From c587302cbf5ef99590727948ce54e443b85bf2dd Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Wed, 7 Aug 2024 10:23:40 -0300
Subject: [PATCH 01/17] Initial commit

---
 .../bedtools_genomecov/config.vsh.yaml        |  79 ++++++++++++++
 src/bedtools/bedtools_genomecov/help.txt      | 101 ++++++++++++++++++
 src/bedtools/bedtools_genomecov/script.sh     |  13 +++
 src/bedtools/bedtools_genomecov/test.sh       |  58 ++++++++++
 4 files changed, 251 insertions(+)
 create mode 100644 src/bedtools/bedtools_genomecov/config.vsh.yaml
 create mode 100644 src/bedtools/bedtools_genomecov/help.txt
 create mode 100644 src/bedtools/bedtools_genomecov/script.sh
 create mode 100644 src/bedtools/bedtools_genomecov/test.sh

diff --git a/src/bedtools/bedtools_genomecov/config.vsh.yaml b/src/bedtools/bedtools_genomecov/config.vsh.yaml
new file mode 100644
index 00000000..fb2b39fe
--- /dev/null
+++ b/src/bedtools/bedtools_genomecov/config.vsh.yaml
@@ -0,0 +1,79 @@
+name: bedtools_genomecov
+namespace: bedtools
+description: |
+  Compute the coverage of a feature file among a genome.
+keywords: [genome coverage, BED]
+links:
+  documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
+  repository: https://github.com/arq5x/bedtools2
+references:
+  doi: 10.1093/bioinformatics/btq033
+license: GPL-2.0, MIT
+requirements:
+  commands: [bedtools]
+authors:
+  - __merge__: /src/_authors/theodoro_gasperin.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        alternatives: -i
+        type: file
+        direction: input
+        description: |
+          The input file (BED/GFF/VCF) to be used.
+        required: true
+        example: input.bed
+
+      - name: --genome
+        alternatives: -g
+        type: file
+        direction: input
+        description: |
+          The genome file to be used.
+        required: true
+        example: genome.txt
+    
+  - name: Outputs
+    arguments:
+      - name: --output
+        type: file
+        direction: output
+        description: | 
+          The output BED file. 
+        required: true
+        example: output.bed
+  
+  - name: Options
+    arguments:
+      - name: --input_bam
+        alternatives: -ibam
+        type: boolean_true
+        description: |
+          The input file is in BAM format.
+          Note: BAM _must_ be sorted by position
+      
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+  - type: docker
+    image: debian:stable-slim
+    setup:
+      - type: apt
+        packages: [bedtools, procps]
+      - type: docker
+        run: |
+          echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
+
+runners:
+  - type: executable
+  - type: nextflow
\ No newline at end of file
diff --git a/src/bedtools/bedtools_genomecov/help.txt b/src/bedtools/bedtools_genomecov/help.txt
new file mode 100644
index 00000000..f13a71d3
--- /dev/null
+++ b/src/bedtools/bedtools_genomecov/help.txt
@@ -0,0 +1,101 @@
+```bash
+bedtools genomecov
+```
+
+Tool:    bedtools genomecov (aka genomeCoverageBed)
+Version: v2.30.0
+Summary: Compute the coverage of a feature file among a genome.
+
+Usage: bedtools genomecov [OPTIONS] -i <bed/gff/vcf> -g <genome>
+
+Options: 
+	-ibam		The input file is in BAM format.
+			Note: BAM _must_ be sorted by position
+
+	-d		Report the depth at each genome position (with one-based coordinates).
+			Default behavior is to report a histogram.
+
+	-dz		Report the depth at each genome position (with zero-based coordinates).
+			Reports only non-zero positions.
+			Default behavior is to report a histogram.
+
+	-bg		Report depth in BedGraph format. For details, see:
+			genome.ucsc.edu/goldenPath/help/bedgraph.html
+
+	-bga		Report depth in BedGraph format, as above (-bg).
+			However with this option, regions with zero 
+			coverage are also reported. This allows one to
+			quickly extract all regions of a genome with 0 
+			coverage by applying: "grep -w 0$" to the output.
+
+	-split		Treat "split" BAM or BED12 entries as distinct BED intervals.
+			when computing coverage.
+			For BAM files, this uses the CIGAR "N" and "D" operations 
+			to infer the blocks for computing coverage.
+			For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds
+			fields (i.e., columns 10,11,12).
+
+	-ignoreD	Ignore local deletions (CIGAR "D" operations) in BAM entries
+			when computing coverage.
+
+	-strand		Calculate coverage of intervals from a specific strand.
+			With BED files, requires at least 6 columns (strand is column 6). 
+			- (STRING): can be + or -
+
+	-pc		Calculate coverage of pair-end fragments.
+			Works for BAM files only
+	-fs		Force to use provided fragment size instead of read length
+			Works for BAM files only
+	-du		Change strand af the mate read (so both reads from the same strand) useful for strand specific
+			Works for BAM files only
+	-5		Calculate coverage of 5" positions (instead of entire interval).
+
+	-3		Calculate coverage of 3" positions (instead of entire interval).
+
+	-max		Combine all positions with a depth >= max into
+			a single bin in the histogram. Irrelevant
+			for -d and -bedGraph
+			- (INTEGER)
+
+	-scale		Scale the coverage by a constant factor.
+			Each coverage value is multiplied by this factor before being reported.
+			Useful for normalizing coverage by, e.g., reads per million (RPM).
+			- Default is 1.0; i.e., unscaled.
+			- (FLOAT)
+
+	-trackline	Adds a UCSC/Genome-Browser track line definition in the first line of the output.
+			- See here for more details about track line definition:
+			      http://genome.ucsc.edu/goldenPath/help/bedgraph.html
+			- NOTE: When adding a trackline definition, the output BedGraph can be easily
+			      uploaded to the Genome Browser as a custom track,
+			      BUT CAN NOT be converted into a BigWig file (w/o removing the first line).
+
+	-trackopts	Writes additional track line definition parameters in the first line.
+			- Example:
+			   -trackopts 'name="My Track" visibility=2 color=255,30,30'
+			   Note the use of single-quotes if you have spaces in your parameters.
+			- (TEXT)
+
+Notes: 
+	(1) The genome file should tab delimited and structured as follows:
+	 <chromName><TAB><chromSize>
+
+	For example, Human (hg19):
+	chr1	249250621
+	chr2	243199373
+	...
+	chr18_gl000207_random	4262
+
+	(2) The input BED (-i) file must be grouped by chromosome.
+	 A simple "sort -k 1,1 <BED> > <BED>.sorted" will suffice.
+
+	(3) The input BAM (-ibam) file must be sorted by position.
+	 A "samtools sort <BAM>" should suffice.
+
+Tips: 
+	One can use the UCSC Genome Browser's MySQL database to extract
+	chromosome sizes. For example, H. sapiens:
+
+	mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
+	"select chrom, size from hg19.chromInfo" > hg19.genome
+
diff --git a/src/bedtools/bedtools_genomecov/script.sh b/src/bedtools/bedtools_genomecov/script.sh
new file mode 100644
index 00000000..6a9543d2
--- /dev/null
+++ b/src/bedtools/bedtools_genomecov/script.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+[[ "$par_input_bam" == "false" ]] && unset par_input_bam
+
+bedtools genomecov \
+    ${par_input_bam:+-ibam "$par_input_bam"} \
+    -i "$par_input" \
+    -g "$par_genome" \
+    > "$par_output"
+    
\ No newline at end of file
diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
new file mode 100644
index 00000000..6d9e52ea
--- /dev/null
+++ b/src/bedtools/bedtools_genomecov/test.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+
+# exit on error
+set -e
+
+## VIASH START
+meta_executable="target/executable/bedtools/bedtools_intersect/bedtools_intersect"
+meta_resources_dir="src/bedtools/bedtools_intersect"
+## VIASH END
+
+#############################################
+# helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+assert_file_not_empty() {
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
+}
+assert_file_contains() {
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+assert_identical_content() {
+  diff -a "$2" "$1" \
+    || (echo "Files are not identical!" && exit 1)
+}
+#############################################
+
+# Create directories for tests
+echo "Creating Test Data..."
+mkdir -p test_data
+
+# create input files
+
+# create expected output files
+
+
+# Test 1: 
+mkdir test1
+cd test1
+
+echo "> Run bedtools_genomecov on BED file"
+# "$meta_executable" \
+#   --input_a "../test_data/featuresA.bed" \
+#   --input_b "../test_data/featuresB.bed" \
+#   --output "output.bed"
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_default.bed"
+echo "- test1 succeeded -"
+
+cd ..
+
+
+
+echo "---- All tests succeeded! ----"
+exit 0

From 6f53e13941e009394d0360307885194bbe3dd09f Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Wed, 7 Aug 2024 10:44:23 -0300
Subject: [PATCH 02/17] Update config.vsh.yaml

