ebanks 30714ec8d9 As per quick chat with Richard Durban, don't increase the mapping quality of realigned reads too much; for now, arbitrarily increase the MQ by 10. We need to figure out a better solution. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3731 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-07 20:12:59 +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	As per quick chat with Richard Durban, don't increase the mapping quality of realigned reads too much; for now, arbitrarily increase the MQ by 10. We need to figure out a better solution.	2010-07-07 20:12:59 +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	Updated md5 - vcf header line change	2010-07-02 21:02:09 +00:00
utils	part two: todo's in combine variants, fixes for InferredGeneticContext, and some other tests and clean-up.	2010-07-05 21:07:53 +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