 @@ def align(target_seq,
         return alignment_path
 
 HIVINTACT_ERRORS_TABLE = [
+    'AlignmentFailed',
+    'InvalidCodon',
     'NonHIV',
     'LongDeletion',
     'InternalInversion',

From 53672414d50951a05b4f6af5e2a2d06bfb4e6727 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Wed, 6 Mar 2024 18:27:21 -0800
Subject: [PATCH 20/47] fix the check for when to use HIVSeqinR results

---
 gene_splicer/utils.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index 5ec660e..87e6220 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -472,9 +472,13 @@ def generate_table_precursor(name, outpath, add_columns=None):
     filtered_path = outpath / (name + '_filtered.csv')
     filtered = pd.read_csv(filtered_path)
     # Load hivseqinr data or HIVIntact results
-    results = get_hivintact_data(name, outpath)
-    if results.empty:
+
+    if any(outpath.glob('hivintact*')):
+        results = get_hivintact_data(name, outpath)
+    elif any(outpath.glob('hivseqinr*')):
         results = get_hivseqinr_data(name, outpath)
+    else:
+        raise RuntimeError("Neither HIVIntact nor HIVSeqinR directory exists.")
 
     try:
         # Assign new columns based on split

From 95ae330a1dc7e0293adcec8e8e2aca1a1de4c1a8 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Wed, 6 Mar 2024 22:19:32 -0800
Subject: [PATCH 21/47] Various code improvements

---
 gene_splicer/utils.py | 51 ++++++++++++++++---------------------------
 1 file changed, 19 insertions(+), 32 deletions(-)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index 87e6220..a658b91 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -12,6 +12,8 @@
 import glob
 from pathlib import Path
 from csv import DictWriter, DictReader
+from itertools import groupby
+from operator import itemgetter
 
 logger = logging.getLogger(__name__)
 
@@ -412,39 +414,26 @@ def align(target_seq,
     ]
 
 def iterate_hivintact_data(name, outpath):
-    intact = {}
+    intact = set()
 
     def get_verdict(SEQID, all_errors):
         ordered = sorted(all_errors, key=HIVINTACT_ERRORS_TABLE.index)
         verdict = ordered[0]
         return [SEQID, verdict]
 
-    for d in glob.glob(str(outpath / 'hivintact*')):
+    for d in outpath.glob('hivintact*'):
         for (SEQID, sequence) in read_fasta(os.path.join(d, 'intact.fasta')):
-            row = [SEQID, 'Intact']
-            intact[SEQID] = True
-            yield row
+            yield [SEQID, 'Intact']
+            intact.add(SEQID)
 
-        sequence_name = None
         with open(os.path.join(d, 'errors.csv'), 'r') as f:
             reader = csv.DictReader(f)
+            grouped = groupby(reader, key=itemgetter('sequence_name'))
+            for sequence_name, errors in grouped:
+                if sequence_name not in intact:
+                    all_errors = [error['error'] for error in errors]
+                    yield get_verdict(sequence_name, all_errors)
 
-            last_name = None
-            all_errors = []
-            for row in reader:
-                sequence_name = row['sequence_name']
-                if sequence_name in intact: continue
-
-                if last_name != sequence_name and last_name is not None:
-                    if all_errors:
-                        yield get_verdict(last_name, all_errors)
-                        all_errors = []
-
-                all_errors.append(row['error'])
-                last_name = sequence_name
-
-        if all_errors:
-            yield get_verdict(sequence_name, all_errors)
 
 def get_hivintact_data(name, outpath):
     column_names = ['SEQID', 'MyVerdict']
@@ -572,16 +561,14 @@ def generate_proviral_landscape_csv(outpath, is_hivintact):
     landscape_rows = []
 
     table_precursor_csv = os.path.join(outpath, 'table_precursor.csv')
-    blastn_csv = glob.glob(
-        os.path.join(outpath, 'hivintact*', 'blast.csv') \
-        if is_hivintact else \
-        os.path.join(
-            outpath,
-            'hivseqinr*',
-            'Results_Intermediate',
-            'Output_Blastn_HXB2MEGA28_tabdelim.txt'
-        )
-    )[0]
+
+    if is_hivintact:
+        subpath = os.path.join(outpath, 'hivintact*', 'blast.csv')
+    else:
+        subpath = os.path.join(outpath, 'hivseqinr*', 'Results_Intermediate', 'Output_Blastn_HXB2MEGA28_tabdelim.txt')
+
+    blastn_csvs = glob.glob(subpath)
+    blastn_csv = blastn_csvs[0]
 
     with open(blastn_csv, 'r') as blastn_file:
         if is_hivintact:

From 9d725a12f15c068a5ac6512e5c1a57b9d6f95e3d Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 8 Jul 2024 14:08:02 -0700
Subject: [PATCH 22/47] Switch to CFEIntact

---
 Pipfile      | 2 +-
 Pipfile.lock | 4 ----
 Singularity  | 2 +-
 setup.py     | 2 +-
 4 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/Pipfile b/Pipfile
index bd1ed10..5ebd2cf 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-intactness-pipeline = {ref = "cfe-1.4", git = "https://github.com/cfe-lab/HIVIntact"}
+cfeintact = {ref = "v1.18.4", git = "https://github.com/cfe-lab/CFEIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index 05f6d7c..ffff191 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -163,10 +163,6 @@
             "markers": "python_version >= '3.5'",
             "version": "==3.4"
         },
-        "intactness-pipeline": {
-            "git": "https://github.com/cfe-lab/HIVIntact",
-            "ref": "739478485deef5fecae47e89d2baaaa16b763aef"
-        },
         "jarowinkler": {
             "hashes": [
                 "sha256:07df473a812772794181885fc8e9950b629809297c8a1c00e06d0376cb6f5611",
diff --git a/Singularity b/Singularity
index 018d4df..513dd05 100644
--- a/Singularity
+++ b/Singularity
@@ -38,7 +38,7 @@ From: ubuntu:22.04
     apt-get install -y ncbi-blast+
 
     echo ===== Installing Python packages ===== >/dev/null
-    pip3 install git+https://github.com/cfe-lab/HIVIntact@cfe-1.4
+    pip3 install git+https://github.com/cfe-lab/CFEIntact@v1.18.4
 
     cd /opt/primer_finder
     pip3 install .
diff --git a/setup.py b/setup.py
index 299c967..1ebaeb7 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'intactness-pipeline @ git+https://github.com/cfe-lab/HIVIntact.git@cfe-1.4',
+        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.18.4',
         'pyyaml'
     ],
     package_data={

From 1c5eca69d7be4587099a1ad65019b2092caeb58c Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 8 Jul 2024 14:09:58 -0700
Subject: [PATCH 23/47] Update Pipfile.lock

---
 Pipfile.lock | 581 ++++++++++++++++++++++-----------------------------
 1 file changed, 249 insertions(+), 332 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index ffff191..e378d44 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "089fff873ef627ba4da8943f369d35baf072b48b4421d4d025abb17d951ffce8"
+            "sha256": "6a9e94b9fb771cdbc70c29e68954211f6778ff1be83c9713a16fe72315bc5a16"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -16,131 +16,148 @@
         ]
     },
     "default": {
-        "appdirs": {
-            "hashes": [
-                "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41",
-                "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"
-            ],
-            "version": "==1.4.4"
+        "aligntools": {
+            "git": "git+https://github.com/cfe-lab/aligntools.git",
+            "ref": "94c65f42b8b2008de4259c837eda4e9378636cb3"
         },
         "biopython": {
             "hashes": [
-                "sha256:11d673698b3d0d6589292ea951fb62cb24ea27d273eca0d08dbbd956690f97f5",
-                "sha256:2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0",
-                "sha256:2f9cfaf16d55ab80d514e7aebe5710dabe4e4ff47ede851031202e33b3249da3",
-                "sha256:35506e39822c52d11cf09a3951e82375ca1bb9303960b4286acf02c9a6f6c4cc",
-                "sha256:3b36ba1bf6395c09a365c53530c9d71f3617763fa2c1d452b3d8948368c0f1de",
-                "sha256:655df416936662c0c8a06a549cb25e1560e1fea5067d850f34fb714b8a3fae6c",
-                "sha256:65b93b513ce9dd7b2ce058720eadf42cd03f312db3409356efeb93123d1320aa",
-                "sha256:6ebfbce0d91796c7aef422ee9dffe8827e07e5abaa94545e006f1f20e965c80b",
-                "sha256:762c6c43a8486b5fcd07f136a3217b87d24755618b9ea9da1f17124ff44c2ad6",
-                "sha256:793c42a376cd63f62f8a088ce39b7dc6b5c55e4e9031d887c434de1595bfa4b8",
-                "sha256:7a168709694e10b338718c18d967edd5b56c237dc88642c22275796007a70000",
-                "sha256:7c5c07123ff5f44c9e6b5369df854a38afd3c0c50ef58498a0ae8f7eb799f3e8",
-                "sha256:811796f8d222aa3869a50e31e54ce62b69106b47cd8bb06934867c0d843297b5",
-                "sha256:8bb0c690c7368f255ed45236bf0f5464b476b8c083c8f634533921af78278261",
-                "sha256:919a2c583cabf9c96d2ae4e1245a6b0376932fb342aca302a0fc198b71ab3275",
-                "sha256:97cbdbed01b2512471f36c74b91658d1dfbdcbf39bc038f6ce5a41c3e60a8fc6",
-                "sha256:9ba33244f0eff830beaa7240065bdb5095d96fded6599b76bbb9ddab45cd2bbd",
-                "sha256:a51d9c1d1b4b634447535da74a644fae59bc234fbbf9001e2dc6b6fbabb98019",
-                "sha256:b09efcb4733c8770f25eab5fe555a96a08f5ab9e1bc36939e08ebf2ffbf3e0f1",
-                "sha256:b37c0d24191e5c96ca02415a5188551980c83a0d518bbc4ffe3c9a5d1fe0ee81",
-                "sha256:ccd729249fd5f586dd4c2a3507c2ea2456825d7e615e97c07c409c850eaf4594",
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@@ -152,124 +169,17 @@
         },
         "gotoh": {
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@@ -300,6 +210,7 @@
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@@ -331,15 +242,16 @@
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@@ -350,10 +262,10 @@
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@@ -386,6 +298,7 @@
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@@ -409,6 +322,7 @@
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@@ -417,46 +331,47 @@
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+                "sha256:dbc5958cb471e5a5af41b0ddaea96a37e74ed289535e8deca404811f6cb0bc3d",
+                "sha256:ddbd2f9713a79e8e7242d7c51f1929611e991d855f414ca9996c20e44a895f7c",
+                "sha256:e16f3d6b491c48c5ae726308e6ab1e18ee830b4cdd6913f2d7f77354b33f91c8",
+                "sha256:e2afe743289273209c992075a5a4913e8d007d569a406ffed0bd080ea02b0633",
+                "sha256:e564c2cf45d2f44a9da56f4e3a26b2236504a496eb4cb0ca7221cd4cc7a9aca9",
+                "sha256:ed550e7442f278af76d9d65af48069f1fb84c9f745ae249c1a183c1e9d1b025c"
             ],
             "index": "pypi",
-            "version": "==7.3.1"
+            "markers": "python_version >= '3.8'",
+            "version": "==7.5.4"
         },
         "exceptiongroup": {
             "hashes": [
-                "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9",
-                "sha256:343280667a4585d195ca1cf9cef84a4e178c4b6cf2274caef9859782b567d5e3"
+                "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad",
+                "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"
             ],
             "markers": "python_version < '3.11'",
-            "version": "==1.1.3"
+            "version": "==1.2.1"
         },
         "iniconfig": {
             "hashes": [
@@ -560,27 +476,28 @@
         },
         "packaging": {
             "hashes": [
-                "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61",
-                "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"
+                "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002",
+                "sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124"
             ],
-            "markers": "python_version >= '3.7'",
-            "version": "==23.1"
+            "markers": "python_version >= '3.8'",
+            "version": "==24.1"
         },
         "pluggy": {
             "hashes": [
-                "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12",
-                "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"
+                "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1",
+                "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==1.3.0"
+            "version": "==1.5.0"
         },
         "pytest": {
             "hashes": [
-                "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002",
-                "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"
+                "sha256:c434598117762e2bd304e526244f67bf66bbd7b5d6cf22138be51ff661980343",
+                "sha256:de4bb8104e201939ccdc688b27a89a7be2079b22e2bd2b07f806b6ba71117977"
             ],
             "index": "pypi",
-            "version": "==7.4.2"
+            "markers": "python_version >= '3.8'",
+            "version": "==8.2.2"
         },
         "tomli": {
             "hashes": [

