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[ah_var_store] VCF max alt alleles [VS-1334] [VS-1357] (#8806)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| version 1.0 | ||
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| import "GvsUtils.wdl" as Utils | ||
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| workflow GvsTieoutVcfMaxAltAlleles { | ||
| input { | ||
| String unfiltered_output_gcs_path | ||
| String filtered_output_gcs_path | ||
| Int max_alt_alleles | ||
| String? variants_docker | ||
| } | ||
|
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| if (!defined(variants_docker)) { | ||
| call Utils.GetToolVersions | ||
| } | ||
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| String effective_variants_docker = select_first([variants_docker, GetToolVersions.variants_docker]) | ||
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| call Tieout { | ||
| input: | ||
| unfiltered_output_gcs_path = unfiltered_output_gcs_path, | ||
| filtered_output_gcs_path = filtered_output_gcs_path, | ||
| max_alt_alleles = max_alt_alleles, | ||
| variants_docker = effective_variants_docker, | ||
| } | ||
| } | ||
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| task Tieout { | ||
| input { | ||
| String unfiltered_output_gcs_path | ||
| String filtered_output_gcs_path | ||
| Int max_alt_alleles | ||
| String variants_docker | ||
| } | ||
| command <<< | ||
| # Prepend date, time and pwd to xtrace log entries. | ||
| PS4='\D{+%F %T} \w $ ' | ||
| set -o errexit -o nounset -o pipefail -o xtrace | ||
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| mkdir unfiltered filtered compare | ||
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| cd unfiltered | ||
| gcloud storage cp '~{unfiltered_output_gcs_path}/*' . | ||
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| cd .. | ||
| cd filtered | ||
| gcloud storage cp '~{filtered_output_gcs_path}/*' . | ||
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| cd .. | ||
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| for unfiltered in unfiltered/*.vcf.gz | ||
| do | ||
| base="$(basename $unfiltered)" | ||
| filtered="filtered/${base}" | ||
| out=${base%-*} | ||
| bcftools isec $filtered $unfiltered -p compare/${out} | ||
| done | ||
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| # Identify the 'isec' output files that represent entries which are "private" to either VCF file being compared. | ||
| find . -name README.txt | xargs grep -h private | awk '{print $1}' > private_files.txt | ||
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| # Turn off errexit, the grep below is expected to return non-zero | ||
| set +o errexit | ||
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| # Find all the private files, print out all the ALTs, look for any lines that do *not* have at least two commas. | ||
| # All ALT entries are expected to have two or more commas because the maximum number of ALT alleles was specified | ||
| # as two. So the unfiltered file would have entries like ALT1,ALT2,...,ALTN while the filtered file would not, | ||
| # and these should be the only differences between the two files. | ||
| cat private_files.txt | xargs -n 1 bcftools query -f '%ALT\n' | grep -E -v ',.*,' > unexpected.txt | ||
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| rc=$? | ||
| if [[ $rc -eq 0 ]] | ||
| then | ||
| echo "Unexpected ALTs found, see 'unexpected' output for details." 1>&2 | ||
| exit 1 | ||
| fi | ||
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| set -o errexit | ||
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| # Similar to above, except making sure that we did observe some filtered sites. At the time of this | ||
| # writing there are 4001 sites filtered for > 2 entries; conservatively setting the threshold at 1000. | ||
| filtered_count=$(cat private_files.txt | xargs -n 1 bcftools query -f '%ALT\n' | grep -E ',.*,' | wc -l) | ||
| if [[ $filtered_count -lt 1000 ]] | ||
| then | ||
| echo "Unexpectedly found fewer than 1000 filtered ALTs, see 'tarball' output for details." 1>&2 | ||
| exit 1 | ||
| fi | ||
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| tar cfvz tieout.tgz compare | ||
| >>> | ||
| output { | ||
| File tarball = "tieout.tgz" | ||
| File unexpected = "unexpected.txt" | ||
| } | ||
| runtime { | ||
| docker: variants_docker | ||
| } | ||
| } |
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