hanna 186c799ffc Class to read an .fai file. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@405 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-14 17:37:18 +00:00
..
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	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
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
FastaSequenceIndex.java	Class to read an .fai file.	2009-04-14 17:37:18 +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	Added lots of assertions to check for problems. The current GenomeLoc needs to be cleaned up and refactored but at least it runs. We need unit tests ASAP	2009-04-14 00:53:08 +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	Some utility methods for creating pileups of secondary bases and secondary quals.	2009-04-14 13:57:54 +00:00
xReadLines.java	Documentation and cleanup of xReadLines.	2009-03-25 15:36:21 +00:00