From 3a0bf9decc34514bf2b60bcac157603051820b76 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 8 Jul 2024 15:01:31 -0700
Subject: [PATCH 24/47] Update cfeintact command

---
 gene_splicer/primer_finder.py | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/gene_splicer/primer_finder.py b/gene_splicer/primer_finder.py
index 40a15f4..adf50b7 100644
--- a/gene_splicer/primer_finder.py
+++ b/gene_splicer/primer_finder.py
@@ -534,17 +534,11 @@ def run(contigs_csv,
                 working_path: Path = outpath / f'hivintact_{i}'
                 working_path.mkdir(exist_ok=True)
                 with (working_path / 'hiv-intact.log').open('w') as log_file:
-                    subprocess.run(['proviral',
-                                    'intact',
+                    subprocess.run(['cfeintact',
+                                    'check',
                                     '--working-folder', working_path,
                                     '--subtype=B',
-                                    '--run-hypermut',
-                                    '--check-long-deletion',
-                                    '--check-nonhiv',
-                                    '--check-scramble',
-                                    '--check-internal-inversion',
-                                    '--include-small-orfs',
-                                    '--output-csv',
+                                    '--ignore-distance',
                                     str(no_primers_fasta)],
                                    check=True,
                                    stdout=log_file,

From 2345afa1ce17776bfa4f2ff9fbf46dc7d7b1d6ae Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 8 Jul 2024 16:34:42 -0700
Subject: [PATCH 25/47] Bump CFEIntact version

---
 Pipfile      | 2 +-
 Pipfile.lock | 4 ++--
 Singularity  | 2 +-
 setup.py     | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Pipfile b/Pipfile
index 5ebd2cf..bfaafec 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-cfeintact = {ref = "v1.18.4", git = "https://github.com/cfe-lab/CFEIntact"}
+cfeintact = {ref = "v1.18.7", git = "https://github.com/cfe-lab/CFEIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index e378d44..3d2ec57 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "6a9e94b9fb771cdbc70c29e68954211f6778ff1be83c9713a16fe72315bc5a16"
+            "sha256": "36616db9203b94cf93d14a00eecbce256e4080aa6e791656ffb40776ad8979e9"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -61,7 +61,7 @@
         },
         "cfeintact": {
             "git": "https://github.com/cfe-lab/CFEIntact",
-            "ref": "a6ea095998a894e795c89a896a5fdc83ed9bc715"
+            "ref": "2e8a134b01053f4a33ba676b5d4f404911321166"
         },
         "charset-normalizer": {
             "hashes": [
diff --git a/Singularity b/Singularity
index 513dd05..af9501c 100644
--- a/Singularity
+++ b/Singularity
@@ -38,7 +38,7 @@ From: ubuntu:22.04
     apt-get install -y ncbi-blast+
 
     echo ===== Installing Python packages ===== >/dev/null
-    pip3 install git+https://github.com/cfe-lab/CFEIntact@v1.18.4
+    pip3 install git+https://github.com/cfe-lab/CFEIntact@v1.18.7
 
     cd /opt/primer_finder
     pip3 install .
diff --git a/setup.py b/setup.py
index 1ebaeb7..6500d8f 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.18.4',
+        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.18.7',
         'pyyaml'
     ],
     package_data={

From bc1d1ea6aa0fa7cfc3bf61340d43ec4839a6f866 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 8 Jul 2024 16:51:29 -0700
Subject: [PATCH 26/47] Use CFEIntact's python API instead of operating
 system's shell

---
 gene_splicer/primer_finder.py | 40 +++++++++++++++++++++++------------
 1 file changed, 27 insertions(+), 13 deletions(-)

diff --git a/gene_splicer/primer_finder.py b/gene_splicer/primer_finder.py
index adf50b7..ad3232a 100644
--- a/gene_splicer/primer_finder.py
+++ b/gene_splicer/primer_finder.py
@@ -6,6 +6,7 @@
 from operator import itemgetter
 import os
 from tarfile import TarFile
+import cfeintact
 
 import pandas as pd
 from pathlib import Path
@@ -531,19 +532,32 @@ def run(contigs_csv,
                     archive_hivseqinr_results(working_path,
                                               hivseqinr_results_tar)
             if run_hivintact:
-                working_path: Path = outpath / f'hivintact_{i}'
-                working_path.mkdir(exist_ok=True)
-                with (working_path / 'hiv-intact.log').open('w') as log_file:
-                    subprocess.run(['cfeintact',
-                                    'check',
-                                    '--working-folder', working_path,
-                                    '--subtype=B',
-                                    '--ignore-distance',
-                                    str(no_primers_fasta)],
-                                   check=True,
-                                   stdout=log_file,
-                                   stderr=subprocess.STDOUT,
-                                   cwd=working_path)
+                working_path = outpath / f'hivintact_{i}'
+                log_file_path = working_path / 'hiv-intact.log'
+                os.makedirs(working_path, exist_ok=True)
+
+                logger = cfeintact.logger
+                file_handler = logging.FileHandler(log_file_path)
+                logger.addHandler(file_handler)
+
+                cfeintact.check(
+                    working_dir=working_path,
+                    input_file=str(no_primers_fasta),
+                    subtype="B",
+                    check_packaging_signal=True,
+                    check_rre=True,
+                    check_major_splice_donor_site=True,
+                    check_hypermut=True,
+                    check_long_deletion=True,
+                    check_nonhiv=True,
+                    check_scramble=True,
+                    check_internal_inversion=True,
+                    check_unknown_nucleotides=True,
+                    check_small_orfs=True,
+                    check_distance=False,
+                    output_csv=True,
+                )
+
                 if hivintact_results_tar is not None:
                     archive_hivintact_results(working_path,
                                               hivintact_results_tar)

From 514221c930f61453ae6c3dd0c620beb928be3813 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 8 Jul 2024 16:52:25 -0700
Subject: [PATCH 27/47] Do not install cfeintact twice

---
 Singularity | 2 --
 1 file changed, 2 deletions(-)

diff --git a/Singularity b/Singularity
index af9501c..4a91529 100644
--- a/Singularity
+++ b/Singularity
@@ -38,8 +38,6 @@ From: ubuntu:22.04
     apt-get install -y ncbi-blast+
 
     echo ===== Installing Python packages ===== >/dev/null
-    pip3 install git+https://github.com/cfe-lab/CFEIntact@v1.18.7
-
     cd /opt/primer_finder
     pip3 install .
 

From 18199519b097475fc7464d8ab95b9212b0bc3996 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 9 Jul 2024 10:56:38 -0700
Subject: [PATCH 28/47] Fix column name of CFEIntact errors.csv

---
 gene_splicer/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index a658b91..875fe95 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -428,7 +428,7 @@ def get_verdict(SEQID, all_errors):
 
         with open(os.path.join(d, 'errors.csv'), 'r') as f:
             reader = csv.DictReader(f)
-            grouped = groupby(reader, key=itemgetter('sequence_name'))
+            grouped = groupby(reader, key=itemgetter('qseqid'))
             for sequence_name, errors in grouped:
                 if sequence_name not in intact:
                     all_errors = [error['error'] for error in errors]

From 05aac4f7fd48d6bf2f586ff46894be4aa483c0dc Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 9 Jul 2024 11:48:52 -0700
Subject: [PATCH 29/47] Improve reading of .SAM files

The data section does not always begin at line 3.
This improvement makes the code able to handle those situations where
it does not.
---
 gene_splicer/utils.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index 875fe95..effd718 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -334,7 +334,17 @@ def splice_aligned_genes(query, target, samfile, annotation):
 
 
 def load_samfile(samfile_path):
-    result = pd.read_table(samfile_path, skiprows=2, header=None)
+    # Open the SAM file and find the starting point for data
+    with open(samfile_path, 'r') as file:
+        # Skip meta fields
+        lines = file.readlines()
+        data_start_index = 0
+        for i, line in enumerate(lines):
+            if not line.startswith('@'):
+                data_start_index = i
+                break
+
+    result = pd.read_table(samfile_path, skiprows=data_start_index, header=None)
     result['cigar'] = result.apply(split_cigar, axis=1)
     return result
 

From 49022e0da2bdb3921d5e11fe36a801b9863cb70b Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 9 Jul 2024 14:02:50 -0700
Subject: [PATCH 30/47] Small refactoring of utils.py

---
 gene_splicer/utils.py | 76 ++++++++++++++++++++++++++-----------------
 1 file changed, 47 insertions(+), 29 deletions(-)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index effd718..d00c09c 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -3,6 +3,7 @@
 import os
 import re
 import typing
+from typing import TextIO, Mapping, Dict, Set, List, Iterable, Tuple
 
 import yaml
 import json
@@ -423,45 +424,62 @@ def align(target_seq,
     'FrameshiftInOrf',
     ]
 
-def iterate_hivintact_data(name, outpath):
+def iterate_hivintact_verdicts_1(directory: Path, intact: Set[str] = set()) -> Iterable[Tuple[str, str]]:
     intact = set()
 
-    def get_verdict(SEQID, all_errors):
+    def get_verdict(SEQID: str, all_errors) -> Tuple[str, str]:
         ordered = sorted(all_errors, key=HIVINTACT_ERRORS_TABLE.index)
         verdict = ordered[0]
-        return [SEQID, verdict]
+        return (SEQID, verdict)
 