---
 .../bedtools_genomecov/config.vsh.yaml        | 125 +++++++++++++++++-
 1 file changed, 124 insertions(+), 1 deletion(-)

diff --git a/src/bedtools/bedtools_genomecov/config.vsh.yaml b/src/bedtools/bedtools_genomecov/config.vsh.yaml
index fb2b39fe..40e9a97e 100644
--- a/src/bedtools/bedtools_genomecov/config.vsh.yaml
+++ b/src/bedtools/bedtools_genomecov/config.vsh.yaml
@@ -2,7 +2,7 @@ name: bedtools_genomecov
 namespace: bedtools
 description: |
   Compute the coverage of a feature file among a genome.
-keywords: [genome coverage, BED]
+keywords: [genome coverage, BED, GFF, VCF, BAM]
 links:
   documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
   repository: https://github.com/arq5x/bedtools2
@@ -55,6 +55,129 @@ argument_groups:
           The input file is in BAM format.
           Note: BAM _must_ be sorted by position
       
+      - name: --depth
+        alternatives: -d
+        type: boolean_true
+        description: |
+          Report the depth at each genome position (with one-based coordinates).
+          Default behavior is to report a histogram.
+
+      - name: --depth_zero
+        alternatives: -dz
+        type: boolean_true
+        description: |
+          Report the depth at each genome position (with zero-based coordinates).
+          Reports only non-zero positions.
+          Default behavior is to report a histogram.
+
+      - name: --bed_graph
+        alternatives: -bg
+        type: boolean_true
+        description: |
+          Report depth in BedGraph format. For details, see:
+          genome.ucsc.edu/goldenPath/help/bedgraph.html
+
+      - name: --bed_graph_zero_coverage
+        alternatives: -bga
+        type: boolean_true
+        description: |
+          Report depth in BedGraph format, as above (-bg).
+          However with this option, regions with zero 
+          coverage are also reported. This allows one to
+          quickly extract all regions of a genome with 0 
+          coverage by applying: "grep -w 0$" to the output.
+
+      - name: --split
+        type: boolean_true
+        description: |
+          Treat "split" BAM or BED12 entries as distinct BED intervals.
+          when computing coverage.
+          For BAM files, this uses the CIGAR "N" and "D" operations 
+          to infer the blocks for computing coverage.
+          For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds
+          fields (i.e., columns 10,11,12).
+
+      - name: --ignore_deletion
+        alternatives: -ignoreD
+        type: boolean_true
+        description: |
+          Ignore local deletions (CIGAR "D" operations) in BAM entries
+          when computing coverage.
+
+      - name: --strand
+        type: string
+        description: |
+          Calculate coverage of intervals from a specific strand.
+          With BED files, requires at least 6 columns (strand is column 6). 
+          - (STRING): can be + or -
+
+      - name: --pair_end_coverage
+        alternatives: -pc
+        type: boolean_true
+        description: |
+          Calculate coverage of pair-end fragments.
+          Works for BAM files only
+
+      - name: --fragment_size
+        alternatives: -fs
+        type: boolean_true
+        description: |
+          Force to use provided fragment size instead of read length
+          Works for BAM files only
+
+      - name: --du
+        type: boolean_true
+        description: |
+          Change strand af the mate read (so both reads from the same strand) useful for strand specific
+          Works for BAM files only
+
+      - name: --5_prime
+        alternatives: -5
+        type: boolean_true
+        description: |
+          Calculate coverage of 5" positions (instead of entire interval).
+
+      - name: --3_prime
+        alternatives: -3
+        type: boolean_true
+        description: |
+          Calculate coverage of 3" positions (instead of entire interval).
+
+      - name: --max
+        type: integer
+        description: |
+          Combine all positions with a depth >= max into
+          a single bin in the histogram. Irrelevant
+          for -d and -bedGraph
+          - (INTEGER)
+
+      - name: --scale
+        type: double
+        description: |
+          Scale the coverage by a constant factor.
+          Each coverage value is multiplied by this factor before being reported.
+          Useful for normalizing coverage by, e.g., reads per million (RPM).
+          - Default is 1.0; i.e., unscaled.
+          - (FLOAT)
+
+      - name: --trackline
+        type: boolean_true
+        description: |
+          Adds a UCSC/Genome-Browser track line definition in the first line of the output.
+          - See here for more details about track line definition:
+                http://genome.ucsc.edu/goldenPath/help/bedgraph.html
+          - NOTE: When adding a trackline definition, the output BedGraph can be easily
+                uploaded to the Genome Browser as a custom track,
+                BUT CAN NOT be converted into a BigWig file (w/o removing the first line).
+      
+      - name: --trackopts
+        type: string
+        description: |
+          Writes additional track line definition parameters in the first line.
+          - Example:
+            -trackopts 'name="My Track" visibility=2 color=255,30,30'
+            Note the use of single-quotes if you have spaces in your parameters.
+          - (TEXT)
 
 resources:
   - type: bash_script

From da6e11fb8045311e8614e8c7dfb4005b46669f78 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Wed, 7 Aug 2024 10:51:31 -0300
Subject: [PATCH 03/17] Update script.sh

---
 src/bedtools/bedtools_genomecov/script.sh | 28 +++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/src/bedtools/bedtools_genomecov/script.sh b/src/bedtools/bedtools_genomecov/script.sh
index 6a9543d2..5dac5946 100644
--- a/src/bedtools/bedtools_genomecov/script.sh
+++ b/src/bedtools/bedtools_genomecov/script.sh
@@ -4,9 +4,37 @@
 ## VIASH END
 
 [[ "$par_input_bam" == "false" ]] && unset par_input_bam
+[[ "$par_depth" == "false" ]] && unset par_depth
+[[ "$par_depth_zero" == "false" ]] && unset par_depth_zero
+[[ "$par_bed_graph" == "false" ]] && unset par_bed_graph
+[[ "$par_bed_graph_zero_coverage" == "false" ]] && unset par_bed_graph_zero_coverage
+[[ "$par_split" == "false" ]] && unset par_split
+[[ "$par_ignore_deletion" == "false" ]] && unset par_ignore_deletion
+[[ "$par_pair_end_coverage" == "false" ]] && unset par_pair_end_coverage
+[[ "$par_fragment_size" == "false" ]] && unset par_fragment_size
+[[ "$par_du" == "false" ]] && unset par_du
+[[ "$par_5_prime" == "false" ]] && unset par_5_prime
+[[ "$par_3_prime" == "false" ]] && unset par_3_prime
+[[ "$par_trackline" == "false" ]] && unset par_trackline
 
 bedtools genomecov \
     ${par_input_bam:+-ibam "$par_input_bam"} \
+    ${par_depth:+-d} \
+    ${par_depth_zero:+-dz} \
+    ${par_bed_graph:+-bg} \
+    ${par_bed_graph_zero_coverage:+-bga} \
+    ${par_split:+-split} \
+    ${par_ignore_deletion:+-ignoreD} \
+    ${par_pair_end_coverage:+-pc} \
+    ${par_fragment_size:+-fs} \
+    ${par_du:+-du} \
+    ${par_5_prime:+-5} \
+    ${par_3_prime:+-3} \
+    ${par_trackline:+-trackline} \
+    ${par_strand:+-strand "$par_strand"} \
+    ${par_max:+-max "$par_max"} \
+    ${par_scale:+-scale "$par_scale"} \
+    ${par_trackopts:+-trackopts "$par_trackopts"} \
     -i "$par_input" \
     -g "$par_genome" \
     > "$par_output"

From bac80a5572370d8239f9d4ceb2b2c7c9e05da028 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Wed, 7 Aug 2024 11:08:40 -0300
Subject: [PATCH 04/17] update on test.sh

---
 src/bedtools/bedtools_genomecov/test.sh       | 25 +++++++++++++------
 .../bedtools_genomecov/test_data/example.bed  |  2 ++
 .../bedtools_genomecov/test_data/genome.txt   |  3 +++
 3 files changed, 22 insertions(+), 8 deletions(-)
 create mode 100644 src/bedtools/bedtools_genomecov/test_data/example.bed
 create mode 100644 src/bedtools/bedtools_genomecov/test_data/genome.txt

diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
index 6d9e52ea..5305438f 100644
--- a/src/bedtools/bedtools_genomecov/test.sh
+++ b/src/bedtools/bedtools_genomecov/test.sh
@@ -29,9 +29,18 @@ assert_identical_content() {
 echo "Creating Test Data..."
 mkdir -p test_data
 
