hanna 56f6847456 Changed interface from contig,pos,length to more common contig,start,stop interface. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@441 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-16 00:04:41 +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
fasta	Changed interface from contig,pos,length to more common contig,start,stop interface.	2009-04-16 00:04:41 +00:00
BaseUtils.java	Added some methods to return the cross-talk partner base of a given base or base index.	2009-04-14 14:49:12 +00:00
BasicPileup.java	General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.	2009-04-14 22:13:10 +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	Meaningful assert messages	2009-04-15 19:12:28 +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
Pileup.java	General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.	2009-04-14 22:13:10 +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
ReadBackedPileup.java	Slight code cleanup	2009-04-14 22:21:36 +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	General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.	2009-04-14 22:13:10 +00:00
xReadLines.java	Documentation and cleanup of xReadLines.	2009-03-25 15:36:21 +00:00