-    for d in outpath.glob('hivintact*'):
-        for (SEQID, sequence) in read_fasta(os.path.join(d, 'intact.fasta')):
-            yield [SEQID, 'Intact']
-            intact.add(SEQID)
+    for (SEQID, sequence) in read_fasta(os.path.join(directory, 'intact.fasta')):
+        yield (SEQID, 'Intact')
+        intact.add(SEQID)
 
-        with open(os.path.join(d, 'errors.csv'), 'r') as f:
-            reader = csv.DictReader(f)
-            grouped = groupby(reader, key=itemgetter('qseqid'))
-            for sequence_name, errors in grouped:
-                if sequence_name not in intact:
-                    all_errors = [error['error'] for error in errors]
-                    yield get_verdict(sequence_name, all_errors)
+    with open(os.path.join(directory, 'errors.csv'), 'r') as f:
+        reader = csv.DictReader(f)
+        grouped = groupby(reader, key=itemgetter('qseqid'))
+        for sequence_name, errors in grouped:
+            if sequence_name not in intact:
+                all_errors = [error['error'] for error in errors]
+                yield get_verdict(sequence_name, all_errors)
 
 
-def get_hivintact_data(name, outpath):
+def iterate_hivintact_verdicts(outpath: Path) -> Iterable[Tuple[str, str]]:
+    intact: Set[str] = set()
+
+    for directory in outpath.glob('hivintact*'):
+        yield from iterate_hivintact_verdicts_1(directory, intact)
+
+
+def get_hivintact_verdicts(name, outpath):
     column_names = ['SEQID', 'MyVerdict']
-    data = iterate_hivintact_data(name, outpath)
+    data = iterate_hivintact_verdicts(outpath)
     return pd.DataFrame(data, columns=column_names)
 
-def get_hivseqinr_data(name, outpath):
-    seqinr_paths = glob.glob(
-        str(outpath / 'hivseqinr*' / 'Results_Final' /
-            'Output_MyBigSummary_DF_FINAL.csv'))
-    parts = []
+
+def iterate_hivseqinr_verdicts_1(directory: Path) -> Iterable[Tuple[str, str]]:
+    path = directory / 'Output_MyBigSummary_DF_FINAL.csv'
+    if not path.is_file():
+        return
+
+    with path.open() as fd:
+        reader = csv.DictReader(fd)
+        for row in reader:
+            yield (row["SEQID"], row["MyVerdict"])
+
+
+def iterate_hivseqinr_verdicts(outpath: Path) -> Iterable[Tuple[str, str]]:
+    seqinr_paths = outpath.glob('hivseqinr*/Results_Final/Output_MyBigSummary_DF_FINAL.csv')
     for path in seqinr_paths:
-        if not os.path.isfile(path):
-            continue
-        part = pd.read_csv(path)
-        parts.append(part)
-    # seqinr = pd.read_csv(seqinr_path)
-    return pd.concat(parts)
+        yield from iterate_hivseqinr_verdicts_1(path)
+
+
+def get_hivseqinr_verdicts(name, outpath):
+    column_names = ['SEQID', 'MyVerdict']
+    data = iterate_hivseqinr_verdicts(outpath)
+    return pd.DataFrame(data, columns=column_names)
+
 
 def generate_table_precursor(name, outpath, add_columns=None):
     # Output csv
@@ -473,9 +491,9 @@ def generate_table_precursor(name, outpath, add_columns=None):
     # Load hivseqinr data or HIVIntact results
 
     if any(outpath.glob('hivintact*')):
-        results = get_hivintact_data(name, outpath)
+        results = get_hivintact_verdicts(name, outpath)
     elif any(outpath.glob('hivseqinr*')):
-        results = get_hivseqinr_data(name, outpath)
+        results = get_hivseqinr_verdicts(name, outpath)
     else:
         raise RuntimeError("Neither HIVIntact nor HIVSeqinR directory exists.")
 

From 3d53ae8fdd673b2a921fb58d32edc6905c62d789 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 9 Jul 2024 14:04:02 -0700
Subject: [PATCH 31/47] Add a separate proviral_landscapes.py script

---
 gene_splicer/landscapes.py | 205 +++++++++++++++++++++++++++++++++++++
 1 file changed, 205 insertions(+)
 create mode 100644 gene_splicer/landscapes.py

diff --git a/gene_splicer/landscapes.py b/gene_splicer/landscapes.py
new file mode 100644
index 0000000..a5f7dc7
--- /dev/null
+++ b/gene_splicer/landscapes.py
@@ -0,0 +1,205 @@
+import csv
+import logging
+import os
+import re
+import typing
+from typing import TextIO, Mapping, Dict, Set, List, Iterable, Tuple
+import argparse
+import sys
+
+import json
+import shutil
+import subprocess as sp
+import glob
+from pathlib import Path
+from csv import DictWriter, DictReader
+from itertools import groupby
+from operator import itemgetter
+
+from gene_splicer.utils import (
+    iterate_hivintact_verdicts_1,
+    iterate_hivseqinr_verdicts_1,
+    LEFT_PRIMER_END, RIGHT_PRIMER_START,
+)
+
+
+logger = logging.getLogger(__name__)
+
+
+def generate_proviral_landscape_csv_1_cont(blastn_reader: csv.DictReader,
+                                           landscape_writer: csv.DictWriter,
+                                           verdicts: Mapping[str, str],
+                                           ) -> None:
+
+    for row in blastn_reader:
+        if row['qseqid'] in ['8E5LAV', 'HXB2']:
+            # skip the positive control rows
+            continue
+
+        ref_start = int(row['sstart'])
+        ref_end = int(row['send'])
+        if ref_end <= LEFT_PRIMER_END or ref_start >= RIGHT_PRIMER_START:
+            # skip unspecific matches of LTR at start and end
+            continue
+
+        qseqid = row['qseqid']
+        try:
+            [run_name, sample_name, _, _] = qseqid.split('::')
+        except ValueError:
+            [run_name, sample_name] = [None, qseqid]
+
+        is_inverted = ''
+        if ref_end < ref_start:
+            # automatically recognize inverted regions
+            new_end = ref_start
+            ref_start = ref_end
+            ref_end = new_end
+            is_inverted = 'yes'
+
+        verdict = verdicts.get(sample_name)
+        landscape_entry = {'ref_start': ref_start,
+                           'ref_end': ref_end,
+                           'samp_name': sample_name,
+                           'run_name': run_name,
+                           'is_inverted': is_inverted,
+                           'is_defective': verdict is not None,
+                           'defect': verdict,
+                           }
+
+        landscape_writer.writerow(landscape_entry)
+
+
+def get_hivintact_verdicts_1_map(details_dir: Path) -> Mapping[str, str]:
+    ret: Dict[str, str] = {}
+
+    for [qseqid, verdict] in iterate_hivintact_verdicts_1(details_dir):
+        ret[qseqid] = verdict
+
+    return ret
+
+
+def get_hivseqinr_verdicts_1_map(details_dir: Path) -> Mapping[str, str]:
+    ret: Dict[str, str] = {}
+
+    for [qseqid, verdict] in iterate_hivseqinr_verdicts_1(details_dir):
+        ret[qseqid] = verdict
+
+    return ret
+
+
+def generate_proviral_landscape_csv_1(landscape_writer: csv.DictWriter,
+                                      details_dir: Path,
+                                      ) -> None:
+    is_hivintact = (details_dir / "holistic.csv").exists()
+    if is_hivintact:
+        verdicts = get_hivintact_verdicts_1_map(details_dir)
+        blastn_path = details_dir / "blast.csv"
+    else:
+        verdicts = get_hivseqinr_verdicts_1_map(details_dir)
+        blastn_path = details_dir / "Results_Intermediate" / "Output_Blastn_HXB2MEGA28_tabdelim.txt"
+
+    with blastn_path.open() as blastn_file:
+        if is_hivintact:
+            blastn_reader = DictReader(blastn_file)
+        else:
+            blastn_columns = ['qseqid',
+                              'qlen',
+                              'sseqid',
+                              'sgi',
+                              'slen',
+                              'qstart',
+                              'qend',
+                              'sstart',
+                              'send',
+                              'evalue',
+                              'bitscore',
+                              'length',
+                              'pident',
+                              'nident',
+                              'btop',
+                              'stitle',
+                              'sstrand']
+            blastn_reader = DictReader(blastn_file, fieldnames=blastn_columns, delimiter='\t')
+
+        return generate_proviral_landscape_csv_1_cont(
+            blastn_reader,
+            landscape_writer,
+            verdicts,
+        )
+
+
+
+class UserError(RuntimeError):
+    def __init__(self, fmt: str, *fmt_args: object):
+        self.fmt = fmt
+        self.fmt_args = fmt_args
+        self.code = 1
+
+
+def dir_path(string: str) -> Path:
+    if os.path.exists(string) and os.path.isdir(string):
+        return Path(string)
+    else:
+        raise UserError("Path %r does not exist or is not a directory.", string)
+
+
+def cli_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description="Generate Proviral Landscape CSV.")
+
+    parser.add_argument("--details_dir", type=dir_path, required=True,
+                        help="Directory containing details files for verdicts.")
+
+    parser.add_argument("--output", type=argparse.FileType("wt"), required=True,
+                        help="Output CSV file for proviral landscape.")
+
+    verbosity_group = parser.add_mutually_exclusive_group()
+    verbosity_group.add_argument('--verbose', action='store_true',
+                                 help='Increase output verbosity.')
+    verbosity_group.add_argument('--no-verbose', action='store_true',
+                                 help='Normal output verbosity.', default=True)
+    verbosity_group.add_argument('--debug', action='store_true',
+                                 help='Maximum output verbosity.')
+    verbosity_group.add_argument('--quiet', action='store_true',
+                                 help='Minimize output verbosity.')
+
+    return parser
+
+
+def main(argv: list) -> int:
+    parser = cli_parser()
+    args = parser.parse_args(argv)
+    if args.quiet:
+        logger.setLevel(logging.ERROR)
+    elif args.verbose:
+        logger.setLevel(logging.INFO)
+    elif args.debug:
+        logger.setLevel(logging.DEBUG)
+    else:
+        logger.setLevel(logging.WARN)
+
+    logger.debug("Start.")
+
+    fieldnames = ['ref_start', 'ref_end', 'samp_name', 'run_name', 'is_inverted', 'is_defective', 'defect']
+
+    landscape_writer = csv.DictWriter(args.output, fieldnames=fieldnames)
+    landscape_writer.writeheader()
+    generate_proviral_landscape_csv_1(landscape_writer, args.details_dir)
+
+    logger.debug("Done.")
+    return 0
+
+
+if __name__ == '__main__':
+    try:
+        rc = main(sys.argv[1:])
+    except BrokenPipeError:
+        logger.debug("Broken pipe.")
+        rc = 0
+    except KeyboardInterrupt:
+        logger.debug("Interrupted.")
+        rc = 1
+    except UserError as e:
+        logger.fatal(e.fmt, *e.fmt_args)
+        rc = e.code
+
+    sys.exit(rc)

From c1698b4ce83cd34a196165415d6d0a37961d7bbb Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 9 Jul 2024 16:00:18 -0700
Subject: [PATCH 32/47] Fix defect column value for intact sequences