-# create input files
-
-# create expected output files
+# Create and populate input files
+printf "chr1\t248956422\nchr3\t242193529\nchr2\t198295559\n" > "test_data/genome.txt"
+printf "chr2:172936693-172938111\t128\t228\tmy_read/1\t37\t+\nchr2:172936693-172938111\t428\t528\tmy_read/2\t37\t-\n" > "test_data/example.bed"
+printf "chr2:172936693-172938111\t128\t228\tmy_read/1\t60\t+\t128\t228\t255,0,0\t1\t100\t0\nchr2:172936693-172938111\t428\t528\tmy_read/2\t60\t-\t428\t528\t255,0,0\t1\t100\t0\n" > "test_data/example.bed12"
+# Create and populate example.gff file
+printf "##gff-version 3\n" > "test_data/example.gff"
+printf "chr1\t.\tgene\t1000\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/example.gff"
+printf "chr3\t.\tmRNA\t1000\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/example.gff"
+printf "chr1\t.\texon\t1000\t1200\t.\t+\t.\tID=exon1;Parent=transcript1\n" >> "test_data/example.gff"
+printf "chr2\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/example.gff"
+printf "chr1\t.\tCDS\t1000\t1200\t.\t+\t0\tID=cds1;Parent=transcript1\n" >> "test_data/example.gff"
+printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/example.gff"
 
 
 # Test 1: 
@@ -39,15 +48,15 @@ mkdir test1
 cd test1
 
 echo "> Run bedtools_genomecov on BED file"
-# "$meta_executable" \
-#   --input_a "../test_data/featuresA.bed" \
-#   --input_b "../test_data/featuresB.bed" \
-#   --output "output.bed"
+"$meta_executable" \
+  --input "../test_data/example.bed" \
+  --genome "../test_data/genome.txt" \
+  --output "output.bed"
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_default.bed"
+#assert_identical_content "output.bed" "../test_data/expected_default.bed"
 echo "- test1 succeeded -"
 
 cd ..
diff --git a/src/bedtools/bedtools_genomecov/test_data/example.bed b/src/bedtools/bedtools_genomecov/test_data/example.bed
new file mode 100644
index 00000000..09df88eb
--- /dev/null
+++ b/src/bedtools/bedtools_genomecov/test_data/example.bed
@@ -0,0 +1,2 @@
+chr2	128	228	my_read/1	37	+
+chr2	428	528	my_read/2	37	-
diff --git a/src/bedtools/bedtools_genomecov/test_data/genome.txt b/src/bedtools/bedtools_genomecov/test_data/genome.txt
new file mode 100644
index 00000000..460c34fe
--- /dev/null
+++ b/src/bedtools/bedtools_genomecov/test_data/genome.txt
@@ -0,0 +1,3 @@
+chr1	248956422
+chr2	198295559
+chr3	242193529

From 6a81a19c61faa0b412584671db0bee75dd367e24 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Thu, 8 Aug 2024 09:48:07 -0300
Subject: [PATCH 05/17] bug fixing

---
 .../bedtools_genomecov/config.vsh.yaml        |  4 +-
 src/bedtools/bedtools_genomecov/script.sh     |  8 ++--
 src/bedtools/bedtools_genomecov/test.sh       | 38 +++++++++++++------
 3 files changed, 32 insertions(+), 18 deletions(-)

diff --git a/src/bedtools/bedtools_genomecov/config.vsh.yaml b/src/bedtools/bedtools_genomecov/config.vsh.yaml
index 40e9a97e..452153b5 100644
--- a/src/bedtools/bedtools_genomecov/config.vsh.yaml
+++ b/src/bedtools/bedtools_genomecov/config.vsh.yaml
@@ -131,13 +131,13 @@ argument_groups:
           Change strand af the mate read (so both reads from the same strand) useful for strand specific
           Works for BAM files only
 
-      - name: --5_prime
+      - name: --five_prime
         alternatives: -5
         type: boolean_true
         description: |
           Calculate coverage of 5" positions (instead of entire interval).
 
-      - name: --3_prime
+      - name: --three_prime
         alternatives: -3
         type: boolean_true
         description: |
diff --git a/src/bedtools/bedtools_genomecov/script.sh b/src/bedtools/bedtools_genomecov/script.sh
index 5dac5946..06a120b7 100644
--- a/src/bedtools/bedtools_genomecov/script.sh
+++ b/src/bedtools/bedtools_genomecov/script.sh
@@ -13,8 +13,8 @@
 [[ "$par_pair_end_coverage" == "false" ]] && unset par_pair_end_coverage
 [[ "$par_fragment_size" == "false" ]] && unset par_fragment_size
 [[ "$par_du" == "false" ]] && unset par_du
-[[ "$par_5_prime" == "false" ]] && unset par_5_prime
-[[ "$par_3_prime" == "false" ]] && unset par_3_prime
+[[ "$par_five_prime" == "false" ]] && unset par_five_prime
+[[ "$par_three_prime" == "false" ]] && unset par_three_prime
 [[ "$par_trackline" == "false" ]] && unset par_trackline
 
 bedtools genomecov \
@@ -28,8 +28,8 @@ bedtools genomecov \
     ${par_pair_end_coverage:+-pc} \
     ${par_fragment_size:+-fs} \
     ${par_du:+-du} \
-    ${par_5_prime:+-5} \
-    ${par_3_prime:+-3} \
+    ${par_five_prime:+-5} \
+    ${par_three_prime:+-3} \
     ${par_trackline:+-trackline} \
     ${par_strand:+-strand "$par_strand"} \
     ${par_max:+-max "$par_max"} \
diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
index 5305438f..40cff0ff 100644
--- a/src/bedtools/bedtools_genomecov/test.sh
+++ b/src/bedtools/bedtools_genomecov/test.sh
@@ -30,18 +30,19 @@ echo "Creating Test Data..."
 mkdir -p test_data
 
 # Create and populate input files
-printf "chr1\t248956422\nchr3\t242193529\nchr2\t198295559\n" > "test_data/genome.txt"
-printf "chr2:172936693-172938111\t128\t228\tmy_read/1\t37\t+\nchr2:172936693-172938111\t428\t528\tmy_read/2\t37\t-\n" > "test_data/example.bed"
-printf "chr2:172936693-172938111\t128\t228\tmy_read/1\t60\t+\t128\t228\t255,0,0\t1\t100\t0\nchr2:172936693-172938111\t428\t528\tmy_read/2\t60\t-\t428\t528\t255,0,0\t1\t100\t0\n" > "test_data/example.bed12"
-# Create and populate example.gff file
-printf "##gff-version 3\n" > "test_data/example.gff"
-printf "chr1\t.\tgene\t1000\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/example.gff"
-printf "chr3\t.\tmRNA\t1000\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/example.gff"
-printf "chr1\t.\texon\t1000\t1200\t.\t+\t.\tID=exon1;Parent=transcript1\n" >> "test_data/example.gff"
-printf "chr2\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/example.gff"
-printf "chr1\t.\tCDS\t1000\t1200\t.\t+\t0\tID=cds1;Parent=transcript1\n" >> "test_data/example.gff"
-printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/example.gff"
+printf "chr1\t248956422\nchr2\t198295559\nchr3\t242193529\n" > "test_data/genome.txt"
+printf "chr2\t128\t228\tmy_read/1\t37\t+\nchr2\t428\t528\tmy_read/2\t37\t-\n" > "test_data/example.bed"
+printf "chr2\t128\t228\tmy_read/1\t60\t+\t128\t228\t255,0,0\t1\t100\t0\nchr2\t428\t528\tmy_read/2\t60\t-\t428\t528\t255,0,0\t1\t100\t0\n" > "test_data/example.bed12"
 
+# expected output
+cat > "test_data/expected_default.bed" <<EOF
+chr2	0	198295359	198295559	0.999999
+chr2	1	200	198295559	1.0086e-06
+chr1	0	248956422	248956422	1
+chr3	0	242193529	242193529	1
+genome	0	689445310	689445510	1
+genome	1	200	689445510	2.90088e-07
+EOF
 
 # Test 1: 
 mkdir test1
@@ -56,11 +57,24 @@ echo "> Run bedtools_genomecov on BED file"
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-#assert_identical_content "output.bed" "../test_data/expected_default.bed"
+assert_identical_content "output.bed" "../test_data/expected_default.bed"
 echo "- test1 succeeded -"
 
 cd ..
 
