Test Result : VariantContextConverterSuite

0 failures (±0) , 1 skipped (±0)
195 tests (±0)
Took 0.31 sec.

All Tests

Test nameDurationStatus
1000G membership set adam->htsjdk0 msPassed
1000G membership set going htsjdk->adam1 msPassed
Convert ADAM SNV w/ genotypes but bad SB to htsjdk with lenient validation4 msPassed
Convert ADAM SNV w/ genotypes but bad SB to htsjdk with strict validation1 msPassed
Convert ADAM SNV w/ genotypes to htsjdk1 msPassed
Convert ADAM site-only SNV to htsjdk1 msPassed
Convert ADAM variant context with failing filters to htsjdk0 msPassed
Convert ADAM variant context with multiple names to htsjdk0 msPassed
Convert ADAM variant context with no filters applied to htsjdk0 msPassed
Convert ADAM variant context with no names to htsjdk0 msPassed
Convert ADAM variant context with null filters applied to htsjdk0 msPassed
Convert ADAM variant context with one name to htsjdk0 msPassed
Convert ADAM variant context with passing filters to htsjdk1 msPassed
Convert gVCF reference records to ADAM2 msPassed
Convert htsjdk SNV w/ genotypes w/ phase information to ADAM3 msPassed
Convert htsjdk SNV with different genotype filters to ADAM1 msPassed
Convert htsjdk SNV with different variant filters to ADAM2 msPassed
Convert htsjdk multi-allelic SNVs to ADAM and back to htsjdk4 msPassed
Convert htsjdk multi-allelic sites-only SNVs to ADAM2 msPassed
Convert htsjdk site-only CNV to ADAM1 msPassed
Convert htsjdk site-only SNV to ADAM1 msPassed
Convert htsjdk variant context with multiple IDs to ADAM0 msPassed
Convert htsjdk variant context with no IDs to ADAM0 msPassed
Convert htsjdk variant context with one ID to ADAM0 msPassed
Convert somatic htsjdk site-only SNV to ADAM0 msPassed
VCF FORMAT attribute Number=0 Type=Flag adam->htsjdk not supported1 msPassed
VCF FORMAT attribute Number=0 Type=Flag htsjdk->adam is not supported0 msPassed
VCF FORMAT attribute Number=1 Type=Integer adam->htsjdk0 msPassed
VCF FORMAT attribute Number=1 Type=Integer htsjdk->adam1 msPassed
VCF FORMAT attribute Number=4 Type=Float htsjdk->adam2 msPassed
VCF FORMAT attribute Number=4 Type=Integer adam->htsjdk1 msPassed
VCF FORMAT attribute Number=4 Type=Integer htsjdk->adam1 msPassed
VCF FORMAT attribute Number=A Type=Integer adam->htsjdk0 msPassed
VCF FORMAT attribute Number=A Type=Integer htsjdk->adam1 msPassed
VCF FORMAT attribute Number=G Type=String htsjdk->adam1 msPassed
VCF FORMAT attribute Number=R Type=Integer adam->htsjdk1 msPassed
VCF FORMAT attribute Number=R Type=Integer htsjdk->adam0 msPassed
VCF FORMAT attribute Number=R Type=String adam->htsjdk1 msPassed
VCF FORMAT attribute Number=R Type=String htsjdk->adam1 msPassed
VCF INFO attribute Number=0 Type=Flag adam->htsjdk0 msPassed
VCF INFO attribute Number=0 Type=Flag htsjdk->adam1 msPassed
VCF INFO attribute Number=1 Type=Integer adam->htsjdk1 msPassed
VCF INFO attribute Number=1 Type=Integer htsjdk->adam0 msPassed
VCF INFO attribute Number=4 Type=Flag adam->htsjdk unsupported, strict0 msSkipped
VCF INFO attribute Number=4 Type=Float htsjdk->adam0 msPassed
VCF INFO attribute Number=4 Type=Integer adam->htsjdk0 msPassed
VCF INFO attribute Number=4 Type=Integer htsjdk->adam1 msPassed
VCF INFO attribute Number=A Type=Integer adam->htsjdk1 msPassed
VCF INFO attribute Number=A Type=Integer htsjdk->adam1 msPassed
VCF INFO attribute Number=G Type=String adam->htsjdk not supported1 msPassed
VCF INFO attribute Number=G Type=String htsjdk->adam not supported1 msPassed
VCF INFO attribute Number=R Type=Integer adam->htsjdk1 msPassed