---
 gene_splicer/landscapes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gene_splicer/landscapes.py b/gene_splicer/landscapes.py
index a5f7dc7..62b4456 100644
--- a/gene_splicer/landscapes.py
+++ b/gene_splicer/landscapes.py
@@ -63,7 +63,7 @@ def generate_proviral_landscape_csv_1_cont(blastn_reader: csv.DictReader,
                            'run_name': run_name,
                            'is_inverted': is_inverted,
                            'is_defective': verdict is not None,
-                           'defect': verdict,
+                           'defect': verdict or 'Intact',
                            }
 
         landscape_writer.writerow(landscape_entry)

From 0925e737f05710155f180bb333b8edd6ba46278b Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 9 Jul 2024 16:47:41 -0700
Subject: [PATCH 33/47] Move all landscapes stuff to landscapes.py

---
 gene_splicer/landscapes.py | 16 ++++++++
 gene_splicer/sample.py     |  3 +-
 gene_splicer/utils.py      | 79 --------------------------------------
 3 files changed, 18 insertions(+), 80 deletions(-)

diff --git a/gene_splicer/landscapes.py b/gene_splicer/landscapes.py
index 62b4456..2fa6c3e 100644
--- a/gene_splicer/landscapes.py
+++ b/gene_splicer/landscapes.py
@@ -128,6 +128,22 @@ def generate_proviral_landscape_csv_1(landscape_writer: csv.DictWriter,
         )
 
 
+def generate_proviral_landscape_csv(outpath: Path, is_hivintact: bool):
+    proviral_landscape_csv = os.path.join(outpath, 'proviral_landscape.csv')
+
+    if is_hivintact:
+        subpath = 'hivintact*'
+    else:
+        subpath = 'hivseqinr*'
+
+    landscape_columns = ['samp_name', 'run_name', 'ref_start', 'ref_end', 'defect', 'is_inverted', 'is_defective']
+    with open(proviral_landscape_csv, 'w') as landscape_file:
+        landscape_writer = csv.DictWriter(landscape_file, fieldnames=landscape_columns)
+        landscape_writer.writeheader()
+
+        for details_dir in outpath.glob(subpath):
+            generate_proviral_landscape_csv_1(landscape_writer, details_dir)
+
 
 class UserError(RuntimeError):
     def __init__(self, fmt: str, *fmt_args: object):
diff --git a/gene_splicer/sample.py b/gene_splicer/sample.py
index 076ce3c..d00e7fa 100644
--- a/gene_splicer/sample.py
+++ b/gene_splicer/sample.py
@@ -7,6 +7,7 @@
 import gene_splicer.gene_splicer as gene_splicer
 import gene_splicer.primer_finder as primer_finder
 import gene_splicer.utils as utils
+import gene_splicer.landscapes as landscapes
 
 
 def parse_args():
@@ -115,7 +116,7 @@ def main():
     for file in fasta_files:
         gene_splicer.run(file, outdir=outpath)
     utils.generate_table_precursor(name=run_name, outpath=outpath)
-    utils.generate_proviral_landscape_csv(outpath, is_hivintact=args.hivintact)
+    landscapes.generate_proviral_landscape_csv(outpath, is_hivintact=args.hivintact)
     copy_output(outpath / 'outcome_summary.csv', args.outcome_summary_csv)
     copy_output(outpath / (run_name + '_conseqs_primer_analysis.csv'),
                 args.conseqs_primers_csv)
diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index d00c09c..44ff8cd 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -584,85 +584,6 @@ def generate_table_precursor_2(hivseqinr_resultsfile, filtered_file,
     return table_precursorfile
 
 
-def generate_proviral_landscape_csv(outpath, is_hivintact):
-    proviral_landscape_csv = os.path.join(outpath, 'proviral_landscape.csv')
-    landscape_rows = []
-
-    table_precursor_csv = os.path.join(outpath, 'table_precursor.csv')
-
-    if is_hivintact:
-        subpath = os.path.join(outpath, 'hivintact*', 'blast.csv')
-    else:
-        subpath = os.path.join(outpath, 'hivseqinr*', 'Results_Intermediate', 'Output_Blastn_HXB2MEGA28_tabdelim.txt')
-
-    blastn_csvs = glob.glob(subpath)
-    blastn_csv = blastn_csvs[0]
-
-    with open(blastn_csv, 'r') as blastn_file:
-        if is_hivintact:
-            blastn_reader = DictReader(blastn_file)
-        else:
-            blastn_columns = ['qseqid',
-                              'qlen',
-                              'sseqid',
-                              'sgi',
-                              'slen',
-                              'qstart',
-                              'qend',
-                              'sstart',
-                              'send',
-                              'evalue',
-                              'bitscore',
-                              'length',
-                              'pident',
-                              'nident',
-                              'btop',
-                              'stitle',
-                              'sstrand']
-            blastn_reader = DictReader(blastn_file, fieldnames=blastn_columns, delimiter='\t')
-
-        for row in blastn_reader:
-            if row['qseqid'] in ['8E5LAV', 'HXB2']:
-                # skip the positive control rows
-                continue
-            ref_start = int(row['sstart'])
-            ref_end = int(row['send'])
-            if ref_end <= LEFT_PRIMER_END or ref_start >= RIGHT_PRIMER_START:
-                # skip unspecific matches of LTR at start and end
-                continue
-            [run_name, sample_name, _, _] = row['qseqid'].split('::')
-            is_inverted = ''
-            if ref_end < ref_start:
-                # automatically recognize inverted regions
-                new_end = ref_start
-                ref_start = ref_end
-                ref_end = new_end
-                is_inverted = 'yes'
-            landscape_entry = {'ref_start': ref_start,
-                               'ref_end': ref_end,
-                               'samp_name': sample_name,
-                               'run_name': run_name,
-                               'is_inverted': is_inverted,
-                               'is_defective': ''}
-            # is_defective is empty for now, will be filled manually
-            landscape_rows.append(landscape_entry)
-
-    with open(table_precursor_csv, 'r') as tab_prec:
-        tab_prec_reader = DictReader(tab_prec)
-        for row in tab_prec_reader:
-            samp_name = row['sample']
-            verdict = row['MyVerdict']
-            for entry in landscape_rows:
-                if entry['samp_name'] == samp_name:
-                    entry['defect'] = verdict
-
-    landscape_columns = ['samp_name', 'run_name', 'ref_start', 'ref_end', 'defect', 'is_inverted', 'is_defective']
-    with open(proviral_landscape_csv, 'w') as landscape_file:
-        landscape_writer = csv.DictWriter(landscape_file, fieldnames=landscape_columns)
-        landscape_writer.writeheader()
-        landscape_writer.writerows(landscape_rows)
-
-
 def get_softclipped_region(query, alignment, alignment_path):
     try:
         size, op = alignment.iloc[0]['cigar'][0]

From c1ed309dcad6a61b2dee0a1da99e0439fda97b62 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 12 Jul 2024 14:48:07 -0700
Subject: [PATCH 34/47] Bump CFEIntact version

---
 Pipfile      |   2 +-
 Pipfile.lock | 116 +++++++++++++++++++++++++--------------------------
 setup.py     |   2 +-
 3 files changed, 60 insertions(+), 60 deletions(-)