+# Test 2: ibam option and pair end option and fragment size option
+
+# Test 3: depth option
+
+# Test 4: strand option
+
+# Test 5: 5' end option
+
+# Test 6: max option
+
+# Test 7: scale option
+
+# Test 8: trackopts option
 
 
 echo "---- All tests succeeded! ----"

From 278ff8ab2ea93ef8ddbec57c41bce2d6bbc38ead Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Thu, 8 Aug 2024 10:26:39 -0300
Subject: [PATCH 06/17] adding ibam option tests

---
 .../bedtools_genomecov/config.vsh.yaml        |  19 +++--
 src/bedtools/bedtools_genomecov/script.sh     |  10 +--
 src/bedtools/bedtools_genomecov/test.sh       |  78 +++++++++++++++++-
 .../bedtools_genomecov/test_data/example.bam  | Bin 0 -> 334 bytes
 4 files changed, 91 insertions(+), 16 deletions(-)
 create mode 100644 src/bedtools/bedtools_genomecov/test_data/example.bam

diff --git a/src/bedtools/bedtools_genomecov/config.vsh.yaml b/src/bedtools/bedtools_genomecov/config.vsh.yaml
index 452153b5..9035858c 100644
--- a/src/bedtools/bedtools_genomecov/config.vsh.yaml
+++ b/src/bedtools/bedtools_genomecov/config.vsh.yaml
@@ -24,8 +24,15 @@ argument_groups:
         direction: input
         description: |
           The input file (BED/GFF/VCF) to be used.
-        required: true
         example: input.bed
+      
+      - name: --input_bam
+        alternatives: -ibam
+        type: file
+        description: |
+          The input file is in BAM format.
+          Note: BAM _must_ be sorted by positions.
+          --genome option is ignored!
 
       - name: --genome
         alternatives: -g
@@ -33,7 +40,6 @@ argument_groups:
         direction: input
         description: |
           The genome file to be used.
-        required: true
         example: genome.txt
     
   - name: Outputs
@@ -48,13 +54,7 @@ argument_groups:
   
   - name: Options
     arguments:
-      - name: --input_bam
-        alternatives: -ibam
-        type: boolean_true
-        description: |
-          The input file is in BAM format.
-          Note: BAM _must_ be sorted by position
-      
+
       - name: --depth
         alternatives: -d
         type: boolean_true
@@ -186,6 +186,7 @@ resources:
 test_resources:
   - type: bash_script
     path: test.sh
+  - path: test_data
 
 engines:
   - type: docker
diff --git a/src/bedtools/bedtools_genomecov/script.sh b/src/bedtools/bedtools_genomecov/script.sh
index 06a120b7..39c4d0db 100644
--- a/src/bedtools/bedtools_genomecov/script.sh
+++ b/src/bedtools/bedtools_genomecov/script.sh
@@ -18,15 +18,12 @@
 [[ "$par_trackline" == "false" ]] && unset par_trackline
 
 bedtools genomecov \
-    ${par_input_bam:+-ibam "$par_input_bam"} \
     ${par_depth:+-d} \
     ${par_depth_zero:+-dz} \
     ${par_bed_graph:+-bg} \
     ${par_bed_graph_zero_coverage:+-bga} \
     ${par_split:+-split} \
     ${par_ignore_deletion:+-ignoreD} \
-    ${par_pair_end_coverage:+-pc} \
-    ${par_fragment_size:+-fs} \
     ${par_du:+-du} \
     ${par_five_prime:+-5} \
     ${par_three_prime:+-3} \
@@ -35,7 +32,10 @@ bedtools genomecov \
     ${par_max:+-max "$par_max"} \
     ${par_scale:+-scale "$par_scale"} \
     ${par_trackopts:+-trackopts "$par_trackopts"} \
-    -i "$par_input" \
-    -g "$par_genome" \
+    ${par_input_bam:+-ibam "$par_input_bam"} \
+    ${par_input:+-i "$par_input"} \
+    ${par_genome:+-g "$par_genome"} \
+    ${par_pair_end_coverage:+-pc} \
+    ${par_fragment_size:+-fs} \
     > "$par_output"
     
\ No newline at end of file
diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
index 40cff0ff..57510982 100644
--- a/src/bedtools/bedtools_genomecov/test.sh
+++ b/src/bedtools/bedtools_genomecov/test.sh
@@ -8,6 +8,9 @@ meta_executable="target/executable/bedtools/bedtools_intersect/bedtools_intersec
 meta_resources_dir="src/bedtools/bedtools_intersect"
 ## VIASH END
 
+# directory of the bam file
+test_data="$meta_resources_dir/test_data"
+
 #############################################
 # helper functions
 assert_file_exists() {
@@ -34,7 +37,7 @@ printf "chr1\t248956422\nchr2\t198295559\nchr3\t242193529\n" > "test_data/genome
 printf "chr2\t128\t228\tmy_read/1\t37\t+\nchr2\t428\t528\tmy_read/2\t37\t-\n" > "test_data/example.bed"
 printf "chr2\t128\t228\tmy_read/1\t60\t+\t128\t228\t255,0,0\t1\t100\t0\nchr2\t428\t528\tmy_read/2\t60\t-\t428\t528\t255,0,0\t1\t100\t0\n" > "test_data/example.bed12"
 
-# expected output
+# expected outputs
 cat > "test_data/expected_default.bed" <<EOF
 chr2	0	198295359	198295559	0.999999
 chr2	1	200	198295559	1.0086e-06
@@ -43,6 +46,24 @@ chr3	0	242193529	242193529	1
 genome	0	689445310	689445510	1
 genome	1	200	689445510	2.90088e-07
 EOF
+cat > "test_data/expected_ibam.bed" <<EOF
+chr2:172936693-172938111	0	1218	1418	0.858956
+chr2:172936693-172938111	1	200	1418	0.141044
+genome	0	1218	1418	0.858956
+genome	1	200	1418	0.141044
+EOF
+cat > "test_data/expected_ibam_pc.bed" <<EOF
+chr2:172936693-172938111	0	1018	1418	0.717913
+chr2:172936693-172938111	1	400	1418	0.282087
+genome	0	1018	1418	0.717913
+genome	1	400	1418	0.282087
+EOF
+cat > "test_data/expected_ibam_fs.bed" <<EOF
+chr2:172936693-172938111	0	1218	1418	0.858956
+chr2:172936693-172938111	1	200	1418	0.141044
+genome	0	1218	1418	0.858956
+genome	1	200	1418	0.141044
+EOF
 
 # Test 1: 
 mkdir test1
@@ -62,7 +83,22 @@ echo "- test1 succeeded -"
 
 cd ..
 
-# Test 2: ibam option and pair end option and fragment size option
+# Test 2: ibam option 
+mkdir test2
+cd test2
+
+echo "> Run bedtools_genomecov on BAM file with -ibam"
+"$meta_executable" \
+  --input_bam "$test_data/example.bam" \
+  --output "output.bed" \
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_ibam.bed"
+echo "- test2 succeeded -"
+
+cd ..
 
 # Test 3: depth option
 
@@ -76,6 +112,44 @@ cd ..
 
 # Test 8: trackopts option
 
+# Test 9: bedgraph option
+
+# Test 10: ibam pc options
+mkdir test10
+cd test10
+
+echo "> Run bedtools_genomecov on BAM file with -ibam, -pc"
+"$meta_executable" \
+  --input_bam "$test_data/example.bam" \
+  --output "output.bed" \
+  --fragment_size \
+  --pair_end_coverage \
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_ibam_pc.bed"
+echo "- test10 succeeded -"
+
+cd ..
+
+# Test 11: ibam fs options
+mkdir test11
+cd test11
+
+echo "> Run bedtools_genomecov on BAM file with -ibam, -fs"
+"$meta_executable" \
+  --input_bam "$test_data/example.bam" \
+  --output "output.bed" \
+  --fragment_size \
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_ibam_fs.bed"
+echo "- test11 succeeded -"
+
+cd ..
 
 echo "---- All tests succeeded! ----"
 exit 0
diff --git a/src/bedtools/bedtools_genomecov/test_data/example.bam b/src/bedtools/bedtools_genomecov/test_data/example.bam
new file mode 100644
index 0000000000000000000000000000000000000000..ffc075ab83a83a98ed1edbf88b26cc27ad8946c6
GIT binary patch
literal 334
zcmb2|=3rp}f&Xj_PR>jWAq>SuUsA6mBqS7Y@IB%Aw%O~PhS4S?6Z1_bX2zRMuCZ>`
z;o;@Ato^fw$CpQUheTtRYNNz-r#8JXHa3Ry>s4lk0?m>~GxQF_-U<7&m>dP#pU;|5
z)~CHK)-&PMX8(zQnRkjz7tzu&Q_9lpm^;_nXXDZb**~)OH9hZA+GbYw!F2!1eU^u&
z=6?J8db>^n+vnS58VqGOpQde!^LhT^FPno$sK1R;RVb&i_o5|>-LG;Kg??MHCx&;~
ziZww?R#r16X1LX_ZFYQZ=WBLl9Y-y@V*W$>-;Wo3eOwoN_@m-GsXhDI<L7O#D!rR*
zAbon#WHIeSf_p=Iw@vX;QcA7~nW$-K`s?tN6@ejF_co|EotL|LtN#%rrst#?n85)E
FA^@Dlf^q-=

literal 0
HcmV?d00001


From 887ac00bfb1441d1dce467a430d284516e473495 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Thu, 8 Aug 2024 10:39:37 -0300
Subject: [PATCH 07/17] depthzero and strand option tests

