add more tests to samtools/index

CHANGELOG.md

@@ -35,6 +35,9 @@
     - `salmon/salmon_index`: Create a salmon index for the transcriptome to use Salmon in the mapping-based mode (PR #24).
     - `salmon/salmon_quant`: Transcript quantification from RNA-seq data (PR #24).
 
+* `samtools`: 
+    - `samtools/index`: Index SAM/BAM/CRAM files.
+
 ## MAJOR CHANGES
 
 ## MINOR CHANGES

src/samtools/index/config.vsh.yaml

@@ -1,7 +1,7 @@
 name: samtools_index
 namespace: samtools
-description: Index BAM files
-keywords: [stats, mapping, counts, chromosome, bam, sam, cram]
+description: Index SAM/BAM/CRAM files
+keywords: [index, bam, sam, cram]
 links:
   homepage: https://www.htslib.org/
   documentation: https://www.htslib.org/doc/samtools-index.html
@@ -13,47 +13,46 @@ license: MIT/Expat
 argument_groups:
   - name: Inputs
     arguments:
-      - name: --bam
-        alternatives: -b
+      - name: --input
         type: file
-        description: BAM input file.
-      - name: "--bam_csi_index"
-        type: boolean
-        description: Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
+        description: Input file name
+        required: true
+        must_exist: true
   - name: Outputs
     arguments:
-      - name: --output_bai
-        alternatives: [ -o, --output ]
+      - name: --output
+        alternatives: -o
         type: file
-        description: BAM index
-        direction: output
+        description: Output file name
         required: true
         must_exist: false
         example: out.bam.bai
-        must_exist: false
-      - name: --output_csi
-        alternatives: [ -c, --csi ]
-        type: file
-        description: CSI index
-        direction: output
-        default: out.bam.csi
-      - name: --min-shift
-        alternatives: -m
-        type: integer
-        description: Create a CSI index, with a minimum interval size of 2^INT.
-        default: 0
   - name: Options
     arguments:
-      - name: --individual
-        alternatives: -M
+      - name: --bai
+        alternatives: -b
+        type: boolean_true
+        description: Generate BAM index
+      - name: --csi
+        alternatives: -c
+        type: boolean_true
+        description: |
+          Create a CSI index for BAM files instead of the traditional BAI 
+          index. This will be required for genomes with larger chromosome 
+          sizes.
+      - name: --min_shift
+        alternatives: -m
         type: integer
+        description: |
+          Create a CSI index, with a minimum interval size of 2^INT.
+      - name: --multiple
+        alternatives: -M
+        type: boolean_true
         description: |
           Interpret all filename arguments as alignment files to
           be indexed individually. (Without -M, filename arguments
           are interpreted solely as per the second synopsis.)
 
