Eric Banks 5dfa863caa Fully stranded implementation of RR (plus bug fix for insertions and het compression). ... Now only filtered reads are unstranded. All consensus reads have strand, so that we emit 2 consensus reads in general now: one for each strand. This involved some refactoring of the sliding window which cleaned it up a lot. Also included is a bug fix: insertions downstream of a variant region weren't triggering a stop to the compression.		2013-07-25 14:48:53 -04:00
..
annotator	Fix bug introduced recently in the VariantAnnotator where only the last -comp was being annotated at a site.	2013-07-05 00:04:52 -04:00
beagle	Simpler FILTER and info field encoding for BeagleOutputToVCF	2013-06-14 15:56:13 -04:00
bqsr	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -04:00
compression/reducereads	Fully stranded implementation of RR (plus bug fix for insertions and het compression).	2013-07-25 14:48:53 -04:00
diagnostics	Update MD5s and the Diagnose Target scala script	2013-05-13 12:06:17 -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	Last feature request from Reich/Paavo labs: the allSitePLs feature in UG worked but not quite filled requirements. What's needed is the ability to have all 10 PLs for EVERY site, regardless of whether they are variant or not. Previous version only emitted the 10 PLs in reference sites. Problem is that, if all PLs are emitted in all sites and every single site is quad-allelic (only way to have the PLs printed out in a valid way) then the ability to filter variants and to use the INFO fields may be compromised.	2013-07-18 12:54:52 -04:00
haplotypecaller	A whole slew of improvements to the Haplotype Caller and related code.	2013-07-12 10:09:10 -04:00
indels	Another fix for the Indel Realigner that arises because of secondary alignments.	2013-06-21 16:59:22 -04:00
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	CombineVariants no longer adds PASS to unfiltered records	2013-05-20 16:53:51 -04:00