diff --git a/Pipfile b/Pipfile
index bfaafec..568ffdc 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-cfeintact = {ref = "v1.18.7", git = "https://github.com/cfe-lab/CFEIntact"}
+cfeintact = {ref = "v1.18.8", git = "https://github.com/cfe-lab/CFEIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index 3d2ec57..a5ed682 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "36616db9203b94cf93d14a00eecbce256e4080aa6e791656ffb40776ad8979e9"
+            "sha256": "9c092e800c5352454e25bd0df1a17c2ff2722892d620bb4869c7da671a1df741"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -61,7 +61,7 @@
         },
         "cfeintact": {
             "git": "https://github.com/cfe-lab/CFEIntact",
-            "ref": "2e8a134b01053f4a33ba676b5d4f404911321166"
+            "ref": "7c67d4ba867ccb3d5469bb34e39d3a4a9c2b293d"
         },
         "charset-normalizer": {
             "hashes": [
@@ -367,11 +367,11 @@
         },
         "setuptools": {
             "hashes": [
-                "sha256:b8b8060bb426838fbe942479c90296ce976249451118ef566a5a0b7d8b78fb05",
-                "sha256:bd63e505105011b25c3c11f753f7e3b8465ea739efddaccef8f0efac2137bac1"
+                "sha256:f171bab1dfbc86b132997f26a119f6056a57950d058587841a0082e8830f9dc5",
+                "sha256:fe384da74336c398e0d956d1cae0669bc02eed936cdb1d49b57de1990dc11ffc"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==70.2.0"
+            "version": "==70.3.0"
         },
         "six": {
             "hashes": [
@@ -401,62 +401,62 @@
     "develop": {
         "coverage": {
             "hashes": [
-                "sha256:018a12985185038a5b2bcafab04ab833a9a0f2c59995b3cec07e10074c78635f",
-                "sha256:02ff6e898197cc1e9fa375581382b72498eb2e6d5fc0b53f03e496cfee3fac6d",
-                "sha256:042183de01f8b6d531e10c197f7f0315a61e8d805ab29c5f7b51a01d62782747",
-                "sha256:1014fbf665fef86cdfd6cb5b7371496ce35e4d2a00cda501cf9f5b9e6fced69f",
-                "sha256:1137f46adb28e3813dec8c01fefadcb8c614f33576f672962e323b5128d9a68d",
-                "sha256:16852febd96acd953b0d55fc842ce2dac1710f26729b31c80b940b9afcd9896f",
-                "sha256:2174e7c23e0a454ffe12267a10732c273243b4f2d50d07544a91198f05c48f47",
-                "sha256:2214ee920787d85db1b6a0bd9da5f8503ccc8fcd5814d90796c2f2493a2f4d2e",
-                "sha256:3257fdd8e574805f27bb5342b77bc65578e98cbc004a92232106344053f319ba",
-                "sha256:3684bc2ff328f935981847082ba4fdc950d58906a40eafa93510d1b54c08a66c",
-                "sha256:3a6612c99081d8d6134005b1354191e103ec9705d7ba2754e848211ac8cacc6b",
-                "sha256:3d7564cc09dd91b5a6001754a5b3c6ecc4aba6323baf33a12bd751036c998be4",
-                "sha256:44da56a2589b684813f86d07597fdf8a9c6ce77f58976727329272f5a01f99f7",
-                "sha256:5013ed890dc917cef2c9f765c4c6a8ae9df983cd60dbb635df8ed9f4ebc9f555",
-                "sha256:54317c2b806354cbb2dc7ac27e2b93f97096912cc16b18289c5d4e44fc663233",
-                "sha256:56b4eafa21c6c175b3ede004ca12c653a88b6f922494b023aeb1e836df953ace",
-                "sha256:581ea96f92bf71a5ec0974001f900db495488434a6928a2ca7f01eee20c23805",
-                "sha256:5cd64adedf3be66f8ccee418473c2916492d53cbafbfcff851cbec5a8454b136",
-                "sha256:5df54843b88901fdc2f598ac06737f03d71168fd1175728054c8f5a2739ac3e4",
-                "sha256:65e528e2e921ba8fd67d9055e6b9f9e34b21ebd6768ae1c1723f4ea6ace1234d",
-                "sha256:6aae5cce399a0f065da65c7bb1e8abd5c7a3043da9dceb429ebe1b289bc07806",
-                "sha256:6cfb5a4f556bb51aba274588200a46e4dd6b505fb1a5f8c5ae408222eb416f99",
-                "sha256:7076b4b3a5f6d2b5d7f1185fde25b1e54eb66e647a1dfef0e2c2bfaf9b4c88c8",
-                "sha256:73ca8fbc5bc622e54627314c1a6f1dfdd8db69788f3443e752c215f29fa87a0b",
-                "sha256:79b356f3dd5b26f3ad23b35c75dbdaf1f9e2450b6bcefc6d0825ea0aa3f86ca5",
-                "sha256:7a892be37ca35eb5019ec85402c3371b0f7cda5ab5056023a7f13da0961e60da",
-                "sha256:8192794d120167e2a64721d88dbd688584675e86e15d0569599257566dec9bf0",
-                "sha256:820bc841faa502e727a48311948e0461132a9c8baa42f6b2b84a29ced24cc078",
-                "sha256:8f894208794b164e6bd4bba61fc98bf6b06be4d390cf2daacfa6eca0a6d2bb4f",
-                "sha256:a04e990a2a41740b02d6182b498ee9796cf60eefe40cf859b016650147908029",
-                "sha256:a44963520b069e12789d0faea4e9fdb1e410cdc4aab89d94f7f55cbb7fef0353",
-                "sha256:a6bb74ed465d5fb204b2ec41d79bcd28afccf817de721e8a807d5141c3426638",
-                "sha256:ab73b35e8d109bffbda9a3e91c64e29fe26e03e49addf5b43d85fc426dde11f9",
-                "sha256:aea072a941b033813f5e4814541fc265a5c12ed9720daef11ca516aeacd3bd7f",
-                "sha256:b1ccf5e728ccf83acd313c89f07c22d70d6c375a9c6f339233dcf792094bcbf7",
-                "sha256:b385d49609f8e9efc885790a5a0e89f2e3ae042cdf12958b6034cc442de428d3",
-                "sha256:b3d45ff86efb129c599a3b287ae2e44c1e281ae0f9a9bad0edc202179bcc3a2e",
-                "sha256:b4a474f799456e0eb46d78ab07303286a84a3140e9700b9e154cfebc8f527016",
-                "sha256:b95c3a8cb0463ba9f77383d0fa8c9194cf91f64445a63fc26fb2327e1e1eb088",
-                "sha256:c5986ee7ea0795a4095ac4d113cbb3448601efca7f158ec7f7087a6c705304e4",
-                "sha256:cdd31315fc20868c194130de9ee6bfd99755cc9565edff98ecc12585b90be882",
-                "sha256:cef4649ec906ea7ea5e9e796e68b987f83fa9a718514fe147f538cfeda76d7a7",
-                "sha256:d05c16cf4b4c2fc880cb12ba4c9b526e9e5d5bb1d81313d4d732a5b9fe2b9d53",
-                "sha256:d2e344d6adc8ef81c5a233d3a57b3c7d5181f40e79e05e1c143da143ccb6377d",
-                "sha256:d45d3cbd94159c468b9b8c5a556e3f6b81a8d1af2a92b77320e887c3e7a5d080",
-                "sha256:db14f552ac38f10758ad14dd7b983dbab424e731588d300c7db25b6f89e335b5",
-                "sha256:dbc5958cb471e5a5af41b0ddaea96a37e74ed289535e8deca404811f6cb0bc3d",
-                "sha256:ddbd2f9713a79e8e7242d7c51f1929611e991d855f414ca9996c20e44a895f7c",
-                "sha256:e16f3d6b491c48c5ae726308e6ab1e18ee830b4cdd6913f2d7f77354b33f91c8",
-                "sha256:e2afe743289273209c992075a5a4913e8d007d569a406ffed0bd080ea02b0633",
-                "sha256:e564c2cf45d2f44a9da56f4e3a26b2236504a496eb4cb0ca7221cd4cc7a9aca9",
-                "sha256:ed550e7442f278af76d9d65af48069f1fb84c9f745ae249c1a183c1e9d1b025c"
+                "sha256:0086cd4fc71b7d485ac93ca4239c8f75732c2ae3ba83f6be1c9be59d9e2c6382",
+                "sha256:01c322ef2bbe15057bc4bf132b525b7e3f7206f071799eb8aa6ad1940bcf5fb1",
+                "sha256:03cafe82c1b32b770a29fd6de923625ccac3185a54a5e66606da26d105f37dac",
+                "sha256:044a0985a4f25b335882b0966625270a8d9db3d3409ddc49a4eb00b0ef5e8cee",
+                "sha256:07ed352205574aad067482e53dd606926afebcb5590653121063fbf4e2175166",
+                "sha256:0d1b923fc4a40c5832be4f35a5dab0e5ff89cddf83bb4174499e02ea089daf57",
+                "sha256:0e7b27d04131c46e6894f23a4ae186a6a2207209a05df5b6ad4caee6d54a222c",
+                "sha256:1fad32ee9b27350687035cb5fdf9145bc9cf0a094a9577d43e909948ebcfa27b",
+                "sha256:289cc803fa1dc901f84701ac10c9ee873619320f2f9aff38794db4a4a0268d51",
+                "sha256:3c59105f8d58ce500f348c5b56163a4113a440dad6daa2294b5052a10db866da",
+                "sha256:46c3d091059ad0b9c59d1034de74a7f36dcfa7f6d3bde782c49deb42438f2450",
+                "sha256:482855914928c8175735a2a59c8dc5806cf7d8f032e4820d52e845d1f731dca2",
+                "sha256:49c76cdfa13015c4560702574bad67f0e15ca5a2872c6a125f6327ead2b731dd",
+                "sha256:4b03741e70fb811d1a9a1d75355cf391f274ed85847f4b78e35459899f57af4d",
+                "sha256:4bea27c4269234e06f621f3fac3925f56ff34bc14521484b8f66a580aacc2e7d",
+                "sha256:4d5fae0a22dc86259dee66f2cc6c1d3e490c4a1214d7daa2a93d07491c5c04b6",
+                "sha256:543ef9179bc55edfd895154a51792b01c017c87af0ebaae092720152e19e42ca",
+                "sha256:54dece71673b3187c86226c3ca793c5f891f9fc3d8aa183f2e3653da18566169",
+                "sha256:6379688fb4cfa921ae349c76eb1a9ab26b65f32b03d46bb0eed841fd4cb6afb1",
+                "sha256:65fa405b837060db569a61ec368b74688f429b32fa47a8929a7a2f9b47183713",
+                "sha256:6616d1c9bf1e3faea78711ee42a8b972367d82ceae233ec0ac61cc7fec09fa6b",
+                "sha256:6fe885135c8a479d3e37a7aae61cbd3a0fb2deccb4dda3c25f92a49189f766d6",
+                "sha256:7221f9ac9dad9492cecab6f676b3eaf9185141539d5c9689d13fd6b0d7de840c",
+                "sha256:76d5f82213aa78098b9b964ea89de4617e70e0d43e97900c2778a50856dac605",
+                "sha256:7792f0ab20df8071d669d929c75c97fecfa6bcab82c10ee4adb91c7a54055463",
+                "sha256:831b476d79408ab6ccfadaaf199906c833f02fdb32c9ab907b1d4aa0713cfa3b",
+                "sha256:9146579352d7b5f6412735d0f203bbd8d00113a680b66565e205bc605ef81bc6",
+                "sha256:9cc44bf0315268e253bf563f3560e6c004efe38f76db03a1558274a6e04bf5d5",
+                "sha256:a73d18625f6a8a1cbb11eadc1d03929f9510f4131879288e3f7922097a429f63",
+                "sha256:a8659fd33ee9e6ca03950cfdcdf271d645cf681609153f218826dd9805ab585c",
+                "sha256:a94925102c89247530ae1dab7dc02c690942566f22e189cbd53579b0693c0783",
+                "sha256:ad4567d6c334c46046d1c4c20024de2a1c3abc626817ae21ae3da600f5779b44",
+                "sha256:b2e16f4cd2bc4d88ba30ca2d3bbf2f21f00f382cf4e1ce3b1ddc96c634bc48ca",
+                "sha256:bbdf9a72403110a3bdae77948b8011f644571311c2fb35ee15f0f10a8fc082e8",
+                "sha256:beb08e8508e53a568811016e59f3234d29c2583f6b6e28572f0954a6b4f7e03d",
+                "sha256:c4cbe651f3904e28f3a55d6f371203049034b4ddbce65a54527a3f189ca3b390",
+                "sha256:c7b525ab52ce18c57ae232ba6f7010297a87ced82a2383b1afd238849c1ff933",
+                "sha256:ca5d79cfdae420a1d52bf177de4bc2289c321d6c961ae321503b2ca59c17ae67",
+                "sha256:cdab02a0a941af190df8782aafc591ef3ad08824f97850b015c8c6a8b3877b0b",
+                "sha256:d17c6a415d68cfe1091d3296ba5749d3d8696e42c37fca5d4860c5bf7b729f03",
+                "sha256:d39bd10f0ae453554798b125d2f39884290c480f56e8a02ba7a6ed552005243b",
+                "sha256:d4b3cd1ca7cd73d229487fa5caca9e4bc1f0bca96526b922d61053ea751fe791",
+                "sha256:d50a252b23b9b4dfeefc1f663c568a221092cbaded20a05a11665d0dbec9b8fb",
+                "sha256:da8549d17489cd52f85a9829d0e1d91059359b3c54a26f28bec2c5d369524807",
+                "sha256:dcd070b5b585b50e6617e8972f3fbbee786afca71b1936ac06257f7e178f00f6",
+                "sha256:ddaaa91bfc4477d2871442bbf30a125e8fe6b05da8a0015507bfbf4718228ab2",
+                "sha256:df423f351b162a702c053d5dddc0fc0ef9a9e27ea3f449781ace5f906b664428",
+                "sha256:dff044f661f59dace805eedb4a7404c573b6ff0cdba4a524141bc63d7be5c7fd",
+                "sha256:e7e128f85c0b419907d1f38e616c4f1e9f1d1b37a7949f44df9a73d5da5cd53c",
+                "sha256:ed8d1d1821ba5fc88d4a4f45387b65de52382fa3ef1f0115a4f7a20cdfab0e94",
+                "sha256:f2501d60d7497fd55e391f423f965bbe9e650e9ffc3c627d5f0ac516026000b8",
+                "sha256:f7db0b6ae1f96ae41afe626095149ecd1b212b424626175a6633c2999eaad45b"
             ],
             "index": "pypi",
             "markers": "python_version >= '3.8'",
-            "version": "==7.5.4"
+            "version": "==7.6.0"
         },
         "exceptiongroup": {
             "hashes": [
diff --git a/setup.py b/setup.py
index 6500d8f..2abf644 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.18.7',
+        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.18.8',
         'pyyaml'
     ],
     package_data={

