Mark DePristo 29319bf222 Improved allele trimming code in GATKVariantContextUtils ... -- Now supports trimming the alleles from both the reverse and forward direction. -- Added lots of unit tests for forwrad allele trimming, as well as creating VC from forward and reverse trimming. -- Added docs and tests for the code, to bring it up to GATK spec		2013-02-21 12:01:43 -05:00
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alignment	Refactored GATKDocs categories some more ( GSATDG-62 )	2013-02-13 16:49:18 -05:00
commandline	Added an option to print out the version string	2013-02-15 12:42:59 -05:00
gatk	Added new ReadFilter that allows users to specifically reassign one single mapping quality to a different value. Useful for TopHat and other RNA-seq software users.	2013-02-20 01:24:45 -05:00
jna	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
queue	change the default VCFs gatherer of the GATK (not just the UG)	2013-01-18 15:03:12 -05:00
tools	Move some VCF/VariantContext methods back to the GATK based on feedback	2013-01-29 16:56:55 -05:00
utils	Improved allele trimming code in GATKVariantContextUtils	2013-02-21 12:01:43 -05:00