---
 src/bedtools/bedtools_genomecov/test.sh       | 48 +++++++++++++++++++
 .../test_data/example_dz.bed                  |  1 +
 2 files changed, 49 insertions(+)
 create mode 100644 src/bedtools/bedtools_genomecov/test_data/example_dz.bed

diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
index 57510982..1f62db8d 100644
--- a/src/bedtools/bedtools_genomecov/test.sh
+++ b/src/bedtools/bedtools_genomecov/test.sh
@@ -36,6 +36,7 @@ mkdir -p test_data
 printf "chr1\t248956422\nchr2\t198295559\nchr3\t242193529\n" > "test_data/genome.txt"
 printf "chr2\t128\t228\tmy_read/1\t37\t+\nchr2\t428\t528\tmy_read/2\t37\t-\n" > "test_data/example.bed"
 printf "chr2\t128\t228\tmy_read/1\t60\t+\t128\t228\t255,0,0\t1\t100\t0\nchr2\t428\t528\tmy_read/2\t60\t-\t428\t528\t255,0,0\t1\t100\t0\n" > "test_data/example.bed12"
+printf "chr2\t100\t103\n" > "test_data/example_dz.bed"
 
 # expected outputs
 cat > "test_data/expected_default.bed" <<EOF
@@ -64,6 +65,19 @@ chr2:172936693-172938111	1	200	1418	0.141044
 genome	0	1218	1418	0.858956
 genome	1	200	1418	0.141044
 EOF
+cat > "test_data/expected_dz.bed" <<EOF
+chr2	100	1
+chr2	101	1
+chr2	102	1
+EOF
+cat > "test_data/expected_strand.bed" <<EOF
+chr2	0	198295459	198295559	1
+chr2	1	100	198295559	5.04298e-07
+chr1	0	248956422	248956422	1
+chr3	0	242193529	242193529	1
+genome	0	689445410	689445510	1
+genome	1	100	689445510	1.45044e-07
+EOF
 
 # Test 1: 
 mkdir test1
@@ -101,8 +115,42 @@ echo "- test2 succeeded -"
 cd ..
 
 # Test 3: depth option
+mkdir test3
+cd test3
+
+echo "> Run bedtools_genomecov on BED file with -dz"
+"$meta_executable" \
+  --input "../test_data/example_dz.bed" \
+  --genome "../test_data/genome.txt" \
+  --output "output.bed" \
+  --depth_zero
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_dz.bed"
+echo "- test3 succeeded -"
+
+cd ..
 
 # Test 4: strand option
+mkdir test4
+cd test4
+
+echo "> Run bedtools_genomecov on BED file with -strand"
+"$meta_executable" \
+  --input "../test_data/example.bed" \
+  --genome "../test_data/genome.txt" \
+  --output "output.bed" \
+  --strand "-" \
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_strand.bed"
+echo "- test4 succeeded -"
+
+cd ..
 
 # Test 5: 5' end option
 
diff --git a/src/bedtools/bedtools_genomecov/test_data/example_dz.bed b/src/bedtools/bedtools_genomecov/test_data/example_dz.bed
new file mode 100644
index 00000000..a5b1a250
--- /dev/null
+++ b/src/bedtools/bedtools_genomecov/test_data/example_dz.bed
@@ -0,0 +1 @@
+chr2	100	103

From f264e22abd0307152425e738c04e4cb194548bc9 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Thu, 8 Aug 2024 10:48:28 -0300
Subject: [PATCH 08/17] 5prime and max tests

---
 src/bedtools/bedtools_genomecov/test.sh | 60 +++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
index 1f62db8d..a5bae97c 100644
--- a/src/bedtools/bedtools_genomecov/test.sh
+++ b/src/bedtools/bedtools_genomecov/test.sh
@@ -78,6 +78,15 @@ chr3	0	242193529	242193529	1
 genome	0	689445410	689445510	1
 genome	1	100	689445510	1.45044e-07
 EOF
+cat > "test_data/expected_5.bed" <<EOF
+chr2	0	198295557	198295559	1
+chr2	1	2	198295559	1.0086e-08
+chr1	0	248956422	248956422	1
+chr3	0	242193529	242193529	1
+genome	0	689445508	689445510	1
+genome	1	2	689445510	2.90088e-09
+EOF
+
 
 # Test 1: 
 mkdir test1
@@ -153,10 +162,61 @@ echo "- test4 succeeded -"
 cd ..
 
 # Test 5: 5' end option
+mkdir test5
+cd test5
+
+echo "> Run bedtools_genomecov on BED file with -5"
+"$meta_executable" \
+  --input "../test_data/example.bed" \
+  --genome "../test_data/genome.txt" \
+  --output "output.bed" \
+  --five_prime \
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_5.bed"
+echo "- test5 succeeded -"
+
+cd ..
 
 # Test 6: max option
+mkdir test6
+cd test6
+
+echo "> Run bedtools_genomecov on BED file with -max"
+"$meta_executable" \
+  --input "../test_data/example.bed" \
+  --genome "../test_data/genome.txt" \
+  --output "output.bed" \
+  --max 100 \
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_default.bed"
+echo "- test6 succeeded -"
+
+cd ..
 
 # Test 7: scale option
+# mkdir test7
+# cd test7
+
+# echo "> Run bedtools_genomecov on BED file with bedgraph and scale"
+# "$meta_executable" \
+#   --input "../test_data/example.bed" \
+#   --genome "../test_data/genome.txt" \
+#   --output "output.bed" \
+#   --scale 100 \
+
+# # checks
+# assert_file_exists "output.bed"
+# assert_file_not_empty "output.bed"
+# assert_identical_content "output.bed" "../test_data/expected_default.bed"
+# echo "- test7 succeeded -"
+
+# cd ..
 
 # Test 8: trackopts option
 

From 7a27fe5efc634db272abc195e4a29ab3f0e99cc8 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Thu, 8 Aug 2024 11:23:18 -0300
Subject: [PATCH 09/17] more tests

---
 src/bedtools/bedtools_genomecov/test.sh       | 125 ++++++++++++++----
 .../test_data/example.bed12                   |   2 +
 2 files changed, 103 insertions(+), 24 deletions(-)
 create mode 100644 src/bedtools/bedtools_genomecov/test_data/example.bed12

diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
index a5bae97c..cf262fc7 100644
--- a/src/bedtools/bedtools_genomecov/test.sh
+++ b/src/bedtools/bedtools_genomecov/test.sh
@@ -86,7 +86,29 @@ chr3	0	242193529	242193529	1
 genome	0	689445508	689445510	1
 genome	1	2	689445510	2.90088e-09
 EOF
-
+cat > "test_data/expected_bg_scale.bed" <<EOF
+chr2	128	228	100
+chr2	428	528	100
+EOF
+cat > "test_data/expected_trackopts.bed" <<EOF
+track type=bedGraph name=example
+chr2	128	228	1
+chr2	428	528	1
+EOF
+cat > "test_data/expected_split.bed" <<EOF
+chr2	0	198295359	198295559	0.999999
+chr2	1	200	198295559	1.0086e-06
+chr1	0	248956422	248956422	1
+chr3	0	242193529	242193529	1
+genome	0	689445310	689445510	1
+genome	1	200	689445510	2.90088e-07
+EOF
+cat > "test_data/expected_ignoreD_du.bed" <<EOF
+chr2:172936693-172938111	0	1218	1418	0.858956
+chr2:172936693-172938111	1	200	1418	0.141044
+genome	0	1218	1418	0.858956
+genome	1	200	1418	0.141044
+EOF
 
 # Test 1: 
 mkdir test1
@@ -199,32 +221,49 @@ echo "- test6 succeeded -"
 
 cd ..
 
-# Test 7: scale option
-# mkdir test7
-# cd test7
+# Test 7: bedgraph and scale option
+mkdir test7
+cd test7
 
-# echo "> Run bedtools_genomecov on BED file with bedgraph and scale"
-# "$meta_executable" \
-#   --input "../test_data/example.bed" \
-#   --genome "../test_data/genome.txt" \
-#   --output "output.bed" \
-#   --scale 100 \
+echo "> Run bedtools_genomecov on BED file with -bg and -scale"
+"$meta_executable" \
+  --input "../test_data/example.bed" \
+  --genome "../test_data/genome.txt" \
+  --output "output.bed" \
+  --bed_graph \
+  --scale 100 \
 
-# # checks
-# assert_file_exists "output.bed"
-# assert_file_not_empty "output.bed"
-# assert_identical_content "output.bed" "../test_data/expected_default.bed"
-# echo "- test7 succeeded -"
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_bg_scale.bed"
+echo "- test7 succeeded -"
 
-# cd ..
+cd ..
 