From eea015180947ab6ea5b626776c1ac22ef212503b Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Tue, 16 Jul 2024 13:49:53 -0700
Subject: [PATCH 35/47] Bump CFEIntact version

---
 Pipfile      |  2 +-
 Pipfile.lock | 10 +++++-----
 setup.py     |  2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/Pipfile b/Pipfile
index 568ffdc..d5fedd9 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-cfeintact = {ref = "v1.18.8", git = "https://github.com/cfe-lab/CFEIntact"}
+cfeintact = {ref = "v1.18.9", git = "https://github.com/cfe-lab/CFEIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index a5ed682..d4f807c 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "9c092e800c5352454e25bd0df1a17c2ff2722892d620bb4869c7da671a1df741"
+            "sha256": "ac639c5687670e64465782b1d6c4d508b3ba6c84f1b22f1225c3c3efffdbac4c"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -61,7 +61,7 @@
         },
         "cfeintact": {
             "git": "https://github.com/cfe-lab/CFEIntact",
-            "ref": "7c67d4ba867ccb3d5469bb34e39d3a4a9c2b293d"
+            "ref": "513b7ce5b332df7601f3a2ac723506ea5ec755a6"
         },
         "charset-normalizer": {
             "hashes": [
@@ -460,11 +460,11 @@
         },
         "exceptiongroup": {
             "hashes": [
-                "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad",
-                "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"
+                "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b",
+                "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"
             ],
             "markers": "python_version < '3.11'",
-            "version": "==1.2.1"
+            "version": "==1.2.2"
         },
         "iniconfig": {
             "hashes": [
diff --git a/setup.py b/setup.py
index 2abf644..57d3048 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.18.8',
+        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.18.9',
         'pyyaml'
     ],
     package_data={

From 6d18b36e6af442fb41c2648f8d123abb6613d564 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 26 Jul 2024 14:28:15 -0700
Subject: [PATCH 36/47] Bump CFEIntact version

---
 Pipfile      |  2 +-
 Pipfile.lock | 16 ++++++++--------
 setup.py     |  2 +-
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/Pipfile b/Pipfile
index d5fedd9..fc2f73c 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-cfeintact = {ref = "v1.18.9", git = "https://github.com/cfe-lab/CFEIntact"}
+cfeintact = {ref = "v1.18.10", git = "https://github.com/cfe-lab/CFEIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index d4f807c..0094cbe 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "ac639c5687670e64465782b1d6c4d508b3ba6c84f1b22f1225c3c3efffdbac4c"
+            "sha256": "242d7f1c41b5fee2859daea64f75c76bbb03977c462f29e9920e9ca16f4dff82"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -61,7 +61,7 @@
         },
         "cfeintact": {
             "git": "https://github.com/cfe-lab/CFEIntact",
-            "ref": "513b7ce5b332df7601f3a2ac723506ea5ec755a6"
+            "ref": "6e1a09b878ca1e8ac851b4e7ddcf58e813f69628"
         },
         "charset-normalizer": {
             "hashes": [
@@ -367,11 +367,11 @@
         },
         "setuptools": {
             "hashes": [
-                "sha256:f171bab1dfbc86b132997f26a119f6056a57950d058587841a0082e8830f9dc5",
-                "sha256:fe384da74336c398e0d956d1cae0669bc02eed936cdb1d49b57de1990dc11ffc"
+                "sha256:032d42ee9fb536e33087fb66cac5f840eb9391ed05637b3f2a76a7c8fb477936",
+                "sha256:33874fdc59b3188304b2e7c80d9029097ea31627180896fb549c578ceb8a0855"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==70.3.0"
+            "version": "==71.1.0"
         },
         "six": {
             "hashes": [
@@ -492,12 +492,12 @@
         },
         "pytest": {
             "hashes": [
-                "sha256:c434598117762e2bd304e526244f67bf66bbd7b5d6cf22138be51ff661980343",
-                "sha256:de4bb8104e201939ccdc688b27a89a7be2079b22e2bd2b07f806b6ba71117977"
+                "sha256:4ba08f9ae7dcf84ded419494d229b48d0903ea6407b030eaec46df5e6a73bba5",
+                "sha256:c132345d12ce551242c87269de812483f5bcc87cdbb4722e48487ba194f9fdce"
             ],
             "index": "pypi",
             "markers": "python_version >= '3.8'",
-            "version": "==8.2.2"
+            "version": "==8.3.2"
         },
         "tomli": {
             "hashes": [
diff --git a/setup.py b/setup.py
index 57d3048..abbd699 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.18.9',
+        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.18.10',
         'pyyaml'
     ],
     package_data={

From 2b9a7b657423800e793e09f26d92b8349bd38a13 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Sat, 27 Jul 2024 10:36:32 -0700
Subject: [PATCH 37/47] Bump CFEIntact version

---
 Pipfile      | 2 +-
 Pipfile.lock | 4 ++--
 setup.py     | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Pipfile b/Pipfile
index fc2f73c..9157cca 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-cfeintact = {ref = "v1.18.10", git = "https://github.com/cfe-lab/CFEIntact"}
+cfeintact = {ref = "v1.19.0", git = "https://github.com/cfe-lab/CFEIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index 0094cbe..301cc74 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "242d7f1c41b5fee2859daea64f75c76bbb03977c462f29e9920e9ca16f4dff82"
+            "sha256": "9423d0d698fd4b562f454550c5ddc78abb8d2b7111295abbe3a8d2c35d4922b6"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -61,7 +61,7 @@
         },
         "cfeintact": {
             "git": "https://github.com/cfe-lab/CFEIntact",
-            "ref": "6e1a09b878ca1e8ac851b4e7ddcf58e813f69628"
+            "ref": "ec42d6735f519ee8051175ff999e467825072040"
         },
         "charset-normalizer": {
             "hashes": [
diff --git a/setup.py b/setup.py
index abbd699..16da194 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.18.10',
+        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.19.0',
         'pyyaml'
     ],
     package_data={

From e68bfe57e3fbe19dbe1dd51914739b5db578df43 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Sat, 27 Jul 2024 13:00:05 -0700
Subject: [PATCH 38/47] Update CFEIntact errors table

---
 gene_splicer/utils.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index 44ff8cd..4370a7f 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -422,6 +422,8 @@ def align(target_seq,
     'InsertionInOrf',
     'InternalStopInOrf',
     'FrameshiftInOrf',
+    'MutatedStopCodon',
+    'MutatedStartCodon',
     ]
 
 def iterate_hivintact_verdicts_1(directory: Path, intact: Set[str] = set()) -> Iterable[Tuple[str, str]]:

From 75fcf9c86d0f58858dd5aaa4772947c3d65c5bc2 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Sat, 27 Jul 2024 23:28:02 -0700
Subject: [PATCH 39/47] Bump CFEIntact version

---
 Pipfile      | 2 +-
 Pipfile.lock | 4 ++--
 setup.py     | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Pipfile b/Pipfile
index 9157cca..c192f84 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-cfeintact = {ref = "v1.19.0", git = "https://github.com/cfe-lab/CFEIntact"}
+cfeintact = {ref = "v1.20.0", git = "https://github.com/cfe-lab/CFEIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index 301cc74..ed45be5 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "9423d0d698fd4b562f454550c5ddc78abb8d2b7111295abbe3a8d2c35d4922b6"
+            "sha256": "95e509a36a7c664fbc0a32dc26e768b6549de116d55171959a711fd3efc00091"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -61,7 +61,7 @@
         },
         "cfeintact": {
             "git": "https://github.com/cfe-lab/CFEIntact",
-            "ref": "ec42d6735f519ee8051175ff999e467825072040"
+            "ref": "b1a6156c70ba76d5f911bb72b0f425b6d4358440"
         },
         "charset-normalizer": {
             "hashes": [
diff --git a/setup.py b/setup.py
index 16da194..d0dfcba 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.19.0',
+        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.20.0',
         'pyyaml'
     ],
     package_data={

From 731556b244ede9dda7cf1efdc6d41aa60dbfc6af Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Sun, 28 Jul 2024 00:34:14 -0700
Subject: [PATCH 40/47] Bump CFEIntact version

---
 Pipfile               |  2 +-
 Pipfile.lock          |  4 ++--
 gene_splicer/utils.py | 22 +++++++++++-----------
 setup.py              |  2 +-
 4 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/Pipfile b/Pipfile
index c192f84..aecfbf0 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-cfeintact = {ref = "v1.20.0", git = "https://github.com/cfe-lab/CFEIntact"}
+cfeintact = {ref = "v1.22.0", git = "https://github.com/cfe-lab/CFEIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index ed45be5..e59b2c8 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "95e509a36a7c664fbc0a32dc26e768b6549de116d55171959a711fd3efc00091"
+            "sha256": "56b5477cba506a2df408fcad36d4fc357ecbfd0bedccf9d90ecb7b8e615cb43e"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -61,7 +61,7 @@
         },
         "cfeintact": {
             "git": "https://github.com/cfe-lab/CFEIntact",
-            "ref": "b1a6156c70ba76d5f911bb72b0f425b6d4358440"
+            "ref": "a8387e08d08ab8db2ed5dc70cbe765d74a353e12"
         },
         "charset-normalizer": {
             "hashes": [
diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index 4370a7f..957c5c7 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -405,23 +405,21 @@ def align(target_seq,
         return alignment_path
 
 HIVINTACT_ERRORS_TABLE = [
-    'AlignmentFailed',
-    'InvalidCodon',
     'NonHIV',
     'LongDeletion',
     'InternalInversion',
     'Scramble',
-    'APOBECHypermutationDetected',
+    'APOBECHypermutation',
     'MajorSpliceDonorSiteMutated',
     'PackagingSignalDeletion',
     'PackagingSignalNotComplete',
     'RevResponseElementDeletion',
     'MisplacedORF',
     'WrongORFNumber',
-    'DeletionInOrf',
-    'InsertionInOrf',
-    'InternalStopInOrf',
-    'FrameshiftInOrf',
+    'Deletion',
+    'Insertion',
+    'InternalStop',
+    'Frameshift',
     'MutatedStopCodon',
     'MutatedStartCodon',
     ]
@@ -434,11 +432,13 @@ def get_verdict(SEQID: str, all_errors) -> Tuple[str, str]:
         verdict = ordered[0]
         return (SEQID, verdict)
 
-    for (SEQID, sequence) in read_fasta(os.path.join(directory, 'intact.fasta')):
-        yield (SEQID, 'Intact')
-        intact.add(SEQID)
+    with open(os.path.join(directory, 'holistic.csv'), 'r') as f:
+        reader = csv.DictReader(f)
+        for row in reader:
+            if row["intact"] == "True":
+                intact.add(row["qseqid"])
 
