rpoplin 7f19ff1fa1 Added a new option in the recalibrator to be used by people who have SOLiD data in which only a few of the reads have no-calls in the color space. These reads will be skipped over and left in the bam file untouched. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2857 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-19 15:25:23 +00:00
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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	VariantFiltration now accepts any number of --name --filter expressions, and annotates the VCF file with each name that matches. Very useful	2010-01-29 12:13:08 +00:00
genotyper	Various improvements and fixes:	2010-02-07 04:21:04 +00:00
indels	- Change sortOnDisk option to sortInMemory	2010-02-17 20:52:57 +00:00
recalibration	Added a new option in the recalibrator to be used by people who have SOLiD data in which only a few of the reads have no-calls in the color space. These reads will be skipped over and left in the bam file untouched.	2010-02-19 15:25:23 +00:00
varianteval	Reverting	2010-02-05 15:57:09 +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