diff --git a/src/bcftools/bcftools_stats/config.vsh.yaml b/src/bcftools/bcftools_stats/config.vsh.yaml index b92a3b24..985acf43 100644 --- a/src/bcftools/bcftools_stats/config.vsh.yaml +++ b/src/bcftools/bcftools_stats/config.vsh.yaml @@ -58,7 +58,7 @@ argument_groups: alternatives: --first_only type: boolean_true description: | - Include only 1st allele at multiallelic sites + Include only 1st allele at multiallelic sites. - name: --collapse alternatives: --c @@ -72,7 +72,7 @@ argument_groups: alternatives: --d type: string description: | - Depth distribution: min,max,bin size [0,500,1] + Depth distribution: min,max,bin size. example: 0,500,1 - name: --exclude @@ -88,21 +88,19 @@ argument_groups: description: | tab-delimited file with exons for indel frameshifts statistics. The columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions. - The file is BGZF-compressed and indexed with tabix - e.g. - tabix -s1 -b2 -e3 file.gz + The file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3 file.gz). - name: --apply_filters alternatives: --f type: string description: | - Require at least one of the listed FILTER strings (e.g. "PASS,.") + Require at least one of the listed FILTER strings (e.g. "PASS,."). - name: --fasta_reference alternatives: --F type: file description: | - Faidx indexed reference sequence file to determine INDEL context + Faidx indexed reference sequence file to determine INDEL context. - name: --include alternatives: --i @@ -115,13 +113,13 @@ argument_groups: alternatives: --I type: boolean_true description: | - Collect stats for sites with ID separately (known vs novel) + Collect stats for sites with ID separately (known vs novel). - name: --regions alternatives: --r type: string description: | - Restrict to comma-separated list of regions + Restrict to comma-separated list of regions. - name: --regions_file alternatives: --R @@ -168,7 +166,7 @@ argument_groups: alternatives: --T type: file description: | - Similar to -R but streams rather than index-jumps. + Similar to --regions_file option but streams rather than index-jumps. - name: --targets_overlaps type: string diff --git a/src/bcftools/bcftools_stats/test.sh b/src/bcftools/bcftools_stats/test.sh index 66457352..87c808f9 100644 --- a/src/bcftools/bcftools_stats/test.sh +++ b/src/bcftools/bcftools_stats/test.sh @@ -183,7 +183,7 @@ popd > /dev/null # Test 6: Include, Regions mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null -echo "> Run bcftools_stats on VCF file with include, regions" +echo "> Run bcftools_stats on VCF file with include and regions options" "$meta_executable" \ --input "../example.vcf.gz" \ --output "stats.txt" \ @@ -198,10 +198,10 @@ echo "- test6 succeeded -" popd > /dev/null -# Test 7: Regions Overlap, Samples, Samples File +# Test 7: Regions Overlap, Samples mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null -echo "> Run bcftools_stats on VCF file with regions overlap, samples, and samples file" +echo "> Run bcftools_stats on VCF file with regions overlap, and samples options" "$meta_executable" \ --input "../example.vcf" \ --output "stats.txt" \