-    with open(os.path.join(directory, 'errors.csv'), 'r') as f:
+    with open(os.path.join(directory, 'defects.csv'), 'r') as f:
         reader = csv.DictReader(f)
         grouped = groupby(reader, key=itemgetter('qseqid'))
         for sequence_name, errors in grouped:
diff --git a/setup.py b/setup.py
index d0dfcba..61530de 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.20.0',
+        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.22.0',
         'pyyaml'
     ],
     package_data={

From 9454adea9ed4f80a3f793374af39463c50511689 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 29 Jul 2024 10:31:34 -0700
Subject: [PATCH 41/47] Fix landscape generation based on sample_name

---
 gene_splicer/landscapes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gene_splicer/landscapes.py b/gene_splicer/landscapes.py
index 2fa6c3e..60fe908 100644
--- a/gene_splicer/landscapes.py
+++ b/gene_splicer/landscapes.py
@@ -56,7 +56,7 @@ def generate_proviral_landscape_csv_1_cont(blastn_reader: csv.DictReader,
             ref_end = new_end
             is_inverted = 'yes'
 
-        verdict = verdicts.get(sample_name)
+        verdict = verdicts.get(qseqid)
         landscape_entry = {'ref_start': ref_start,
                            'ref_end': ref_end,
                            'samp_name': sample_name,

From 87aaffb4379c2e2d2e1eea2ac3d4101c0d7f815c Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 29 Jul 2024 14:08:04 -0700
Subject: [PATCH 42/47] Fix ignoring intact sequences in table_precursor and
 landscapes_plots

---
 gene_splicer/landscapes.py |  7 ++++---
 gene_splicer/utils.py      | 10 ++++++++--
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/gene_splicer/landscapes.py b/gene_splicer/landscapes.py
index 60fe908..9da65e7 100644
--- a/gene_splicer/landscapes.py
+++ b/gene_splicer/landscapes.py
@@ -56,14 +56,15 @@ def generate_proviral_landscape_csv_1_cont(blastn_reader: csv.DictReader,
             ref_end = new_end
             is_inverted = 'yes'
 
-        verdict = verdicts.get(qseqid)
+        verdict = verdicts[qseqid]
+        is_defective = verdict != 'Intact'
         landscape_entry = {'ref_start': ref_start,
                            'ref_end': ref_end,
                            'samp_name': sample_name,
                            'run_name': run_name,
                            'is_inverted': is_inverted,
-                           'is_defective': verdict is not None,
-                           'defect': verdict or 'Intact',
+                           'is_defective': is_defective,
+                           'defect': verdict,
                            }
 
         landscape_writer.writerow(landscape_entry)
diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index 957c5c7..4669b90 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -428,8 +428,12 @@ def iterate_hivintact_verdicts_1(directory: Path, intact: Set[str] = set()) -> I
     intact = set()
 
     def get_verdict(SEQID: str, all_errors) -> Tuple[str, str]:
-        ordered = sorted(all_errors, key=HIVINTACT_ERRORS_TABLE.index)
-        verdict = ordered[0]
+        if all_errors:
+            ordered = sorted(all_errors, key=HIVINTACT_ERRORS_TABLE.index)
+            verdict = ordered[0]
+        else:
+            verdict = "Intact"
+
         return (SEQID, verdict)
 
     with open(os.path.join(directory, 'holistic.csv'), 'r') as f:
@@ -437,6 +441,8 @@ def get_verdict(SEQID: str, all_errors) -> Tuple[str, str]:
         for row in reader:
             if row["intact"] == "True":
                 intact.add(row["qseqid"])
+                SEQID = row["qseqid"]
+                yield get_verdict(SEQID, all_errors=[])
 
     with open(os.path.join(directory, 'defects.csv'), 'r') as f:
         reader = csv.DictReader(f)

From 5fc93403ac59a6fbb5ca0619618bb55d8240516a Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 29 Jul 2024 16:34:40 -0700
Subject: [PATCH 43/47] Bump CFEIntact version

---
 Pipfile               |  2 +-
 Pipfile.lock          | 10 +++++-----
 gene_splicer/utils.py | 14 +++++++-------
 setup.py              |  2 +-
 4 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/Pipfile b/Pipfile
index aecfbf0..bad630b 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-cfeintact = {ref = "v1.22.0", git = "https://github.com/cfe-lab/CFEIntact"}
+cfeintact = {ref = "v1.23.0", git = "https://github.com/cfe-lab/CFEIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index e59b2c8..a00bf95 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "56b5477cba506a2df408fcad36d4fc357ecbfd0bedccf9d90ecb7b8e615cb43e"
+            "sha256": "e765cc4af24f9eca7db1eb84af000daab8d3238c01daa3df4f57ddb03d7b8774"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -61,7 +61,7 @@
         },
         "cfeintact": {
             "git": "https://github.com/cfe-lab/CFEIntact",
-            "ref": "a8387e08d08ab8db2ed5dc70cbe765d74a353e12"
+            "ref": "70031d6aff59249eb61495d2c63ae467bef6c408"
         },
         "charset-normalizer": {
             "hashes": [
@@ -367,11 +367,11 @@
         },
         "setuptools": {
             "hashes": [
-                "sha256:032d42ee9fb536e33087fb66cac5f840eb9391ed05637b3f2a76a7c8fb477936",
-                "sha256:33874fdc59b3188304b2e7c80d9029097ea31627180896fb549c578ceb8a0855"
+                "sha256:5a03e1860cf56bb6ef48ce186b0e557fdba433237481a9a625176c2831be15d1",
+                "sha256:8d243eff56d095e5817f796ede6ae32941278f542e0f941867cc05ae52b162ec"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==71.1.0"
+            "version": "==72.1.0"
         },
         "six": {
             "hashes": [
diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index 4669b90..e2c49f9 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -427,9 +427,9 @@ def align(target_seq,
 def iterate_hivintact_verdicts_1(directory: Path, intact: Set[str] = set()) -> Iterable[Tuple[str, str]]:
     intact = set()
 
-    def get_verdict(SEQID: str, all_errors) -> Tuple[str, str]:
-        if all_errors:
-            ordered = sorted(all_errors, key=HIVINTACT_ERRORS_TABLE.index)
+    def get_verdict(SEQID: str, all_defects) -> Tuple[str, str]:
+        if all_defects:
+            ordered = sorted(all_defects, key=HIVINTACT_ERRORS_TABLE.index)
             verdict = ordered[0]
         else:
             verdict = "Intact"
@@ -442,15 +442,15 @@ def get_verdict(SEQID: str, all_errors) -> Tuple[str, str]:
             if row["intact"] == "True":
                 intact.add(row["qseqid"])
                 SEQID = row["qseqid"]
-                yield get_verdict(SEQID, all_errors=[])
+                yield get_verdict(SEQID, all_defects=[])
 
     with open(os.path.join(directory, 'defects.csv'), 'r') as f:
         reader = csv.DictReader(f)
         grouped = groupby(reader, key=itemgetter('qseqid'))
-        for sequence_name, errors in grouped:
+        for sequence_name, defects in grouped:
             if sequence_name not in intact:
-                all_errors = [error['error'] for error in errors]
-                yield get_verdict(sequence_name, all_errors)
+                all_defects = [defect['code'] for defect in defects]
+                yield get_verdict(sequence_name, all_defects)
 
 
 def iterate_hivintact_verdicts(outpath: Path) -> Iterable[Tuple[str, str]]:
diff --git a/setup.py b/setup.py
index 61530de..e00e2ec 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.22.0',
+        'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.23.0',
         'pyyaml'
     ],
     package_data={

From 28950eb74463e0753325dbc6437ec8a58c3ff73b Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 29 Jul 2024 17:03:10 -0700
Subject: [PATCH 44/47] Bump pandas version