VCF INFO attribute Number=R Type=Integer htsjdk->adam1 msPassed
VCF INFO attribute Number=R Type=String adam->htsjdk0 msPassed
VCF INFO attribute Number=R Type=String htsjdk->adam0 msPassed
allele count set adam->htsjdk0 msPassed
allele frequency set adam->htsjdk1 msPassed
ancestral allele set adam->htsjdk0 msPassed
ancestral allele set going htsjdk->adam1 msPassed
cigar set adam->htsjdk0 msPassed
dbsnp membership set adam->htsjdk0 msPassed
dbsnp membership set going htsjdk->adam1 msPassed
extract depth going adam->htsjdk0 msPassed
extract fisher strand bias going adam->htsjdk0 msPassed
extract fisher strand bias going htsjdk->adam1 msPassed
extract genotype likelihoods going adam->htsjdk0 msPassed
extract genotype quality going htsjdk->adam1 msPassed
extract gt read depth going adam->htsjdk0 msPassed
extract gt read depth going htsjdk->adam1 msPassed
extract mapping quality 0 reads going adam->htsjdk1 msPassed
extract min depth going adam->htsjdk0 msPassed
extract min gt read depth going htsjdk->adam0 msPassed
extract mq0 going htsjdk->adam1 msPassed
extract multiple filters going htsjdk->adam1 msPassed
extract phred likelihoods going htsjdk->adam1 msPassed
extract quality going adam->htsjdk0 msPassed
extract rms mapping quality going adam->htsjdk0 msPassed
extract rms mapping quality going htsjdk->adam1 msPassed
extract single filter going htsjdk->adam1 msPassed
extract strand bias going adam->htsjdk1 msPassed
extract strand bias info going htsjdk->adam1 msPassed
filters applied and passed going htsjdk->adam1 msPassed
filters passed adam->htsjdk0 msPassed
filters passed going adam->htsjdk0 msPassed
filters passed going htsjdk->adam0 msPassed
forward read depth set adam->htsjdk0 msPassed
forward read depth without reference forward read depth0 msPassed
hapmap2 membership set adam->htsjdk1 msPassed
hapmap2 membership set going htsjdk->adam1 msPassed
hapmap3 membership set adam->htsjdk0 msPassed
hapmap3 membership set going htsjdk->adam1 msPassed
if filter failed, must have filters adam->htsjdk1 msPassed
if filters applied, must set passed/failed going adam->htsjdk1 msPassed
if filters failed, must set filters failed going adam->htsjdk0 msPassed
malformed strand bias going adam->htsjdk1 msPassed
multiple CIGARs going htsjdk->adam0 msPassed
multiple allele counts going htsjdk->adam1 msPassed
multiple allele frequencies going htsjdk->adam1 msPassed
multiple filters applied and failed going htsjdk->adam1 msPassed
multiple filters failed adam->htsjdk0 msPassed
multiple filters failed going adam->htsjdk0 msPassed
multiple forward read depths going htsjdk->adam0 msPassed
multiple names set going htsjdk->adam1 msPassed
multiple read depths going htsjdk->adam0 msPassed
multiple reverse read depths going htsjdk->adam1 msPassed
no 1000G membership set adam->htsjdk1 msPassed
no 1000G membership set going htsjdk->adam0 msPassed
no CIGAR going htsjdk->adam0 msPassed
no allele count going htsjdk->adam0 msPassed
no allele count set adam->htsjdk0 msPassed
no allele frequency going htsjdk->adam1 msPassed
no allele frequency set adam->htsjdk0 msPassed
no allelic depth going htsjdk->adam1 msPassed
no ancestral allele set adam->htsjdk0 msPassed
no ancestral allele set going htsjdk->adam1 msPassed
no cigar set adam->htsjdk0 msPassed
no dbsnp membership set adam->htsjdk0 msPassed
no dbsnp membership set going htsjdk->adam0 msPassed
no depth going adam->htsjdk0 msPassed
no filter info going adam->htsjdk0 msPassed
no filters applied adam->htsjdk0 msPassed
no filters applied going htsjdk->adam1 msPassed