 # Test 8: trackopts option
+mkdir test8
+cd test8
 
-# Test 9: bedgraph option
+echo "> Run bedtools_genomecov on BED file with -bg and -trackopts"
+"$meta_executable" \
+  --input "../test_data/example.bed" \
+  --genome "../test_data/genome.txt" \
+  --output "output.bed" \
+  --bed_graph \
+  --trackopts "name=example" \
 
-# Test 10: ibam pc options
-mkdir test10
-cd test10
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_trackopts.bed"
+echo "- test8 succeeded -"
+
+cd ..
+
+# Test 9: ibam pc options
+mkdir test9
+cd test9
 
 echo "> Run bedtools_genomecov on BAM file with -ibam, -pc"
 "$meta_executable" \
@@ -237,13 +276,13 @@ echo "> Run bedtools_genomecov on BAM file with -ibam, -pc"
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
 assert_identical_content "output.bed" "../test_data/expected_ibam_pc.bed"
-echo "- test10 succeeded -"
+echo "- test9 succeeded -"
 
 cd ..
 
-# Test 11: ibam fs options
-mkdir test11
-cd test11
+# Test 10: ibam fs options
+mkdir test10
+cd test10
 
 echo "> Run bedtools_genomecov on BAM file with -ibam, -fs"
 "$meta_executable" \
@@ -255,9 +294,47 @@ echo "> Run bedtools_genomecov on BAM file with -ibam, -fs"
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
 assert_identical_content "output.bed" "../test_data/expected_ibam_fs.bed"
+echo "- test10 succeeded -"
+
+cd ..
+
+# Test 11: split 
+mkdir test11
+cd test11
+
+echo "> Run bedtools_genomecov on BED12 file with -split"
+"$meta_executable" \
+  --input "../test_data/example.bed12" \
+  --genome "../test_data/genome.txt" \
+  --output "output.bed" \
+  --split \
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_split.bed"
 echo "- test11 succeeded -"
 
 cd ..
 
+# Test 12: ignore deletion and du
+mkdir test12
+cd test12
+
+echo "> Run bedtools_genomecov on BAM file with -ignoreD and -du"
+"$meta_executable" \
+  --input_bam "$test_data/example.bam" \
+  --output "output.bed" \
+  --ignore_deletion \
+  --du \
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_ignoreD_du.bed"
+echo "- test12 succeeded -"
+
+cd ..
+
 echo "---- All tests succeeded! ----"
 exit 0
diff --git a/src/bedtools/bedtools_genomecov/test_data/example.bed12 b/src/bedtools/bedtools_genomecov/test_data/example.bed12
new file mode 100644
index 00000000..58c7a75d
--- /dev/null
+++ b/src/bedtools/bedtools_genomecov/test_data/example.bed12
@@ -0,0 +1,2 @@
+chr2	128	228	my_read/1	60	+	128	228	255,0,0	1	100	0
+chr2	428	528	my_read/2	60	-	428	528	255,0,0	1	100	0

From d3b46757182943d25c0aeef6f4a2d49d458978f4 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Thu, 8 Aug 2024 11:25:24 -0300
Subject: [PATCH 10/17] Changelog

---
 CHANGELOG.md                                             | 2 +-
 src/bedtools/bedtools_genomecov/test_data/example.bed    | 2 --
 src/bedtools/bedtools_genomecov/test_data/example.bed12  | 2 --
 src/bedtools/bedtools_genomecov/test_data/example_dz.bed | 1 -
 src/bedtools/bedtools_genomecov/test_data/genome.txt     | 3 ---
 5 files changed, 1 insertion(+), 9 deletions(-)
 delete mode 100644 src/bedtools/bedtools_genomecov/test_data/example.bed
 delete mode 100644 src/bedtools/bedtools_genomecov/test_data/example.bed12
 delete mode 100644 src/bedtools/bedtools_genomecov/test_data/example_dz.bed
 delete mode 100644 src/bedtools/bedtools_genomecov/test_data/genome.txt

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9dd2389c..73a03dc7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,7 +26,7 @@
 * `bedtools`:
   - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
   - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
-
+  - `bedtools/bedtools_genomecov`: Compute the coverage of a feature file (bed/gff/vcf/bam) among a genome (PR #128).
 
 ## MINOR CHANGES
 
diff --git a/src/bedtools/bedtools_genomecov/test_data/example.bed b/src/bedtools/bedtools_genomecov/test_data/example.bed
deleted file mode 100644
index 09df88eb..00000000
--- a/src/bedtools/bedtools_genomecov/test_data/example.bed
+++ /dev/null
@@ -1,2 +0,0 @@
-chr2	128	228	my_read/1	37	+
-chr2	428	528	my_read/2	37	-
diff --git a/src/bedtools/bedtools_genomecov/test_data/example.bed12 b/src/bedtools/bedtools_genomecov/test_data/example.bed12
deleted file mode 100644
index 58c7a75d..00000000
--- a/src/bedtools/bedtools_genomecov/test_data/example.bed12
+++ /dev/null
@@ -1,2 +0,0 @@
-chr2	128	228	my_read/1	60	+	128	228	255,0,0	1	100	0
-chr2	428	528	my_read/2	60	-	428	528	255,0,0	1	100	0
diff --git a/src/bedtools/bedtools_genomecov/test_data/example_dz.bed b/src/bedtools/bedtools_genomecov/test_data/example_dz.bed
deleted file mode 100644
index a5b1a250..00000000
--- a/src/bedtools/bedtools_genomecov/test_data/example_dz.bed
+++ /dev/null
@@ -1 +0,0 @@
-chr2	100	103
diff --git a/src/bedtools/bedtools_genomecov/test_data/genome.txt b/src/bedtools/bedtools_genomecov/test_data/genome.txt
deleted file mode 100644
index 460c34fe..00000000
--- a/src/bedtools/bedtools_genomecov/test_data/genome.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-chr1	248956422
-chr2	198295559
-chr3	242193529

From f979eacdc80077d71228a0e8c94ceeb817abc06a Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Mon, 12 Aug 2024 00:19:25 +0200
Subject: [PATCH 11/17] Update config.vsh.yaml

---
 src/bedtools/bedtools_genomecov/config.vsh.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/bedtools/bedtools_genomecov/config.vsh.yaml b/src/bedtools/bedtools_genomecov/config.vsh.yaml
index 9035858c..2646735d 100644
--- a/src/bedtools/bedtools_genomecov/config.vsh.yaml
+++ b/src/bedtools/bedtools_genomecov/config.vsh.yaml
@@ -8,7 +8,7 @@ links:
   repository: https://github.com/arq5x/bedtools2
 references:
   doi: 10.1093/bioinformatics/btq033
-license: GPL-2.0, MIT
+license: MIT
 requirements:
   commands: [bedtools]
 authors:

From d5ff055f5d66714a17428cad6aba53b63423cfac Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Mon, 12 Aug 2024 21:18:48 +0200
Subject: [PATCH 12/17] Update config.vsh.yaml

---
 src/bedtools/bedtools_genomecov/config.vsh.yaml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/bedtools/bedtools_genomecov/config.vsh.yaml b/src/bedtools/bedtools_genomecov/config.vsh.yaml
index 2646735d..0dddd7c7 100644
--- a/src/bedtools/bedtools_genomecov/config.vsh.yaml
+++ b/src/bedtools/bedtools_genomecov/config.vsh.yaml
@@ -4,8 +4,10 @@ description: |
   Compute the coverage of a feature file among a genome.
 keywords: [genome coverage, BED, GFF, VCF, BAM]
 links:
+  homepage: https://bedtools.readthedocs.io/en/latest/#
   documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
   repository: https://github.com/arq5x/bedtools2
+  issue_tracker: https://github.com/arq5x/bedtools2/issues
 references:
   doi: 10.1093/bioinformatics/btq033
 license: MIT
@@ -32,7 +34,7 @@ argument_groups:
         description: |
           The input file is in BAM format.
           Note: BAM _must_ be sorted by positions.
-          --genome option is ignored!
+          '--genome' option is ignored if you use '--input_bam' option!
 
       - name: --genome
         alternatives: -g
@@ -106,10 +108,10 @@ argument_groups:
 
       - name: --strand
         type: string
+        choices: ["+", "-"]
         description: |
           Calculate coverage of intervals from a specific strand.
           With BED files, requires at least 6 columns (strand is column 6). 
-          - (STRING): can be + or -
 
       - name: --pair_end_coverage
         alternatives: -pc
@@ -145,6 +147,7 @@ argument_groups:
 
       - name: --max
         type: integer
+        min: 0
         description: |
           Combine all positions with a depth >= max into
           a single bin in the histogram. Irrelevant
@@ -153,6 +156,7 @@ argument_groups:
 
       - name: --scale
         type: double
+        min: 0
         description: |
           Scale the coverage by a constant factor.
           Each coverage value is multiplied by this factor before being reported.