---
 Pipfile      |  2 +-
 Pipfile.lock | 60 ++++++++++++++++++++++++++++------------------------
 setup.py     |  2 +-
 3 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/Pipfile b/Pipfile
index bad630b..d46c6eb 100644
--- a/Pipfile
+++ b/Pipfile
@@ -7,7 +7,7 @@ name = "pypi"
 gotoh = {subdirectory = "micall/alignment", ref = "v7.7.0", git = "https://github.com/cfe-lab/MiCall.git"}
 numpy = "==1.25.1"
 python-levenshtein = "==0.12.0"
-pandas = "==2.0.2"
+pandas = "==2.2.2"
 requests = "==2.31.0"
 pyyaml = "*"
 cfeintact = {ref = "v1.23.0", git = "https://github.com/cfe-lab/CFEIntact"}
diff --git a/Pipfile.lock b/Pipfile.lock
index a00bf95..bcf2914 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "e765cc4af24f9eca7db1eb84af000daab8d3238c01daa3df4f57ddb03d7b8774"
+            "sha256": "627846a347fac9a0d82e30a61f395bc23a45f30344dcf8144eeb2abebc84d9d0"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -215,35 +215,39 @@
         },
         "pandas": {
             "hashes": [
-                "sha256:02755de164da6827764ceb3bbc5f64b35cb12394b1024fdf88704d0fa06e0e2f",
-                "sha256:0a1e0576611641acde15c2322228d138258f236d14b749ad9af498ab69089e2d",
-                "sha256:1eb09a242184092f424b2edd06eb2b99d06dc07eeddff9929e8667d4ed44e181",
-                "sha256:30a89d0fec4263ccbf96f68592fd668939481854d2ff9da709d32a047689393b",
-                "sha256:50e451932b3011b61d2961b4185382c92cc8c6ee4658dcd4f320687bb2d000ee",
-                "sha256:51a93d422fbb1bd04b67639ba4b5368dffc26923f3ea32a275d2cc450f1d1c86",
-                "sha256:598e9020d85a8cdbaa1815eb325a91cfff2bb2b23c1442549b8a3668e36f0f77",
-                "sha256:66d00300f188fa5de73f92d5725ced162488f6dc6ad4cecfe4144ca29debe3b8",
-                "sha256:69167693cb8f9b3fc060956a5d0a0a8dbfed5f980d9fd2c306fb5b9c855c814c",
-                "sha256:6d6d10c2142d11d40d6e6c0a190b1f89f525bcf85564707e31b0a39e3b398e08",
-                "sha256:713f2f70abcdade1ddd68fc91577cb090b3544b07ceba78a12f799355a13ee44",
-                "sha256:7376e13d28eb16752c398ca1d36ccfe52bf7e887067af9a0474de6331dd948d2",
-                "sha256:77550c8909ebc23e56a89f91b40ad01b50c42cfbfab49b3393694a50549295ea",
-                "sha256:7b21cb72958fc49ad757685db1919021d99650d7aaba676576c9e88d3889d456",
-                "sha256:9ebb9f1c22ddb828e7fd017ea265a59d80461d5a79154b49a4207bd17514d122",
-                "sha256:a18e5c72b989ff0f7197707ceddc99828320d0ca22ab50dd1b9e37db45b010c0",
-                "sha256:a6b5f14cd24a2ed06e14255ff40fe2ea0cfaef79a8dd68069b7ace74bd6acbba",
-                "sha256:b42b120458636a981077cfcfa8568c031b3e8709701315e2bfa866324a83efa8",
-                "sha256:c4af689352c4fe3d75b2834933ee9d0ccdbf5d7a8a7264f0ce9524e877820c08",
-                "sha256:c7319b6e68de14e6209460f72a8d1ef13c09fb3d3ef6c37c1e65b35d50b5c145",
-                "sha256:cf3f0c361a4270185baa89ec7ab92ecaa355fe783791457077473f974f654df5",
-                "sha256:dd46bde7309088481b1cf9c58e3f0e204b9ff9e3244f441accd220dd3365ce7c",
-                "sha256:dd5476b6c3fe410ee95926873f377b856dbc4e81a9c605a0dc05aaccc6a7c6c6",
-                "sha256:e69140bc2d29a8556f55445c15f5794490852af3de0f609a24003ef174528b79",
-                "sha256:f908a77cbeef9bbd646bd4b81214cbef9ac3dda4181d5092a4aa9797d1bc7774"
+                "sha256:001910ad31abc7bf06f49dcc903755d2f7f3a9186c0c040b827e522e9cef0863",
+                "sha256:0ca6377b8fca51815f382bd0b697a0814c8bda55115678cbc94c30aacbb6eff2",
+                "sha256:0cace394b6ea70c01ca1595f839cf193df35d1575986e484ad35c4aeae7266c1",
+                "sha256:1cb51fe389360f3b5a4d57dbd2848a5f033350336ca3b340d1c53a1fad33bcad",
+                "sha256:2925720037f06e89af896c70bca73459d7e6a4be96f9de79e2d440bd499fe0db",
+                "sha256:3e374f59e440d4ab45ca2fffde54b81ac3834cf5ae2cdfa69c90bc03bde04d76",
+                "sha256:40ae1dffb3967a52203105a077415a86044a2bea011b5f321c6aa64b379a3f51",
+                "sha256:43498c0bdb43d55cb162cdc8c06fac328ccb5d2eabe3cadeb3529ae6f0517c32",
+                "sha256:4abfe0be0d7221be4f12552995e58723c7422c80a659da13ca382697de830c08",
+                "sha256:58b84b91b0b9f4bafac2a0ac55002280c094dfc6402402332c0913a59654ab2b",
+                "sha256:640cef9aa381b60e296db324337a554aeeb883ead99dc8f6c18e81a93942f5f4",
+                "sha256:66b479b0bd07204e37583c191535505410daa8df638fd8e75ae1b383851fe921",
+                "sha256:696039430f7a562b74fa45f540aca068ea85fa34c244d0deee539cb6d70aa288",
+                "sha256:6d2123dc9ad6a814bcdea0f099885276b31b24f7edf40f6cdbc0912672e22eee",
+                "sha256:8635c16bf3d99040fdf3ca3db669a7250ddf49c55dc4aa8fe0ae0fa8d6dcc1f0",
+                "sha256:873d13d177501a28b2756375d59816c365e42ed8417b41665f346289adc68d24",
+                "sha256:8e5a0b00e1e56a842f922e7fae8ae4077aee4af0acb5ae3622bd4b4c30aedf99",
+                "sha256:8e90497254aacacbc4ea6ae5e7a8cd75629d6ad2b30025a4a8b09aa4faf55151",
+                "sha256:9057e6aa78a584bc93a13f0a9bf7e753a5e9770a30b4d758b8d5f2a62a9433cd",
+                "sha256:90c6fca2acf139569e74e8781709dccb6fe25940488755716d1d354d6bc58bce",
+                "sha256:92fd6b027924a7e178ac202cfbe25e53368db90d56872d20ffae94b96c7acc57",
+                "sha256:9dfde2a0ddef507a631dc9dc4af6a9489d5e2e740e226ad426a05cabfbd7c8ef",
+                "sha256:9e79019aba43cb4fda9e4d983f8e88ca0373adbb697ae9c6c43093218de28b54",
+                "sha256:a77e9d1c386196879aa5eb712e77461aaee433e54c68cf253053a73b7e49c33a",
+                "sha256:c7adfc142dac335d8c1e0dcbd37eb8617eac386596eb9e1a1b77791cf2498238",
+                "sha256:d187d355ecec3629624fccb01d104da7d7f391db0311145817525281e2804d23",
+                "sha256:ddf818e4e6c7c6f4f7c8a12709696d193976b591cc7dc50588d3d1a6b5dc8772",
+                "sha256:e9b79011ff7a0f4b1d6da6a61aa1aa604fb312d6647de5bad20013682d1429ce",
+                "sha256:eee3a87076c0756de40b05c5e9a6069c035ba43e8dd71c379e68cab2c20f16ad"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
-            "version": "==2.0.2"
+            "markers": "python_version >= '3.9'",
+            "version": "==2.2.2"
         },
         "python-dateutil": {
             "hashes": [
diff --git a/setup.py b/setup.py
index e00e2ec..813dd68 100644
--- a/setup.py
+++ b/setup.py
@@ -8,7 +8,7 @@
         'gotoh @ git+https://github.com/cfe-lab/MiCall.git@v7.7.0#egg=gotoh&subdirectory=micall/alignment',
         'numpy==1.25.1',
         'python-Levenshtein==0.12.0',
-        'pandas==2.0.2',
+        'pandas==2.2.2',
         'requests==2.31.0',
         'cfeintact @ git+https://github.com/cfe-lab/CFEIntact.git@v1.23.0',
         'pyyaml'

From 6098677bdf7b7d90d6a41b2c02b6c811781db5d2 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 29 Jul 2024 17:50:15 -0700
Subject: [PATCH 45/47] Fix reading of SAM files

Instead of using pandas, use the builtin csv module.

Pandas will not parse a SAM file correctly if it does not have regular
number of columns, which some SAM files dont.
---
 gene_splicer/utils.py          | 42 +++++++++++++++++++---------------
 tests/test_utils/test_utils.py |  5 ++--
 2 files changed, 26 insertions(+), 21 deletions(-)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index e2c49f9..4985ba5 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -101,9 +101,9 @@ def csv_to_bed(csvfile, target_name='HXB2', offset_start=0, offset_stop=0):
                 })
 
 
-def split_cigar(row):
+def split_cigar(string):
     pattern = re.compile(r'(\d+)([A-Z])')
-    cigar = re.findall(pattern, row[5])
+    cigar = re.findall(pattern, string)
     return cigar
 
 
@@ -214,11 +214,12 @@ def modify_annot(annot):
 
 def splice_genes(query, target, samfile, annotation):
     results = {}
-    for i, row in samfile.iterrows():
+    for i, row in enumerate(samfile):
         # Subtract 1 to convert target position to zero-base
         target_pos = int(row[3]) - 1
         query_pos = None
-        for size, op in row['cigar']:
+        cigar = row[5]
+        for size, op in split_cigar(cigar):
             size = int(size)
             # logger.debug(f'size: {size}, op: {op}')
             # logger.debug(f'target_pos: {target_pos}, query_pos: {query_pos}')
@@ -277,11 +278,12 @@ def coords_to_genes(coords, query):
 def splice_aligned_genes(query, target, samfile, annotation):
     results = {}
     sequences = {}
-    for i, row in samfile.iterrows():
+    for i, row in enumerate(samfile):
         # Subtract 1 to convert target position to zero-base
         target_pos = int(row[3]) - 1
         query_pos = None
-        for size, op in row['cigar']:
+        cigar = row[5]
+        for size, op in split_cigar(cigar):
             # print(f'size: {size}, op: {op}')
             # print(f'target_pos: {target_pos}, query_pos: {query_pos}')
             size = int(size)
@@ -334,19 +336,17 @@ def splice_aligned_genes(query, target, samfile, annotation):
     return results, sequences
 
 
-def load_samfile(samfile_path):
-    # Open the SAM file and find the starting point for data
+def load_samfile(samfile_path: Path) -> List[List[str]]:
     with open(samfile_path, 'r') as file:
-        # Skip meta fields
-        lines = file.readlines()
-        data_start_index = 0
-        for i, line in enumerate(lines):
-            if not line.startswith('@'):
-                data_start_index = i
-                break
-
-    result = pd.read_table(samfile_path, skiprows=data_start_index, header=None)
-    result['cigar'] = result.apply(split_cigar, axis=1)
+        reader = csv.reader(file, delimiter='\t')
+
+        result = []
+        for row in reader:
+            # Skip header lines (lines starting with '@')
+            if row[0].startswith('@'):
+                continue
+            result.append(row)
+
     return result
 
 
@@ -594,12 +594,16 @@ def generate_table_precursor_2(hivseqinr_resultsfile, filtered_file,
 
 def get_softclipped_region(query, alignment, alignment_path):
     try:
-        size, op = alignment.iloc[0]['cigar'][0]
+        first_match = alignment[0]
     except IndexError:
         logger.warning('No alignment in %s!', alignment_path)
         return
+
+    cigar = first_match[5]
+    size, op = split_cigar(cigar)[0]
     if op != 'S':
         return
+
     size = int(size)
     return query[:size]
 
diff --git a/tests/test_utils/test_utils.py b/tests/test_utils/test_utils.py
index d378d2c..28d0adc 100644
--- a/tests/test_utils/test_utils.py
+++ b/tests/test_utils/test_utils.py
@@ -16,7 +16,8 @@ def test_get_softclip_start():
     # Normally this alignment would be generated by a separate function
     aln_path = example / 'alignment.sam'
     aln = utils.load_samfile(aln_path)
-    size, op = aln.iloc[0]['cigar'][0]
+    cigar = aln[0][5]
+    size, op = utils.split_cigar(cigar)[0]
     size = int(size)
     query_fasta = Fasta(example / 'query.fasta')
     query_sequence = None
@@ -110,4 +111,4 @@ def test_getSamplesFromCascade():
     samples = utils.get_samples_from_cascade(cascade)
     assert len(samples) == 10
     for i in range(10):
-        assert samples[str(i)] == i
\ No newline at end of file
+        assert samples[str(i)] == i

From 9f874dac7e0f57416e2ddc685c527d671d679ef6 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 29 Jul 2024 17:58:11 -0700
Subject: [PATCH 46/47] Add missing UnknownNucleotide CFEIntact defect code

---
 gene_splicer/utils.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index 4985ba5..e7693ae 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -405,6 +405,7 @@ def align(target_seq,
         return alignment_path
 
 HIVINTACT_ERRORS_TABLE = [
+    'UnknownNucleotide',
     'NonHIV',
     'LongDeletion',
     'InternalInversion',

From 92c8d39599925898ccf9f539ef8599449ddd0290 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 29 Jul 2024 17:59:19 -0700
Subject: [PATCH 47/47] Add missing SequenceDivergence CFEIntact defect code

---
 gene_splicer/utils.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gene_splicer/utils.py b/gene_splicer/utils.py
index e7693ae..91cb81a 100644
--- a/gene_splicer/utils.py
+++ b/gene_splicer/utils.py
@@ -423,6 +423,7 @@ def align(target_seq,
     'Frameshift',
     'MutatedStopCodon',
     'MutatedStartCodon',
+    'SequenceDivergence',
     ]
 
 def iterate_hivintact_verdicts_1(directory: Path, intact: Set[str] = set()) -> Iterable[Tuple[str, str]]: