ebanks ca1917507f Various improvements and fixes: ... In indel cleaner: 1. allow the user to specify that he wants to use Picard’s SAMFileWriter sorting on disk instead of having us sort in memory; this is useful if the input consists of long reads. 2. for N-way-out mode: output bams now use the original headers from the corresponding input bams - as opposed to the merged header. This entailed some reworking of the datasources code. 3. intermediate check-in of code that allows user to input known indels to be used as alternate consenses. Not done yet. In UG: fix bug in beagle output for Jared. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2805 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-07 04:21:04 +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	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	RealignerTargetCreator is officially live	2010-01-27 03:41:52 +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
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