Mauricio Carneiro feeab6075f Merging ReduceReads development with unstable repo ... It is time to bring the ReadClipper class to the main repo. Read Clipper has tested functionality for soft and hard clipping reads. I will prepare thorough documentation for it as it will be very useful for the assembler and the GATK in general.		2011-08-22 23:03:03 -04:00
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alignment	Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-07-19 20:25:33 -04:00
analyzecovariates	Added GATKDocs for the VQSR walkers.	2011-08-18 14:00:39 -04:00
commandline	info, not warn, about dynamic type determination	2011-08-22 17:24:51 -04:00
gatk	Further Bug fixes to CountVariants: stratifications were wrong in case genotypes had no-calls, for example if we stratified by sample and a sample had a no-call, this no-call was considered a true variant and counts were incorrectly increased	2011-08-22 20:42:47 -04:00
jna	Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline:	2011-08-22 15:13:27 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
queue	Fixed Queue's tagging of RodBindings.	2011-08-21 02:34:20 -04:00
utils	Merging ReduceReads development with unstable repo	2011-08-22 23:03:03 -04:00