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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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ebanks 47440bc029 - Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads. 
- Reimplemented optimization in UG to not call when there are no non-ref bases.
- Compute reference confidence accurately in UG for ref calls.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2693 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-01-26 21:56:33 +00:00
..
annotator - Fixed output for beagle header 2010-01-21 21:25:56 +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 - Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads. 2010-01-26 21:56:33 +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 Default platform and default read group are no longer set to values by default. The recalibrator throws an exception if needed values are empty in the bam file and the args weren't set by the user. This is done to make it more obvious to the user when the bam file is malformed. Similarly, the recalibrator now refuses to recalibrate any solid reads in which it can't find the color space information with an exception message explaining this. The recalibrator no longer maintains its own version number and instead uses the new global GATK version number. 2010-01-26 18:47:40 +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