depristo 8d13597a27 Temporary command-line support to enable rod walkers, if you know what you are doing this is safe. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2505 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-06 12:15:36 +00:00
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contexts	Can now be constructed with either base pileup or extended event (indel) pileup; has query methods checking what kind of pileup is served by the context, and getter methods return the appropriate pileup. TODO: while it is impossible right now to create a context that contains both types of pileups simultaneously, this restriction is only weakly enforced through the lack of appropriate constructor. Either we keep it this way, or some getters may become ambiguous and have to be fixed!	2009-12-29 20:07:29 +00:00
datasources	Temporary command-line support to enable rod walkers, if you know what you are doing this is safe.	2010-01-06 12:15:36 +00:00
examples	Completed my documentation responsibilities - based on Mark's reasonable assignment and not the one Matt made up while on Meth.	2009-12-13 04:13:30 +00:00
executive	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00
filters	Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark.	2010-01-03 21:31:04 +00:00
io	UnifiedGenotyper now works without -varout or -vf set.	2009-12-29 16:46:24 +00:00
iterators	Compute and cache the length of the longest deletion observed at the site; ReadBackedExtendedEventPileup now has a getter to access that value.	2009-12-30 21:19:39 +00:00
refdata	Converter from HapMap chip genotype data to VCF added; HapMapGenotypeROD adjusted to not convert from Hg18 to b36 formatting of contigs	2009-12-28 01:36:08 +00:00
traversals	Temporary command-line support to enable rod walkers, if you know what you are doing this is safe.	2010-01-06 12:15:36 +00:00
walkers	Give Annotations access to rod data.	2010-01-05 18:53:01 +00:00
CommandLineExecutable.java	First revision of command-line argument support for GenotypeWriter. Also, fixed the damn build.	2009-12-20 19:19:23 +00:00
CommandLineGATK.java	Cleanup of the doc system, and introduce Kiran's concept of a detailed summary	2009-12-12 04:04:37 +00:00
GATKArgumentCollection.java	Temporary command-line support to enable rod walkers, if you know what you are doing this is safe.	2010-01-06 12:15:36 +00:00
GenomeAnalysisEngine.java	Reads now have new traversal flag: generateExtendedEvents(). Support added to GenomeAnalysisEngine and Walker. This is a silent and transparent framework change that no existing code is going to see. The actual code that makes use of the new flag (which is false by default) will be committed separately...	2009-12-28 19:52:44 +00:00
Reads.java	Reads now have new traversal flag: generateExtendedEvents(). Support added to GenomeAnalysisEngine and Walker. This is a silent and transparent framework change that no existing code is going to see. The actual code that makes use of the new flag (which is false by default) will be committed separately...	2009-12-28 19:52:44 +00:00
WalkerManager.java	Cleanup of the doc system, and introduce Kiran's concept of a detailed summary	2009-12-12 04:04:37 +00:00
package-info.java	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00