aaron 72ae81c6de VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include: ... - Tribble is included directly in the GATK repo; those who have access to commit to Tribble can now directly commit from the GATK directory from Intellij; command line users can commit from inside the tribble directory. - Hapmap ROD now in Tribble; all mentions have been switched over. - VariantContext does not know about GenomeLoc; use VariantContextUtils.getLocation(VariantContext vc) to get a genome loc. - VariantContext.getSNPSubstitutionType is now in VariantContextUtils. - This does not include the checked-in project files for Intellij; still running into issues with changes to the iml files being marked as changes by SVN I'll send out an email to GSAMembers with some more details. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3954 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-05 18:47:53 +00:00
..
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	VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:	2010-08-05 18:47:53 +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	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
utils	VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:	2010-08-05 18:47:53 +00:00
BaseTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +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