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Merge pull request #319 from sambrightman/uniquesampleids
Ensure FreeBayes fails on multiple BAMs with conflicting read groups
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| #!/usr/bin/env bash | ||
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| BASH_TAP_ROOT=bash-tap | ||
| source ./bash-tap/bash-tap-bootstrap | ||
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| PATH=../bin:$PATH # for freebayes | ||
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| plan tests 7 | ||
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| ref=$(basename $0).ref | ||
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| trap 'rm -f ${ref}* $(basename $0)*.bam*' EXIT | ||
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| cat >${ref} <<REF | ||
| >ref | ||
| AATCGGCTA | ||
| REF | ||
| samtools faidx ${ref} | ||
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| function run_freebayes() { | ||
| freebayes "$@" \ | ||
| --haplotype-length 0 --min-alternate-count 1 \ | ||
| --min-alternate-fraction 0 --pooled-continuous --report-monomorphic \ | ||
| --ploidy 1 \ | ||
| -f $ref $bam \ | ||
| 2>&1 \ | ||
| | grep -vE "^#" | cut -f1-5 | ||
| } | ||
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| function make_bam() { | ||
| local id=$1 && shift | ||
| local sm=$1 && shift | ||
| local pl=$1 && shift | ||
| local suffix=${1:-} && shift | ||
| local first_snp=${1:-G} && shift | ||
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| local bam="$(basename $0).${id}.${sm}.${pl}${suffix}.bam" | ||
| samtools view -S -b - >${bam} <<SAM | ||
| @HD VN:1.5 SO:coordinate | ||
| @SQ SN:ref LN:9 | ||
| @RG ID:${id} SM:${sm} PL:${pl} | ||
| alt 0 ref 1 30 1=1X1=2X1=1X1=1X * 0 0 A${first_snp}TTAGGTT * RG:Z:${id} | ||
| SAM | ||
| samtools index ${bam} | ||
| echo ${bam} | ||
| } | ||
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| expected=$(cat <<END | ||
| ref 2 . A G | ||
| ref 4 . CG TA | ||
| ref 7 . C G | ||
| ref 9 . A T | ||
| END | ||
| ) | ||
| bam1=$(make_bam "id1" "sample1" "platform1" "a") | ||
| bam2=$(make_bam "id1" "sample1" "platform1" "b") | ||
| is "$(run_freebayes -f ${ref} ${bam1} ${bam2})" "${expected}" "freebayes calls from two identical BAMs" | ||
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| bam1=$(make_bam "id1" "sample1" "platform1") | ||
| bam2=$(make_bam "id2" "sample2" "platform2") | ||
| is "$(run_freebayes -f ${ref} ${bam1} ${bam2})" "${expected}" "freebayes calls from two BAMs with different samples for different read groups" | ||
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| bam1=$(make_bam "id1" "sample1" "platform1") | ||
| bam2=$(make_bam "id2" "sample1" "platform2") | ||
| is "$(run_freebayes -f ${ref} ${bam1} ${bam2})" "${expected}" "freebayes calls from two BAMs with different technologies for different read groups" | ||
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| bam1=$(make_bam "id1" "sample1" "platform1") | ||
| bam2=$(make_bam "id1" "sample2" "platform1") | ||
| expected='ERROR\(freebayes\): multiple samples \(SM\) map to the same read group \(RG\)' | ||
| like "$(run_freebayes -f ${ref} ${bam1} ${bam2})" "${expected}" "freebayes rejects two BAMs with different samples for same read groups" | ||
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| bam1=$(make_bam "id1" "sample1" "platform1") | ||
| bam2=$(make_bam "id1" "sample1" "platform2") | ||
| expected='ERROR\(freebayes\): multiple technologies \(PL\) map to the same read group \(RG\)' | ||
| like "$(run_freebayes -f ${ref} ${bam1} ${bam2})" "${expected}" "freebayes rejects two BAMs with different technologies for same read groups" | ||
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| bam1=$(make_bam "id1" "sample1" "platform1") | ||
| bam2=$(make_bam "id2" "sample2" "platform2" "" "C") | ||
| expected=$(cat <<END | ||
| ref 2 . A C,G | ||
| ref 4 . CG TA | ||
| ref 7 . C G | ||
| ref 9 . A T | ||
| END | ||
| ) | ||
| is "$(run_freebayes -f ${ref} ${bam1} ${bam2})" "${expected}" "freebayes calls multiple alts from two different BAMs" | ||
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| is "$(run_freebayes -f ${ref} ${bam1} ${bam1})" "Error: Duplicate bam file '02_multi_bam.t.id1.sample1.platform1.bam'" "freebayes rejects two BAMs with the same name" |