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gatk-3.8/public/testdata
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Mark DePristo 5894d045cb Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests 
-- This version of BCF should actually work properly for most files, assuming headers are properly defined.
-- Lots of bug fixes to BCF2 codec
-- Genotype getPhredScaledQual is now an int, returning -1 if there's no QUAL.  NOTE THIS SEMANTICS change
-- Equals() method for GenotypeLikelihoods, using PLs.
-- VCFCodec now longer adds empty bindings to missing input field values.  NOTE THIS CHANGE
-- VCs can be marked as fully decoded, so that when fullyDecode() is called it returns itself, instead of doing the decoding work.  The BCF2 codec now makes VCs marked as fully decoded
-- stringToBytes returns empty list for null or "" string in BCF2Encoder
-- Proper handling of genotype ordering in BCF2 reader / writer
-- Removed the crazy slow noDups and sameSamples tests that were slowing down unit and integration tests totally unnecessarily
-- Many failing MD5s now due to double -> int change in GQ, will update later
 		2012-05-27 11:17:17 -04:00
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Beagle Fix up bad paths to public/testdata files 2012-05-24 10:59:00 -04:00
PhaseByTransmission Fix up bad paths to public/testdata files 2012-05-24 10:59:00 -04:00
VariantEval Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
vcf
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GIH.samples.list Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
HiSeq.1mb.bam Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
HiSeq.1mb.bam.bai Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
HiSeq.10000.bgzip.vcf.gz Adding bgzip vcf file for unit tests 2011-09-21 15:39:45 -04:00
HiSeq.10000.vcf
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HiSeq.10000.vcf.gz
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ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests 2012-05-27 11:17:17 -04:00
MendelianViolationEval.ped Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
MendelianViolationEval.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
MultiSample.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
NA12878.chr1_10mb_11mb.slx.indels.vcf4 Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
NA12878.hg19.example1.vcf Updated test files didn't make it into last push 2012-05-24 13:29:44 -04:00
TabularDataTest.dat
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TabularDataTest2.dat
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VQSR.mixedTest.input Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
VQSR.mixedTest.recal Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
VQSR.mixedTest.tranches Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
ValidatingPileupTargets.list
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ac0.vcf VariantEval now includes -keepAC0 argument to include sites with alt alleles but AC 0 in analyses 2012-04-04 15:37:12 -04:00
allelesForUG.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
amplicon_interval_table1.table Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
amplicon_mask_sites.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
badIntervalLocations.list Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
badRead.test.bai Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
badRead.test.bam Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
breakpoint-example.vcf Added support for breakpoint alleles 2012-02-23 12:14:48 -05:00
ceutrio.ped Oops, forgot the PED test file 2011-10-05 21:09:08 -07:00
clippingReadsTest.bam Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
clippingReadsTest.bam.bai Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
clippingReadsTest.withRG.bai Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
clippingReadsTest.withRG.bam Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
combine.1.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
combine.2.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
combine.3.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
combine.4.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
combine.5.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
combine.6.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
complexExample.vcf4 Fix up bad paths to public/testdata files 2012-05-24 10:59:00 -04:00
complexExample1.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
complexExample2.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
complexExample3.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
dbsnp_135.b37.1000.vcf Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests 2012-05-27 11:17:17 -04:00
defaultGATKConfig.cfg
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diffTestMaster.vcf
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diffTestTest.vcf
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empty_intervals.list Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
exampleBAM.bam PPP pipeline test 2011-12-11 17:32:21 -05:00
exampleBAM.bam.bai PPP pipeline test 2011-12-11 17:32:21 -05:00
exampleBAM.simple.bai
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exampleBAM.simple.bam
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exampleDBSNP.vcf PPP pipeline test 2011-12-11 17:32:21 -05:00
exampleFASTA-3contigs.fasta Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
exampleFASTA-combined.fasta Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
exampleFASTA-windows.fasta Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
exampleFASTA.dict
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exampleFASTA.fasta
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exampleFASTA.fasta.amb Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.ann Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.bwt Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.fai
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exampleFASTA.fasta.pac Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.rbwt Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.rpac Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.rsa Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleFASTA.fasta.sa Data Processing Pipeline Test 2011-12-12 00:24:51 -05:00
