depristo c47a5ff5ab Official parallel CountCovariates, passes all integration tests. Now poster-child example of parallelism in GATK (Matt H). Apparent general performance improvements throughout too. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3833 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-19 22:13:18 +00:00
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alignment	Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath.	2010-04-01 17:17:16 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	Official parallel CountCovariates, passes all integration tests. Now poster-child example of parallelism in GATK (Matt H). Apparent general performance improvements throughout too.	2010-07-19 22:13:18 +00:00
oneoffprojects/walkers	fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric!	2010-06-29 21:38:55 +00:00
playground	Solid processing in base quality recalibrator now has several options for how to handle no calls in the color space. --ignore_nocall_colorspace is removed and replace by --solid_nocall_strategy. Fixed some of the @Deprecated tags in BaseUtils. LocusWalkers now filter out FailsVendorQualityCheck reads. HLA caller integration test bam file had bad vendor reads so its integration test changed.	2010-07-19 19:10:29 +00:00
utils	The first step in integrating Jim's tree based index scheme:	2010-07-19 04:49:27 +00:00
BaseTest.java	incremental changes to the VCF4 codec, including allele clipping down to the minimum reference allele; adding unit testing for certain aspects of the parsing. Not ready for prime-time yet.	2010-06-22 06:31:05 +00:00
WalkerTest.java	GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line	2010-06-02 22:26:32 +00:00