Mauricio Carneiro eb6308a0e4 General DiagnoseTargets documentation cleanup ... * remove interval statistic low_median_coverage -- it is already captured by low coverage and coverage gaps. * add gatkdocs to all the parameters * clean up the logic on callable status a bit (still need to be re-worked into a plugin system) * update integration tests		2013-04-22 23:53:09 -04:00
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annotator	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
beagle	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
bqsr	Trivial BQSR bug fixes and improvement	2013-04-11 17:08:35 -04:00
compression/reducereads	Refactored binomial probability code in MathUtils.	2013-04-16 18:19:07 -04:00
diagnostics	General DiagnoseTargets documentation cleanup	2013-04-22 23:53:09 -04:00
diffengine	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
fasta	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
genotyper	UnifiedGenotyper bugfix: don't create haplotypes with 0 bases	2013-04-13 14:57:55 -04:00
haplotypecaller	Bugfix for CommonSuffixSplitter	2013-04-21 19:37:01 -04:00
indels	Fixed IndelRealigner reference length bug (GSA-774)	2013-02-19 16:00:36 -05:00
phasing	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
validation	MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods	2013-03-29 14:52:10 -04:00
varianteval	Move some VCF/VariantContext methods back to the GATK based on feedback	2013-01-29 16:56:55 -05:00
variantrecalibration	Update MD5s for VQSR header change	2013-04-16 11:45:45 -04:00
variantutils	Using --keepOriginalAC in SelectVariants was causing it to emit bad VCFs	2013-04-05 00:53:28 -04:00