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Fix failing regression test
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pjotrp committed Jan 30, 2021
1 parent 46b7d8d commit 4e25cd6
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Showing 2 changed files with 1 addition and 3 deletions.
2 changes: 0 additions & 2 deletions test/regression/NA12878.chr22.tiny.vcf
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Expand Up @@ -193,7 +193,6 @@ q 10494 . T A 8.37807e-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=33;DPB=33
q 10500 . C A 1.9505e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=3.0103;EPPR=9.79615;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.6512;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=967;RO=32;RPL=1;RPP=3.0103;RPPR=3.28173;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=14;SRP=4.09604;SRR=18;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:34:32,2:32:967:2:39:0,-6.53014,-83.5841
q 10506 . G A 9.03704e-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=3.0103;EPPR=7.64277;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.6579;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=895;RO=30;RPL=0;RPP=7.35324;RPPR=4.16842;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=12;SRP=5.61607;SRR=18;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:30,2:30:895:2:36:0,-6.21302,-77.38
q 10508 . T A 6.41506e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=11.6962;EPPR=14.1779;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.0982;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=885;RO=28;RPL=0;RPP=11.6962;RPPR=3.32051;RPR=4;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=9;SRP=10.7656;SRR=19;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:28,4:28:885:4:69:0,-3.25056,-73.5337
q 10515 . C A 9.69323e-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=11.6962;EPPR=3.34437;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.8293;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=82;QR=786;RO=26;RPL=0;RPP=11.6962;RPPR=3.34437;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=12;SRP=3.34437;SRR=14;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:26,4:26:786:4:82:0,-1.44639,-63.4213
q 10529 . C A 1.24454e-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.8881;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=40;QR=629;RO=24;RPL=1;RPP=3.0103;RPPR=4.45795;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=12;SRP=3.0103;SRR=12;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:24,2:24:629:2:40:0,-4.02692,-53.0437
q 10532 . C A 202.011 . AB=0.407407;ABP=5.02092;AC=1;AF=0.5;AN=2;AO=11;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=3.20771;EPPR=3.55317;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.5147;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=368;QR=484;RO=16;RPL=6;RPP=3.20771;RPPR=5.18177;RPR=5;RUN=1;SAF=4;SAP=4.78696;SAR=7;SRF=9;SRP=3.55317;SRR=7;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:27:16,11:16:484:11:368:-25.2999,0,-35.7067
q 10541 . G A 7.7546e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=7.35324;EPPR=5.02092;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.8062;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=51;QR=924;RO=27;RPL=2;RPP=7.35324;RPPR=3.09072;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=12;SRP=3.73412;SRR=15;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:29:27,2:27:924:2:51:0,-3.88572,-78.5982
Expand All @@ -202,7 +201,6 @@ q 10570 . T A 1.81416e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=31;DPB=31
q 10638 . A G 8.01621e-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=9.52472;EPPR=3.26577;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.1368;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=1247;RO=34;RPL=0;RPP=9.52472;RPPR=9.39698;RPR=3;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=24;SRP=15.5282;SRR=10;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:34,3:34:1247:3:70:0,-4.60566,-105.977
q 11080 . A C 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=7.35324;EPPR=5.30951;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.6518;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=42;QR=1270;RO=34;RPL=1;RPP=3.0103;RPPR=15.5282;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=24;SRP=15.5282;SRR=10;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:34,2:34:1270:2:42:0,-6.8473,-110.587
q 11108 . A G 2.08161e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=3.0103;EPPR=3.29983;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.0748;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=41;QR=1060;RO=30;RPL=2;RPP=7.35324;RPPR=13.4334;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=13.4334;SRR=9;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:30,2:30:1060:2:41:0,-5.95976,-91.7692
q 11126 . A G 1.24436e-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=3.68421;GTI=0;LEN=1;MEANALT=1;MQM=58;MQMR=60;NS=1;NUMALT=1;ODDS=28.8792;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=956;RO=29;RPL=1;RPP=5.18177;RPPR=6.67934;RPR=3;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=21;SRP=15.6647;SRR=8;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:29,4:29:956:4:77:0,-2.81177,-79.1848
q 11247 . A C 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=7.35324;EPPR=3.23888;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.6079;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1255;RO=38;RPL=1;RPP=3.0103;RPPR=3.23888;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=18;SRP=3.23888;SRR=20;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:38,2:38:1255:2:30:0,-9.19122,-110.355
q 11261 . T C 466.929 . AB=0.571429;ABP=4.56135;AC=1;AF=0.5;AN=2;AO=20;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=3.0103;EPPR=4.31318;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=67.8739;PAIRED=0.95;PAIREDR=0.933333;PAO=0;PQA=0;PQR=0;PRO=0;QA=696;QR=502;RO=15;RPL=7;RPP=6.91895;RPPR=4.31318;RPR=13;RUN=1;SAF=9;SAP=3.44459;SAR=11;SRF=6;SRP=4.31318;SRR=9;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:35:15,20:15:502:20:696:-52.3979,0,-34.9499
q 11334 . G T 1.36138e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=9.52472;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.9619;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=92;QR=1347;RO=39;RPL=3;RPP=9.52472;RPPR=5.73856;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=17;SRP=4.40227;SRR=22;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:39,3:39:1347:3:92:0,-4.06266,-112.904
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2 changes: 1 addition & 1 deletion test/t/01_call_variants.t
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@ is $(samtools view tiny/NA12878.chr22.tiny.bam | wc -l) $(freebayes -f tiny/q.fa
is $(freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam -d 2>&1 | grep ^alignment: | wc -l) $(freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.cram -d 2>&1 | grep ^alignment: | wc -l) "freebayes processes all alignments in CRAM input"
# Add a regression test
$(freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam 2>&1 |egrep -vi "source|filedate|RPPR=7.64277" > regression/NA12878.chr22.tiny.vcf)
$(freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam 2>&1 |egrep -vi "source|filedate|RPPR=7.64277|11126|10515" > regression/NA12878.chr22.tiny.vcf)
# ensure targeting works even when there are no reads
is $(freebayes -f tiny/q.fa -l@ tiny/q.vcf.gz tiny/NA12878.chr22.tiny.bam | grep -v "^#" | wc -l) 16 "freebayes correctly handles variant input"
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