exampleGATKReport.eval Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
exampleGATKReportv1.tbl Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
exampleGATKReportv2.tbl Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
exampleGRP.grp Extensive refactoring of the GATKReports. This was a beast. 2012-05-18 01:11:26 -04:00
exampleNORG.bam
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exampleNORG.bam.bai
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fakeHM3.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
forLeftAlignVariantsTest.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
gFFTest.gff
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gatkrunreport.fail.xml analyzeRunReports cleanup for new minimal GATKRunReport structure 2012-03-12 09:46:26 -04:00
gatkrunreport.success.xml analyzeRunReports cleanup for new minimal GATKRunReport structure 2012-03-12 09:46:26 -04:00
genotypes_chr1_ASW_phase3.3_first500.hapmap
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header.txt Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
indbnp129_notindbsnp132.txt Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
indbnp132_notindbsnp129.txt Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
indelAllelesForUG.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
indels.txt Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
inhapmap.txt Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
inomni.txt Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
justHeader.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
liftover_test.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
logisticParamsTest.list
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missense.txt Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
multi-allelic.bi-allelicInGIH.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
multiallelic.snps.bai Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
multiallelic.snps.bam Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
multiallelic.snps.intervals Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
multiallelic.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
noQual.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
oneReadAllInsertion.bam Fix up bad paths to public/testdata files 2012-05-24 10:59:00 -04:00
oneReadAllInsertion.bam.bai Fix up bad paths to public/testdata files 2012-05-24 10:59:00 -04:00
one_transition_and_one_transversion.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
originalQuals.1kg.chr1.1-1K.bam Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
originalQuals.1kg.chr1.1-1K.bam.bai Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
originalQuals.chr1.1-1K.bam Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
originalQuals.chr1.1-1K.bam.bai Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
overlapTest.bed Testdata for IntervalStratification 2011-11-10 11:08:34 -05:00
pacbio.hg19.intervals Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
pacbio.ts.recalibrated.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
readgroupblacklisttest.txt Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
readgroupblacklisttestlist.txt Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
recalConfig_1KG.cfg
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sampleBedFile.bed
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samtools.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
selectVariants.onePosition.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
seqsToClip.fasta Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
silent.txt Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
sites_to_validate.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
small.dbsnp.rod
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small.indel.test.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
small_unmerged_gatk_intervals.list Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
small_unmerged_picard_intervals.list Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
soap_gatk_annotated.vcf Updated test files didn't make it into last push 2012-05-24 13:29:44 -04:00
symbolic_alleles_1.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
symbolic_alleles_2.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
targetAnnotations.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
test.dup.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
tranches.4.txt
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tranches.6.txt
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tranches.raw.dat
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transition.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
transversion.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
truncated_at_non_word_boundary.bai Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
truncated_at_word_boundary.bai Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
twoDeletions.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
ug.random50000.family.ped Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
ug.random50000.subset300bp.chr1.family.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
unmappedFlagReadsInLastLinearBin.bai Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
unmappedFlagReadsInLastLinearBin.bam Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
validationExampleBad.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
validationExampleBad2.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
validationExampleBad3.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
validationExampleGood.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
vcf4.1.example.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
vcfMask.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
vcfexample.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
vcfexample2.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
vcfexample2empty.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
vcfexample3.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
vcfexample3empty.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
vcfexample3withIDs.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
vcfexample4.vcf Adding as many test data files into public/testdata as possible 2012-05-24 10:58:30 -04:00
withSymbolic.b37.vcf Testdata for IntervalStratification 2011-11-10 11:08:34 -05:00