no filters going htsjdk->adam0 msPassed
no fisher strand bias going adam->htsjdk0 msPassed
no fisher strand bias going htsjdk->adam1 msPassed
no forward read depth going htsjdk->adam1 msPassed
no forward read depth set adam->htsjdk0 msPassed
no genotype likelihoods going adam->htsjdk0 msPassed
no genotype quality going htsjdk->adam1 msPassed
no gt read depth going adam->htsjdk0 msPassed
no gt read depth going htsjdk->adam0 msPassed
no hapmap2 membership set adam->htsjdk0 msPassed
no hapmap2 membership set going htsjdk->adam0 msPassed
no hapmap3 membership set adam->htsjdk0 msPassed
no hapmap3 membership set going htsjdk->adam0 msPassed
no mapping quality 0 reads going adam->htsjdk0 msPassed
no min depth going adam->htsjdk1 msPassed
no min gt read depth going htsjdk->adam1 msPassed
no mq0 going htsjdk->adam0 msPassed
no names set adam->htsjdk0 msPassed
no names set going htsjdk->adam1 msPassed
no phasing info going adam->htsjdk0 msPassed
no phasing set going htsjdk->adam1 msPassed
no phred likelihood going htsjdk->adam1 msPassed
no qual set adam->htsjdk0 msPassed
no quality going adam->htsjdk0 msPassed
no quality going htsjdk->adam0 msPassed
no read depth going htsjdk->adam1 msPassed
no read depth set adam->htsjdk0 msPassed
no reverse read depth going htsjdk->adam0 msPassed
no reverse read depth set adam->htsjdk0 msPassed
no rms mapping quality going adam->htsjdk0 msPassed
no rms mapping quality going htsjdk->adam0 msPassed
no strand bias going adam->htsjdk0 msPassed
no strand bias info going htsjdk->adam0 msPassed
no validated set adam->htsjdk0 msPassed
no validated set going htsjdk->adam0 msPassed
not somatic going htsjdk->adam0 msPassed
null filters applied adam->htsjdk0 msPassed
phased but no phase set info going htsjdk->adam1 msPassed
phased but no pq going adam->htsjdk0 msPassed
phased but no ps going adam->htsjdk0 msPassed
phased but no ps/pq going adam->htsjdk1 msPassed
phased going adam->htsjdk0 msPassed
qual is set adam->htsjdk0 msPassed
quality set going htsjdk->adam0 msPassed
read depth set adam->htsjdk0 msPassed
read depth without reference read depth1 msPassed
reference forward read depth without forward read depth0 msPassed
reference read depth without read depth0 msPassed
reference reverse read depth without reverse read depth0 msPassed
respect end position for symbolic alts0.19 secPassed
reverse read depth set adam->htsjdk0 msPassed
reverse read depth without reference reverse read depth1 msPassed
set a single name adam->htsjdk0 msPassed
set allelic depth going htsjdk->adam0 msPassed
set multiple names adam->htsjdk0 msPassed
set phase set and extract going htsjdk->adam1 msPassed
single CIGAR going htsjdk->adam1 msPassed
single allele count going htsjdk->adam0 msPassed
single allele frequency going htsjdk->adam1 msPassed
single allele frequency is +Inf going htsjdk->adam0 msPassed
single allele frequency is -Inf going htsjdk->adam1 msPassed
single filter applied and failed going htsjdk->adam1 msPassed
single filter failed adam->htsjdk0 msPassed
single filter failed going adam->htsjdk1 msPassed
single forward read depth going htsjdk->adam1 msPassed
single name set going htsjdk->adam1 msPassed
single read depth going htsjdk->adam1 msPassed
single reverse read depth going htsjdk->adam1 msPassed
somatic going htsjdk->adam1 msPassed
throw iae if missing one component of gt read depth going adam->htsjdk1 msPassed
unphased going adam->htsjdk0 msPassed
validated set adam->htsjdk0 msPassed
validated set going htsjdk->adam1 msPassed