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gatk-3.8/public/java/src/org/broadinstitute/sting
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Eric Banks 9424e8b2ca Initial working version of new interval system in which the argument for -L (and -XL) is allowed to be a rod file (e.g. VCF). Old samtools-style intervals still behave as before. BTI is no longer supported. The merging (union or intersection) of intervals is now consistently applied to all -L (or -XL) intervals, which is nice. More testing needed. 2011-10-26 14:11:49 -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 Forgot that no matter how trivial a change it's a good idea to compile first 2011-10-11 11:18:41 -04:00
commandline Initial working version of new interval system in which the argument for -L (and -XL) is allowed to be a rod file (e.g. VCF). Old samtools-style intervals still behave as before. BTI is no longer supported. The merging (union or intersection) of intervals is now consistently applied to all -L (or -XL) intervals, which is nice. More testing needed. 2011-10-26 14:11:49 -04:00
gatk Initial working version of new interval system in which the argument for -L (and -XL) is allowed to be a rod file (e.g. VCF). Old samtools-style intervals still behave as before. BTI is no longer supported. The merging (union or intersection) of intervals is now consistently applied to all -L (or -XL) intervals, which is nice. More testing needed. 2011-10-26 14:11:49 -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 Initial working version of new interval system in which the argument for -L (and -XL) is allowed to be a rod file (e.g. VCF). Old samtools-style intervals still behave as before. BTI is no longer supported. The merging (union or intersection) of intervals is now consistently applied to all -L (or -XL) intervals, which is nice. More testing needed. 2011-10-26 14:11:49 -04:00