update changelog, add one test

CHANGELOG.md

@@ -41,6 +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).
 
 ## MAJOR CHANGES
 

src/samtools/samtools_view/config.vsh.yaml

@@ -176,18 +176,19 @@ argument_groups:
       alternatives: -q
       type: integer
       description: |
-        Skip alignments with MAPQ smaller than INT [0].
+        Skip alignments with MAPQ smaller than INT.
       default: 0
     - name: --library
       alternatives: -l
       type: string
       description: |
-        Only output alignments in library STR [null].
+        Only output alignments in library STR.
+      default: null
     - name: --min_qlen
       alternatives: -m
       type: integer
       description: |
-        Only output alignments with number of CIGAR bases consuming query sequence ≥ INT [0]
+        Only output alignments with number of CIGAR bases consuming query sequence ≥ INT.
       default: 0
     - name: --expr
       alternatives: -e

src/samtools/samtools_view/test.sh

@@ -63,6 +63,25 @@ diff "$temp_dir/a.count" "$test_dir/a.count" || \
 
 ############################################################################################
 
-echo ">>> All test passed successfully"
+echo ">>> Test 4: ${meta_functionality_name} including only the forward reads from read pairs"
+
+"$meta_executable" \
+   --output "$temp_dir/a.forward" \
+   --excl_flags "147" \
+    --input "$test_dir/a.sam"
+
+echo ">>> Checking whether output exists"
+[ ! -f "$temp_dir/a.forward" ] && echo "File 'a.forward' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$temp_dir/a.forward" ] && echo "File 'a.forward' is empty!" && exit 1
+
+echo ">>> Checking whether output is correct"
+diff "$temp_dir/a.forward" "$test_dir/a.forward" || \
+    (echo "Output file a.forward does not match expected output" && exit 1)
 
+############################################################################################
+
+echo ">>> All test passed successfully"
+rm -rf "${temp_dir}"
 exit 0