weisburd 09c3b15af3 Implemented joins ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3476 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-02 16:28:06 +00:00
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arguments	Support for detecting and automatically excluding reads reading into the adaptor sequence and, if desired, also only showing the first pair when two reads overlap in the fragment. Not enabled, an intermediate check in before updating and verifying the impact on locus walkers everywhere.	2010-05-30 18:00:12 +00:00
contexts	Changes to Depth of Coverage (added maximum base and mapping quality flags; with new integration tests -- because they use b36, and the other test uses hg18, it's in a different class (integration test system can't change refs on the fly). Initial change to VariantAnnotator to allow it to see extended event pilups; you currently have to throw the -dels flag; and it's specified as "very experimental". Yet,all the integration tests pass.	2010-05-21 13:02:01 +00:00
datasources	Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end.	2010-05-26 22:12:25 +00:00
examples	Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes	2010-02-05 21:47:54 +00:00
executive	Support for detecting and automatically excluding reads reading into the adaptor sequence and, if desired, also only showing the first pair when two reads overlap in the fragment. Not enabled, an intermediate check in before updating and verifying the impact on locus walkers everywhere.	2010-05-30 18:00:12 +00:00
filters	Reorganization of SW code for clarity. Totally failure at raw optimization. Discovered that ~50% of reads being cleaned were perfect reference matches. New code comes with flag to look at NM field and not clean perfect matches. Can we turned off with command line option (needed for 1KG bams with bad NM fields). Going to rerun cleaning jobs due to accidentally rebuilding of stable codebase and loss of 2 days of runtime.	2010-05-27 23:16:00 +00:00
io	Fixed UG parallelization bug. Better integration test to catch this in the future.	2010-05-25 21:03:45 +00:00
iterators	Support for detecting and automatically excluding reads reading into the adaptor sequence and, if desired, also only showing the first pair when two reads overlap in the fragment. Not enabled, an intermediate check in before updating and verifying the impact on locus walkers everywhere.	2010-05-30 18:00:12 +00:00
refdata	Added toString()	2010-06-02 16:24:25 +00:00
traversals	Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end.	2010-05-26 22:12:25 +00:00
walkers	Implemented joins	2010-06-02 16:28:06 +00:00
CommandLineExecutable.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
CommandLineGATK.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
DownsampleType.java	Experimental versions of downsampler and Ryan's deduper are now available either	2010-05-19 05:40:05 +00:00
DownsamplingMethod.java	Experimental versions of downsampler and Ryan's deduper are now available either	2010-05-19 05:40:05 +00:00
GATKErrorReport.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
GenomeAnalysisEngine.java	Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:	2010-05-28 14:52:44 +00:00
Reads.java	Experimental versions of downsampler and Ryan's deduper are now available either	2010-05-19 05:40:05 +00:00
WalkerManager.java	Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:	2010-05-28 14:52:44 +00:00
package-info.java	Put a major.minor version into the GATK Javadoc for reading. Also,	2010-01-15 21:48:30 +00:00