-
-   
 resources:
   - type: bash_script
     path: script.sh

src/samtools/index/help.txt

@@ -2,8 +2,12 @@
 samtools index
 ```
 
-Usage: samtools index [-bc] [-m INT] <in.bam> [out.index]
+Usage: samtools index -M [-bc] [-m INT] <in1.bam> <in2.bam>...
+   or: samtools index [-bc] [-m INT] <in.bam> [out.index]
 Options:
-  -b       Generate BAI-format index for BAM files [default]
-  -c       Generate CSI-format index for BAM files
-  -m INT   Set minimum interval size for CSI indices to 2^INT [14]
+  -b, --bai            Generate BAI-format index for BAM files [default]
+  -c, --csi            Generate CSI-format index for BAM files
+  -m, --min-shift INT  Set minimum interval size for CSI indices to 2^INT [14]
+  -M                   Interpret all filename arguments as files to be indexed
+  -o, --output FILE    Write index to FILE [alternative to <out.index> in args]
+  -@, --threads INT    Sets the number of threads [none]

src/samtools/index/script.sh

@@ -4,10 +4,15 @@
 ## VIASH END
 
 set -e
-
-[[ "$par_output_csi" == "false" ]] && unset par_output_csi
+[[ "$par_multiple" == "false" ]] && unset par_multiple
+[[ "$par_bai" == "false" ]] && unset par_bai
+[[ "$par_csi" == "false" ]] && unset par_csi
+[[ "$par_multiple" == "true" ]] && par_multiple="--multiple"
 
 samtools index \
     "$par_input" \
-    ${par_output_csi:+-c} \
+    ${par_csi:+-c} \
+    ${par_bai:+-b} \
+    ${par_min_shift:+-m "par_output_bai"} \
+    ${par_multiple:+-M} \
     -o "$par_output"

src/samtools/index/test.sh

@@ -5,23 +5,86 @@ echo ">>> Testing $meta_functionality_name"
 
 echo ">>> Generating BAM index"
 "$meta_executable" \
-  --input "$test_dir/chr19.bam" \
-  --bam_csi_index false \
-  --output_bai "$test_dir/chr19.bam.bai"
+  --input "$test_dir/a.sorted.bam" \
+  --bai \
+  --output "$test_dir/a.sorted.bam.bai"
 
 echo ">>> Check whether output exists"
-[ ! -f chr19.bam.bai ] && echo "File 'mapt.NA12156.altex.bam.bai' does not exist!" && exit 1
-[ ! -s chr19.bam.bai ] && echo "File 'mapt.NA12156.altex.bam.bai' is empty!" && exit 1
+[ ! -f "$test_dir/a.sorted.bam.bai" ] && echo "File 'a.sorted.bam.bai' does not exist!" && exit 1
+
+echo ">>> Check whether output is empty"
+[ ! -s "$test_dir/a.sorted.bam.bai" ] && echo "File 'a.sorted.bam.bai' is empty!" && exit 1
+
+echo ">>> Check whether output is correct"
+diff "$test_dir/a.sorted.bam.bai" "$test_dir/a_ref.sorted.bam.bai" || \
+  (echo "File 'a.sorted.bam.bai' does not match expected output." && exit 1)
+
+rm "$test_dir/a.sorted.bam.bai"
+
+#################################################################################################
 
 echo ">>> Generating CSI index"
 "$meta_executable" \
-  --input "$test_dir/chr19.bam" \
-  --bam_csi_index true \
-  --output_csi "$test_dir/chr19.bam.csi"
+  --input "$test_dir/a.sorted.bam" \
+  --csi \
+  --output "$test_dir/a.sorted.bam.csi"
+
+echo ">>> Check whether output exists"
+[ ! -f "$test_dir/a.sorted.bam.csi" ] && echo "File 'a.sorted.bam.csi' does not exist!" && exit 1
+
+echo ">>> Check whether output is empty"
+[ ! -s "$test_dir/a.sorted.bam.csi" ] && echo "File 'a.sorted.bam.csi' is empty!" && exit 1
+
+echo ">>> Check whether output is correct"
+diff "$test_dir/a.sorted.bam.csi" "$test_dir/a_ref.sorted.bam.csi" || \
+  (echo "File 'a.sorted.bam.csi' does not match expected output." && exit 1)
+
+rm "$test_dir/a.sorted.bam.csi"
+
+#################################################################################################
+
+echo ">>> Generating bam index with -M option"
+"$meta_executable" \
+  --input "$test_dir/a.sorted.bam" \
+  --bai \
+  --output "$test_dir/a_multiple.sorted.bam.bai" \
+  --multiple
+
+echo ">>> Check whether output exists"
+[ ! -f "$test_dir/a_multiple.sorted.bam.bai" ] && echo "File 'a_multiple.sorted.bam.bai' does not exist!" && exit 1
+
+echo ">>> Check whether output is empty"
+[ ! -s "$test_dir/a_multiple.sorted.bam.bai" ] && echo "File 'a_multiple.sorted.bam.bai' is empty!" && exit 1
+
+echo ">>> Check whether output is correct"
+diff "$test_dir/a_multiple.sorted.bam.bai" "$test_dir/a_multiple_ref.sorted.bam.bai" || \
+  (echo "File 'a_multiple.sorted.bam.bai' does not match expected output." && exit 1)
+
+
+#################################################################################################
+
+echo ">>> Generating BAM index with -m option"
+
+"$meta_executable" \
+  --input "$test_dir/a.sorted.bam" \
+  --min_shift 4 \
+  --bai \
+  --output "$test_dir/a_4.sorted.bam.bai"
 
 echo ">>> Check whether output exists"
-[ ! -f "chr19.bam.csi" ] && echo "File 'mapt.NA12156.altex.bam.csi' does not exist!" && exit 1
-[ ! -s "chr19.bam.csi" ] && echo "File 'mapt.NA12156.altex.bam.csi' is empty!" && exit 1
+[ ! -f "$test_dir/a_4.sorted.bam.bai" ] && echo "File 'a_4.sorted.bam.bai' does not exist!" && exit 1
+
+echo ">>> Check whether output is empty"
+[ ! -s "$test_dir/a_4.sorted.bam.bai" ] && echo "File 'a_4.sorted.bam.bai' is empty!" && exit 1
+
+echo ">>> Check whether output is correct"
+diff "$test_dir/a_4.sorted.bam.bai" "$test_dir/a_4_ref.sorted.bam.bai" || \
+  (echo "File 'a_4.sorted.bam.bai' does not match expected output." && exit 1)
+
+rm "$test_dir/a_4.sorted.bam.bai"
+
+#################################################################################################
+
 
 echo "All tests succeeded!"
 exit 0

src/samtools/index/test_data/script.sh

@@ -6,9 +6,7 @@ if [ ! -d /tmp/idxstats_source ]; then
 fi
 
 cp -r /tmp/idxstats_source/bio/samtools/idxstats/test/mapped/* src/samtools/idxstats/test_data
-# samtools idxstats a.sorted.bam > a.sorted.idxstats
+# samtools index a_ref.sorted.bam -o a_ref.sorted.bam.bai
+# samtools index a_ref.sorted.bam -c a_ref.sorted.bam.csi
+
 
-# dowload test data from nf-core module
-wget https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam
-wget https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai
-# samtools idxstats test.paired_end.sorted.bam > test_ref.paired_end.sorted.idxstats