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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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rpoplin 189829841b The recalibrator now uses all input RODs when looking for known polymorphic sites not just the one named dbsnp. Added an integration test which uses both dbsnp and an input vcf file and skips over the union of the two. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2564 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-01-12 18:50:39 +00:00
..
annotator 1. Fixed small but embarrassing bug in weighted Allele Balance annotation calculation. 2010-01-12 18:33:53 +00:00
concordance Check for division by 0 in annotations 2010-01-07 19:27:15 +00:00
fasta moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 2009-12-29 07:40:48 +00:00
filters moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 2009-12-29 07:40:48 +00:00
genotyper 1. Fixed small but embarrassing bug in weighted Allele Balance annotation calculation. 2010-01-12 18:33:53 +00:00
indels moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 2009-12-29 07:40:48 +00:00
recalibration The recalibrator now uses all input RODs when looking for known polymorphic sites not just the one named dbsnp. Added an integration test which uses both dbsnp and an input vcf file and skips over the union of the two. 2010-01-12 18:50:39 +00:00
DepthOfCoverageIntegrationTest.java moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 2009-12-29 07:40:48 +00:00
PileupWalkerIntegrationTest.java Now that we changed how deletions are represented, got to update MD5... 2009-12-30 22:00:58 +00:00
PrintReadsWalkerTest.java A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records). 2009-10-02 19:35:35 +00:00