kiran 1fb16d54e0 For SAM files that have no alignments and when no reference is specified, contigInfo.getSequence() is null, causing an error when getSequenceName() is called on the resulting null pointer. Check for null instead and return that instead of barfing here. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@374 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-13 00:48:21 +00:00
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cmdLine	Enabled multiple argument for GATK driver; first step towards generalized -rods <name> <type> <file> argument structure	2009-04-08 01:52:13 +00:00
BaseUtils.java	Helpful functions for converting a base (char) to a base index (A:0, C:1, G:2, T:3, alphabetical and consistent with Illumina conventions to minimize confusion.	2009-04-13 00:46:23 +00:00
FastaSequenceFile2.java	moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes.	2009-03-27 14:02:55 +00:00
FileProgressTracker.java	moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes.	2009-03-27 14:02:55 +00:00
GenomeLoc.java	For SAM files that have no alignments and when no reference is specified, contigInfo.getSequence() is null, causing an error when getSequenceName() is called on the resulting null pointer. Check for null instead and return that instead of barfing here.	2009-04-13 00:48:21 +00:00
JVMUtils.java	Refactor common functionality out of WalkerManager and into JVMUtils and PathUtils. Add support for loading walkers from a jar.	2009-03-30 23:20:55 +00:00
Pair.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
PathUtils.java	Refactor common functionality out of WalkerManager and into JVMUtils and PathUtils. Add support for loading walkers from a jar.	2009-03-30 23:20:55 +00:00
Predicate.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
PrimitivePair.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
QualityUtils.java	Added some stuff for retreiving the base index and probability of a compressed base.	2009-04-08 15:52:58 +00:00
RefHanger.java	moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes.	2009-03-27 14:02:55 +00:00
Utils.java	The system now requires a dictionary file for a fasta file, or it throws an error. You can't just operate without a sequence dictionary any longer. We will transition to a GenomeLoc system that assumes a dictionary is available.	2009-04-07 22:19:54 +00:00
xReadLines.java	Documentation and cleanup of xReadLines.	2009-03-25 15:36:21 +00:00