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gatk-3.8/java/src/org/broadinstitute/sting/utils
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depristo d7c0bcc223 Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information. 
All GenomeLoc[] are not ArrayList<GenomeLoc> for clarity and consistency
Parsing now recursively merges contiguous elements chr1:1-10;chr1:11-20 => chr1:1-20
Added support for TraversingByLoci over all reference positions specified by the provided location array.  System dynamically determines which traversal system to use.
Pileup now marks, very clearly, reference positions without covered reads.
Made changes around the codebase to deal with new GenomeLoc structure.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@218 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-03-28 20:37:27 +00:00
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cmdLine Provide out and err PrintStreams to the walkers. 2009-03-27 15:03:32 +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 Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information. 2009-03-28 20:37:27 +00:00
Pair.java Push core / playground lower into the tree. 2009-03-23 23:19:54 +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
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 Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information. 2009-03-28 20:37:27 +00:00
xReadLines.java Documentation and cleanup of xReadLines. 2009-03-25 15:36:21 +00:00