From 007c50eec6427c257669fb6b8805639888140b9a Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Mon, 12 Aug 2024 21:22:50 +0200
Subject: [PATCH 13/17] Update script.sh

---
 src/bedtools/bedtools_genomecov/script.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/bedtools/bedtools_genomecov/script.sh b/src/bedtools/bedtools_genomecov/script.sh
index 39c4d0db..88d3b68f 100644
--- a/src/bedtools/bedtools_genomecov/script.sh
+++ b/src/bedtools/bedtools_genomecov/script.sh
@@ -3,6 +3,9 @@
 ## VIASH START
 ## VIASH END
 
+# Exit on error
+set -eo pipefail
+
 [[ "$par_input_bam" == "false" ]] && unset par_input_bam
 [[ "$par_depth" == "false" ]] && unset par_depth
 [[ "$par_depth_zero" == "false" ]] && unset par_depth_zero

From 77446e2ac80e805293bf0dee76f805879513e40a Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Mon, 12 Aug 2024 21:24:18 +0200
Subject: [PATCH 14/17] Update test.sh

---
 src/bedtools/bedtools_genomecov/test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
index cf262fc7..b2253600 100644
--- a/src/bedtools/bedtools_genomecov/test.sh
+++ b/src/bedtools/bedtools_genomecov/test.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # exit on error
-set -e
+set -eo pipefail
 
 ## VIASH START
 meta_executable="target/executable/bedtools/bedtools_intersect/bedtools_intersect"

From 516e0183314956a0e36dd773a827e8055280def3 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Tue, 13 Aug 2024 11:29:27 +0200
Subject: [PATCH 15/17] TMPDIR

---
 src/bedtools/bedtools_genomecov/test.sh | 152 +++++++++++-------------
 1 file changed, 72 insertions(+), 80 deletions(-)

diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
index b2253600..89d53061 100644
--- a/src/bedtools/bedtools_genomecov/test.sh
+++ b/src/bedtools/bedtools_genomecov/test.sh
@@ -30,16 +30,20 @@ assert_identical_content() {
 
 # Create directories for tests
 echo "Creating Test Data..."
-mkdir -p test_data
+TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
 
 # Create and populate input files
-printf "chr1\t248956422\nchr2\t198295559\nchr3\t242193529\n" > "test_data/genome.txt"
-printf "chr2\t128\t228\tmy_read/1\t37\t+\nchr2\t428\t528\tmy_read/2\t37\t-\n" > "test_data/example.bed"
-printf "chr2\t128\t228\tmy_read/1\t60\t+\t128\t228\t255,0,0\t1\t100\t0\nchr2\t428\t528\tmy_read/2\t60\t-\t428\t528\t255,0,0\t1\t100\t0\n" > "test_data/example.bed12"
-printf "chr2\t100\t103\n" > "test_data/example_dz.bed"
+printf "chr1\t248956422\nchr2\t198295559\nchr3\t242193529\n" > "$TMPDIR/genome.txt"
+printf "chr2\t128\t228\tmy_read/1\t37\t+\nchr2\t428\t528\tmy_read/2\t37\t-\n" > "$TMPDIR/example.bed"
+printf "chr2\t128\t228\tmy_read/1\t60\t+\t128\t228\t255,0,0\t1\t100\t0\nchr2\t428\t528\tmy_read/2\t60\t-\t428\t528\t255,0,0\t1\t100\t0\n" > "$TMPDIR/example.bed12"
+printf "chr2\t100\t103\n" > "$TMPDIR/example_dz.bed"
 
 # expected outputs
-cat > "test_data/expected_default.bed" <<EOF
+cat > "$TMPDIR/expected_default.bed" <<EOF
 chr2	0	198295359	198295559	0.999999
 chr2	1	200	198295559	1.0086e-06
 chr1	0	248956422	248956422	1
@@ -47,30 +51,30 @@ chr3	0	242193529	242193529	1
 genome	0	689445310	689445510	1
 genome	1	200	689445510	2.90088e-07
 EOF
-cat > "test_data/expected_ibam.bed" <<EOF
+cat > "$TMPDIR/expected_ibam.bed" <<EOF
 chr2:172936693-172938111	0	1218	1418	0.858956
 chr2:172936693-172938111	1	200	1418	0.141044
 genome	0	1218	1418	0.858956
 genome	1	200	1418	0.141044
 EOF
-cat > "test_data/expected_ibam_pc.bed" <<EOF
+cat > "$TMPDIR/expected_ibam_pc.bed" <<EOF
 chr2:172936693-172938111	0	1018	1418	0.717913
 chr2:172936693-172938111	1	400	1418	0.282087
 genome	0	1018	1418	0.717913
 genome	1	400	1418	0.282087
 EOF
-cat > "test_data/expected_ibam_fs.bed" <<EOF
+cat > "$TMPDIR/expected_ibam_fs.bed" <<EOF
 chr2:172936693-172938111	0	1218	1418	0.858956
 chr2:172936693-172938111	1	200	1418	0.141044
 genome	0	1218	1418	0.858956
 genome	1	200	1418	0.141044
 EOF
-cat > "test_data/expected_dz.bed" <<EOF
+cat > "$TMPDIR/expected_dz.bed" <<EOF
 chr2	100	1
 chr2	101	1
 chr2	102	1
 EOF
-cat > "test_data/expected_strand.bed" <<EOF
+cat > "$TMPDIR/expected_strand.bed" <<EOF
 chr2	0	198295459	198295559	1
 chr2	1	100	198295559	5.04298e-07
 chr1	0	248956422	248956422	1
@@ -78,7 +82,7 @@ chr3	0	242193529	242193529	1
 genome	0	689445410	689445510	1
 genome	1	100	689445510	1.45044e-07
 EOF
-cat > "test_data/expected_5.bed" <<EOF
+cat > "$TMPDIR/expected_5.bed" <<EOF
 chr2	0	198295557	198295559	1
 chr2	1	2	198295559	1.0086e-08
 chr1	0	248956422	248956422	1
@@ -86,16 +90,16 @@ chr3	0	242193529	242193529	1
 genome	0	689445508	689445510	1
 genome	1	2	689445510	2.90088e-09
 EOF
-cat > "test_data/expected_bg_scale.bed" <<EOF
+cat > "$TMPDIR/expected_bg_scale.bed" <<EOF
 chr2	128	228	100
 chr2	428	528	100
 EOF
-cat > "test_data/expected_trackopts.bed" <<EOF
+cat > "$TMPDIR/expected_trackopts.bed" <<EOF
 track type=bedGraph name=example
 chr2	128	228	1
 chr2	428	528	1
 EOF
-cat > "test_data/expected_split.bed" <<EOF
+cat > "$TMPDIR/expected_split.bed" <<EOF
 chr2	0	198295359	198295559	0.999999
 chr2	1	200	198295559	1.0086e-06
 chr1	0	248956422	248956422	1
@@ -103,7 +107,7 @@ chr3	0	242193529	242193529	1
 genome	0	689445310	689445510	1
 genome	1	200	689445510	2.90088e-07
 EOF
-cat > "test_data/expected_ignoreD_du.bed" <<EOF
+cat > "$TMPDIR/expected_ignoreD_du.bed" <<EOF
 chr2:172936693-172938111	0	1218	1418	0.858956
 chr2:172936693-172938111	1	200	1418	0.141044
 genome	0	1218	1418	0.858956
@@ -111,26 +115,24 @@ genome	1	200	1418	0.141044
 EOF
 
