aaron 7e0f69dab5 Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2410 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-18 22:54:56 +00:00
..
contexts	UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter).	2009-12-16 17:28:09 +00:00
datasources	Temporary hack for Tim Fennell: introduce a sharding strategy that stuffs all data into a single	2009-12-16 21:55:42 +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	Optimizations:	2009-12-16 21:39:58 +00:00
io	Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same.	2009-12-18 22:54:56 +00:00
iterators	Fixed curiously epic failure in read-backed pileup: size() mismatched the numReads-numDeletions at that locus in the case where includeReadsWithDeletionsAtLoci == false, causing failures including bad output from pileup walker. Also fixed up ValidatingPileup to run with the new ReadBackedPileup instead of just compiling successfully.	2009-12-18 22:52:44 +00:00
refdata	Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same.	2009-12-18 22:54:56 +00:00
traversals	Temporary hack for Tim Fennell: introduce a sharding strategy that stuffs all data into a single	2009-12-16 21:55:42 +00:00
walkers	Fixed curiously epic failure in read-backed pileup: size() mismatched the numReads-numDeletions at that locus in the case where includeReadsWithDeletionsAtLoci == false, causing failures including bad output from pileup walker. Also fixed up ValidatingPileup to run with the new ReadBackedPileup instead of just compiling successfully.	2009-12-18 22:52:44 +00:00
CommandLineExecutable.java	Make filters used available to the walker via getToolkit().	2009-12-16 21:26:04 +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	Un-reinventing the wheel. --sleep argument removed.	2009-12-02 20:19:28 +00:00
GenomeAnalysisEngine.java	Fixed NPE in index check with RefWalkers.	2009-12-16 22:37:45 +00:00
Reads.java	Command-line arguments for SamReadFilters.	2009-11-10 23:36:17 +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