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gatk-3.8/java/src/org/broadinstitute/sting/gatk/walkers
History
hanna 21d1eba502 Cleaned division of responsibilities between arguments to map function. Reference has been changed 
from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-08-04 21:01:37 +00:00
..
genotyper Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
indels Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
recalibration Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
Allows.java @Required / @Allows flags for main arguments. 2009-05-19 23:26:17 +00:00
By.java Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along 2009-05-15 21:02:12 +00:00
CountLociWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
CountReadsWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
DataSource.java Added REFERENCE_BASES required annotation for performance 2009-06-18 21:03:57 +00:00
DepthOfCoverageWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
DuplicateWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
LocusWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
LocusWindowWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
NullWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
PileupWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
PileupWithContextWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
PrintLocusContextWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
PrintReadsWalker.java A bit of reorganization to help with more flexible output streams. Pushed construction of data 2009-07-29 23:00:15 +00:00
RMD.java Better support for specifying read filters to apply directly from the walkers. 2009-07-09 23:59:53 +00:00
ReadFilters.java Better support for specifying read filters to apply directly from the walkers. 2009-07-09 23:59:53 +00:00
ReadWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
RefWalker.java Added REFERENCE_BASES required annotation for performance 2009-06-18 21:03:57 +00:00
Requires.java @Required / @Allows flags for main arguments. 2009-05-19 23:26:17 +00:00
SplitSamFileWalker.java A bit of reorganization to help with more flexible output streams. Pushed construction of data 2009-07-29 23:00:15 +00:00
TreeReducible.java N-way parallelism. Works for small test cases. Untested for large test cases. 2009-05-01 19:34:09 +00:00
ValidatingPileupWalker.java Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
Walker.java Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very* 2009-07-29 16:11:45 +00:00
WalkerName.java Make command-line arguments available in walker constructor, provide back door from 2009-03-26 20:45:27 +00:00
package.html More package-level documentation. 2009-06-17 16:28:45 +00:00