depristo 819862e04e major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@918 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-05 23:34:37 +00:00
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dataSources	major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.	2009-06-05 23:34:37 +00:00
executive	We're no longer in the read-dropping business.	2009-06-04 22:37:51 +00:00
iterators	We're no longer in the read-dropping business.	2009-06-04 22:37:51 +00:00
refdata	major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.	2009-06-05 23:34:37 +00:00
traversals	major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.	2009-06-05 23:34:37 +00:00
walkers	Allow user to specify the compression to be used when writing out BAM files.	2009-06-05 08:48:34 +00:00
CommandLineGATK.java	Catch and rethrow the walker's required argument, so that command-line arguments will be displayed when the GATK throws an argument exception.	2009-05-20 19:17:16 +00:00
GATKArgumentCollection.java	Allow user to specify the compression to be used when writing out BAM files.	2009-06-05 08:48:34 +00:00
GenomeAnalysisEngine.java	major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.	2009-06-05 23:34:37 +00:00
LocusContext.java	Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...	2009-05-28 20:13:01 +00:00
OutputTracker.java	Lazy creation of output streams. Only create output streams when absolutely necessary.	2009-05-26 21:56:57 +00:00
Reads.java	enabled underlying filtering of zero mapping quality reads, vastly improves system performance	2009-05-29 14:51:08 +00:00
WalkerManager.java	Farewell, functionalj. You promised much, but you could not deliver.	2009-05-28 01:35:49 +00:00