ebanks aacec3aeb0 rod for binary GELI files (still needs to be tested) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1198 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-08 20:25:56 +00:00
..
datasources	Refactoring; make a better home for the MalformedReadFilteringIterator.	2009-07-08 16:54:20 +00:00
examples	First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool.	2009-06-30 21:59:54 +00:00
executive	Basic infrastructure for filtering malformed reads.	2009-07-06 22:50:22 +00:00
iterators	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
refdata	rod for binary GELI files (still needs to be tested)	2009-07-08 20:25:56 +00:00
traversals	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
walkers	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
CommandLineExecutable.java	initial check-in of an easy way to create command line tools based on the GATK	2009-06-10 17:34:02 +00:00
CommandLineGATK.java	Temporary fix for Eric's problems with SOLiD reads: make sure the command-line argument system takes the --validation-strictness command-line argument into account when creating SAMFileReaders.	2009-07-07 15:18:05 +00:00
GATKArgumentCollection.java	Prep for documenting command-line arguments: delete some arguments that don't make sense any more given	2009-07-01 18:23:35 +00:00
GenomeAnalysisEngine.java	Temporary fix for Eric's problems with SOLiD reads: make sure the command-line argument system takes the --validation-strictness command-line argument into account when creating SAMFileReaders.	2009-07-07 15:18:05 +00:00
LocusContext.java	Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.	2009-06-30 19:17:24 +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	Prep for documenting command-line arguments: delete some arguments that don't make sense any more given	2009-07-01 18:23:35 +00:00
WalkerManager.java	Farewell, functionalj. You promised much, but you could not deliver.	2009-05-28 01:35:49 +00:00
package.html	More package-level documentation.	2009-06-17 16:28:45 +00:00