 # Test 1: 
-mkdir test1
-cd test1
+mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed"
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_default.bed"
+assert_identical_content "output.bed" "../expected_default.bed"
 echo "- test1 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 2: ibam option 
-mkdir test2
-cd test2
+mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null
 
 echo "> Run bedtools_genomecov on BAM file with -ibam"
 "$meta_executable" \
@@ -140,95 +142,90 @@ echo "> Run bedtools_genomecov on BAM file with -ibam"
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_ibam.bed"
+assert_identical_content "output.bed" "../expected_ibam.bed"
 echo "- test2 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 3: depth option
-mkdir test3
-cd test3
+mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -dz"
 "$meta_executable" \
-  --input "../test_data/example_dz.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example_dz.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --depth_zero
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_dz.bed"
+assert_identical_content "output.bed" "../expected_dz.bed"
 echo "- test3 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 4: strand option
-mkdir test4
-cd test4
+mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -strand"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --strand "-" \
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_strand.bed"
+assert_identical_content "output.bed" "../expected_strand.bed"
 echo "- test4 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 5: 5' end option
-mkdir test5
-cd test5
+mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -5"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --five_prime \
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_5.bed"
+assert_identical_content "output.bed" "../expected_5.bed"
 echo "- test5 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 6: max option
-mkdir test6
-cd test6
+mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -max"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --max 100 \
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_default.bed"
+assert_identical_content "output.bed" "../expected_default.bed"
 echo "- test6 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 7: bedgraph and scale option
-mkdir test7
-cd test7
+mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -bg and -scale"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --bed_graph \
   --scale 100 \
@@ -236,19 +233,18 @@ echo "> Run bedtools_genomecov on BED file with -bg and -scale"
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_bg_scale.bed"
+assert_identical_content "output.bed" "../expected_bg_scale.bed"
 echo "- test7 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 8: trackopts option
-mkdir test8
-cd test8
+mkdir "$TMPDIR/test8" && pushd "$TMPDIR/test8" > /dev/null
 
 echo "> Run bedtools_genomecov on BED file with -bg and -trackopts"
 "$meta_executable" \
-  --input "../test_data/example.bed" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --bed_graph \
   --trackopts "name=example" \
@@ -256,14 +252,13 @@ echo "> Run bedtools_genomecov on BED file with -bg and -trackopts"
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_trackopts.bed"
+assert_identical_content "output.bed" "../expected_trackopts.bed"
 echo "- test8 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 9: ibam pc options
-mkdir test9
-cd test9
+mkdir "$TMPDIR/test9" && pushd "$TMPDIR/test9" > /dev/null
 
 echo "> Run bedtools_genomecov on BAM file with -ibam, -pc"
 "$meta_executable" \
@@ -275,14 +270,13 @@ echo "> Run bedtools_genomecov on BAM file with -ibam, -pc"
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_ibam_pc.bed"
+assert_identical_content "output.bed" "../expected_ibam_pc.bed"
 echo "- test9 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 10: ibam fs options
-mkdir test10
-cd test10
+mkdir "$TMPDIR/test10" && pushd "$TMPDIR/test10" > /dev/null
 
 echo "> Run bedtools_genomecov on BAM file with -ibam, -fs"
 "$meta_executable" \
@@ -293,33 +287,31 @@ echo "> Run bedtools_genomecov on BAM file with -ibam, -fs"
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_ibam_fs.bed"
+assert_identical_content "output.bed" "../expected_ibam_fs.bed"
 echo "- test10 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 11: split 
-mkdir test11
-cd test11
+mkdir "$TMPDIR/test11" && pushd "$TMPDIR/test11" > /dev/null
 
 echo "> Run bedtools_genomecov on BED12 file with -split"
 "$meta_executable" \
-  --input "../test_data/example.bed12" \
-  --genome "../test_data/genome.txt" \
+  --input "../example.bed12" \
+  --genome "../genome.txt" \
   --output "output.bed" \
   --split \
 
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_split.bed"
+assert_identical_content "output.bed" "../expected_split.bed"
 echo "- test11 succeeded -"
 
-cd ..
+popd > /dev/null
 
 # Test 12: ignore deletion and du
-mkdir test12
-cd test12
+mkdir "$TMPDIR/test12" && pushd "$TMPDIR/test12" > /dev/null
 
 echo "> Run bedtools_genomecov on BAM file with -ignoreD and -du"
 "$meta_executable" \
@@ -331,10 +323,10 @@ echo "> Run bedtools_genomecov on BAM file with -ignoreD and -du"
 # checks
 assert_file_exists "output.bed"
 assert_file_not_empty "output.bed"
-assert_identical_content "output.bed" "../test_data/expected_ignoreD_du.bed"
+assert_identical_content "output.bed" "../expected_ignoreD_du.bed"
 echo "- test12 succeeded -"
 
-cd ..
+popd > /dev/null
 
 echo "---- All tests succeeded! ----"
 exit 0

From 3b8852763bc9c5975fe9cc8c5363b5767efcb524 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Tue, 20 Aug 2024 19:27:58 +0200
Subject: [PATCH 16/17] Unset Variables

---
 src/bedtools/bedtools_genomecov/script.sh | 34 ++++++++++++++---------
 1 file changed, 21 insertions(+), 13 deletions(-)

diff --git a/src/bedtools/bedtools_genomecov/script.sh b/src/bedtools/bedtools_genomecov/script.sh
index 88d3b68f..28e005fe 100644
--- a/src/bedtools/bedtools_genomecov/script.sh
+++ b/src/bedtools/bedtools_genomecov/script.sh
@@ -6,19 +6,27 @@
 # Exit on error
 set -eo pipefail
 
-[[ "$par_input_bam" == "false" ]] && unset par_input_bam
-[[ "$par_depth" == "false" ]] && unset par_depth
-[[ "$par_depth_zero" == "false" ]] && unset par_depth_zero
-[[ "$par_bed_graph" == "false" ]] && unset par_bed_graph
-[[ "$par_bed_graph_zero_coverage" == "false" ]] && unset par_bed_graph_zero_coverage
-[[ "$par_split" == "false" ]] && unset par_split
-[[ "$par_ignore_deletion" == "false" ]] && unset par_ignore_deletion
-[[ "$par_pair_end_coverage" == "false" ]] && unset par_pair_end_coverage
-[[ "$par_fragment_size" == "false" ]] && unset par_fragment_size
-[[ "$par_du" == "false" ]] && unset par_du
-[[ "$par_five_prime" == "false" ]] && unset par_five_prime
-[[ "$par_three_prime" == "false" ]] && unset par_three_prime
-[[ "$par_trackline" == "false" ]] && unset par_trackline
+# Unset variables
+unset_if_false=(
+    par_input_bam
+    par_depth
+    par_depth_zero
+    par_bed_graph
+    par_bed_graph_zero_coverage
+    par_split
+    par_ignore_deletion
+    par_pair_end_coverage
+    par_fragment_size
+    par_du
+    par_five_prime
+    par_three_prime
+    par_trackline
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 bedtools genomecov \
     ${par_depth:+-d} \

From 1f5adfc3846fb03a7f94e30a2791470e0cc00575 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Tue, 20 Aug 2024 19:57:30 +0200
Subject: [PATCH 17/17] par_trackopts multiple: true

---
 src/bedtools/bedtools_genomecov/config.vsh.yaml | 1 +
 src/bedtools/bedtools_genomecov/script.sh       | 5 ++++-
 src/bedtools/bedtools_genomecov/test.sh         | 3 ++-
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/bedtools/bedtools_genomecov/config.vsh.yaml b/src/bedtools/bedtools_genomecov/config.vsh.yaml
index 0dddd7c7..775587de 100644
--- a/src/bedtools/bedtools_genomecov/config.vsh.yaml
+++ b/src/bedtools/bedtools_genomecov/config.vsh.yaml
@@ -182,6 +182,7 @@ argument_groups:
             -trackopts 'name="My Track" visibility=2 color=255,30,30'
             Note the use of single-quotes if you have spaces in your parameters.
           - (TEXT)
+        multiple: true
 
 resources:
   - type: bash_script
diff --git a/src/bedtools/bedtools_genomecov/script.sh b/src/bedtools/bedtools_genomecov/script.sh
index 28e005fe..20fbd968 100644
--- a/src/bedtools/bedtools_genomecov/script.sh
+++ b/src/bedtools/bedtools_genomecov/script.sh
@@ -28,6 +28,9 @@ for par in ${unset_if_false[@]}; do
     [[ "$test_val" == "false" ]] && unset $par
 done
 
+# Create input array 
+IFS=";" read -ra trackopts <<< $par_trackopts
+
 bedtools genomecov \
     ${par_depth:+-d} \
     ${par_depth_zero:+-dz} \
@@ -42,7 +45,7 @@ bedtools genomecov \
     ${par_strand:+-strand "$par_strand"} \
     ${par_max:+-max "$par_max"} \
     ${par_scale:+-scale "$par_scale"} \
-    ${par_trackopts:+-trackopts "$par_trackopts"} \
+    ${par_trackopts:+-trackopts "${trackopts[*]}"} \
     ${par_input_bam:+-ibam "$par_input_bam"} \
     ${par_input:+-i "$par_input"} \
     ${par_genome:+-g "$par_genome"} \
diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh
index 89d53061..7e4487da 100644
--- a/src/bedtools/bedtools_genomecov/test.sh
+++ b/src/bedtools/bedtools_genomecov/test.sh
@@ -95,7 +95,7 @@ chr2	128	228	100
 chr2	428	528	100
 EOF
 cat > "$TMPDIR/expected_trackopts.bed" <<EOF
-track type=bedGraph name=example
+track type=bedGraph name=example llama=Alpaco
 chr2	128	228	1
 chr2	428	528	1
 EOF
@@ -248,6 +248,7 @@ echo "> Run bedtools_genomecov on BED file with -bg and -trackopts"
   --output "output.bed" \
   --bed_graph \
   --trackopts "name=example" \
+  --trackopts "llama=Alpaco" \
 
 # checks
 assert_file_exists "output.bed"