asivache 0338345bee Fixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3300 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-05 15:42:27 +00:00
..
arguments	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
contexts	Updated to work correctly with extended pileups. Clogged and uses some dirty tricks; pileups/extended pileups need to be redesigned someday	2010-04-20 17:38:09 +00:00
datasources	DbSNP moved over to tribble	2010-05-03 06:02:35 +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	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
filters	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
io	Because of the ugly VCF format, generic addCall() method of GenotypeWriter interface acquired an additional parameter, explicitly specified reference base (in VCF it's the base immediately *before* the event in case of indels, so we got to pass it). All implementing classes are modified to accomodate the change.	2010-04-21 18:19:03 +00:00
iterators	Checking in the reference implementation of the downsampler for back comparison.	2010-04-30 15:41:13 +00:00
refdata	fixes for new package names in tribble 74	2010-05-05 05:47:04 +00:00
traversals	Fare thee well, oh LocusWindowTraversal.	2010-03-29 13:17:26 +00:00
walkers	Fixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error.	2010-05-05 15:42:27 +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
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	DbSNP moved over to tribble	2010-05-03 06:02:35 +00:00
Reads.java	changes to intelligently log overflowing locus pile-ups.	2010-01-20 08:09:48 +00:00
WalkerManager.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +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