Update changelog flagstats

CHANGELOG.md

@@ -29,6 +29,9 @@
 
 * `star/star_align_reads`: Align reads to a reference genome (PR #22).
 
+* `samtools`:
+    - `samtools/flagstat`: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
+
 ## MAJOR CHANGES
 
 ## MINOR CHANGES

src/samtools/flagstat/config.vsh.yaml

@@ -1,6 +1,6 @@
 name: samtools_flagstat
 namespace: samtools
-description: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type..
+description: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type.
 keywords: [ stats, mapping, counts, bam, sam, cram]
 links:
   homepage: https://www.htslib.org/

src/samtools/flagstat/test.sh

@@ -1,44 +1,45 @@
 #!/bin/bash
 
+test_dir="${meta_resources_dir}test_data"
 echo ">>> Testing $meta_functionality_name"
 
 "$meta_executable" \
-  --bam "$meta_resources_dir/test_data/a.bam" \
-  --bai "$meta_resources_dir/test_data/a.bam.bai" \
-  --output "$meta_resources_dir/test_data/a.flagstat"
+  --bam "$test_dir/a.bam" \
+  --bai "$test_dir/a.bam.bai" \
+  --output "$test_dir/a.flagstat"
 
 echo ">>> Checking whether output exists"
-[ ! -f "$meta_resources_dir/test_data/a.flagstat" ] && echo "File 'a.flagstat' does not exist!" && exit 1
+[ ! -f "$test_dir/a.flagstat" ] && echo "File 'a.flagstat' does not exist!" && exit 1
 
 echo ">>> Checking whether output is non-empty"
-[ ! -s "$meta_resources_dir/test_data/a.flagstat" ] && echo "File 'a.flagstat' is empty!" && exit 1
+[ ! -s "$test_dir/a.flagstat" ] && echo "File 'a.flagstat' is empty!" && exit 1
 
 echo ">>> Checking whether output is correct"
-diff "$meta_resources_dir/test_data/a.flagstat" "$meta_resources_dir/test_data/a_ref.flagstat" || \
+diff "$test_dir/a.flagstat" "$test_dir/a_ref.flagstat" || \
     (echo "Output file chr19.flagstat does not match expected output" && exit 1)
 
-rm "$meta_resources_dir/test_data/a.flagstat"
+rm "$test_dir/a.flagstat"
 
 ############################################################################################
 
 echo ">>> Testing $meta_functionality_name with singletons in the input"
 
 "$meta_executable" \
-  --bam "$meta_resources_dir/test_data/test.paired_end.sorted.bam" \
-  --bai "$meta_resources_dir/test_data/test.paired_end.sorted.bam.bai" \
-  --output "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat"
+  --bam "$test_dir/test.paired_end.sorted.bam" \
+  --bai "$test_dir/test.paired_end.sorted.bam.bai" \
+  --output "$test_dir/test.paired_end.sorted.flagstat"
 
 echo ">>> Checking whether output exists"
-[ ! -f "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat" ] && echo "File 'test.paired_end.sorted.flagstat' does not exist!" && exit 1
+[ ! -f "$test_dir/test.paired_end.sorted.flagstat" ] && echo "File 'test.paired_end.sorted.flagstat' does not exist!" && exit 1
 
 echo ">>> Checking whether output is non-empty"
-[ ! -s "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat" ] && echo "File 'test.paired_end.sorted.flagstat' is empty!" && exit 1
+[ ! -s "$test_dir/test.paired_end.sorted.flagstat" ] && echo "File 'test.paired_end.sorted.flagstat' is empty!" && exit 1
 
 echo ">>> Checking whether output is correct"
-diff "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat" "$meta_resources_dir/test_data/test_ref.paired_end.sorted.flagstat" || \
+diff "$test_dir/test.paired_end.sorted.flagstat" "$test_dir/test_ref.paired_end.sorted.flagstat" || \
     (echo "Output file chr19.flagstat does not match expected output" && exit 1)
 
-rm "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat"
+rm "$test_dir/test.paired_end.sorted.flagstat"
 
 
 echo "All tests succeeded!"