add a 4th test, fix option names in the script

CHANGELOG.md

@@ -41,7 +41,7 @@
     - `samtools/samtools_index`: Index SAM/BAM/CRAM files (PR #35).
     - `samtools/samtools_sort`: Sort SAM/BAM/CRAM files (PR #36).
     - `samtools/samtools_stats`: Reports alignment summary statistics for a BAM file (PR #39).
-    - `samtools/samtools_view`: Views and converts SAM/BAM/CRAM files (PR #45).
+    - `samtools/samtools_view`: Views and converts SAM/BAM/CRAM files (PR #48).
 
 ## MAJOR CHANGES
 

src/samtools/samtools_view/config.vsh.yaml

@@ -49,7 +49,6 @@ argument_groups:
       description: |
         Only output alignments overlapping the input BED FILE [null].
     - name: --region_file
-      alternatives: --regions_file
       type: file
       description: |
         Use an index and multi-region iterator to only output alignments overlapping the input BED FILE.
@@ -108,13 +107,13 @@ argument_groups:
         with a known suffix.
     - name: --uncompressed
       alternatives: -u
+      type: boolean_true
       description: |
         Output uncompressed data. This also changes the default output format to BAM,
         but this can be overridden by the explicit format options or using a filename
         with a known suffix.
         This option saves time spent on compression/decompression and is thus preferred
         when the output is piped to another samtools command.
-      type: boolean_true
     - name: --with_header
       type: boolean_true
       description: |
@@ -135,7 +134,7 @@ argument_groups:
       type: boolean_true
       description: |
         Instead of printing the alignments, only count them and print the total number.
-        All filter options, such as --require-flags, --excl-flags, and --min-MQ, are taken
+        All filter options, such as --require_flags, --excl_flags, and --min_MQ, are taken
         into account. The --unmap option is ignored in this mode.
     - name: --output_unselected
       alternatives: -U
@@ -329,6 +328,10 @@ argument_groups:
       type: string
       description: |
         Specify a single output file format option in the form of OPTION or OPTION=VALUE.
+    - name: --write_index
+      type: boolean_true
+      description: |
+        Automatically index the output files.
 
 resources:
   - type: bash_script

src/samtools/samtools_view/script.sh

@@ -18,7 +18,8 @@ set -e
 [[ "$par_fetch_pairs" == "false" ]] && unset par_fetch_pairs
 [[ "$par_customized_index" == "false" ]] && unset par_customized_index
 [[ "$par_no_PG" == "false" ]] && unset par_no_PG
-
+[[ "$par_write_index" == "false" ]] && unset par_write_index
+[[ "$par_remove_B" == "false" ]] && unset par_remove_B
 
 samtools view \
     ${par_bam:+-b} \
@@ -48,8 +49,8 @@ samtools view \
     ${par_min_qlen:+-m "$par_min_qlen"} \
     ${par_expr:+-e "$par_expr"} \
     ${par_require_flags:+-f "$par_require_flags"} \
-    ${par_exclude_flags:+-F "$par_exclude_flags"} \
-    ${par_incl_flags:+--rf "$par_include_flags"} \
+    ${par_excl_flags:+-F "$par_excl_flags"} \
+    ${par_incl_flags:+--rf "$par_incl_flags"} \
     ${par_excl_all_flags:+-G "$par_excl_all_flags"} \
     ${par_subsample:+--subsample "$par_subsample"} \
     ${par_subsample_seed:+--subsample-seed "$par_subsample_seed"} \

src/samtools/samtools_view/test.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 test_dir="${meta_resources_dir}/test_data"
-temp_dir="${meta_resources_dir}/tmp"
+temp_dir="${meta_resources_dir}/out"
 
 ############################################################################################
 
@@ -24,7 +24,7 @@ diff <(samtools view "$temp_dir/a.bam") <(samtools view "$test_dir/a.bam") || \
 
 ############################################################################################
 
-echo ">>> Test 2: ${meta_functionality_name} with --output_format CRAM"
+echo ">>> Test 2: ${meta_functionality_name} with CRAM format output"
 
 "$meta_executable" \
    --cram \
@@ -67,8 +67,8 @@ echo ">>> Test 4: ${meta_functionality_name} including only the forward reads fr
 
 "$meta_executable" \
    --output "$temp_dir/a.forward" \
-   --excl_flags "147" \
-    --input "$test_dir/a.sam"
+   --excl_flags "0x80" \
+   --input "$test_dir/a.sam"
 
 echo ">>> Checking whether output exists"
 [ ! -f "$temp_dir/a.forward" ] && echo "File 'a.forward' does not exist!" && exit 1

src/samtools/samtools_view/test_data/a.forward

@@ -0,0 +1,3 @@
+a1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+b1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+c1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********