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gatk-3.8/java/src/org/broadinstitute/sting/gatk
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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
..
contexts Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
datasources Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
examples Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
executive A bit of reorganization to help with more flexible output streams. Pushed construction of data 2009-07-29 23:00:15 +00:00
filters Major: allow genotyper to optionally output in 1KG format, including outputting the samples in which indels are found. 2009-07-23 19:53:51 +00:00
iterators Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
refdata Made sure all RODs have a (good) toString() method - and use it in the Venn walker. (thanks, Mark) 2009-07-30 14:53:27 +00:00
traversals Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
walkers Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
CommandLineExecutable.java Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very* 2009-07-29 16:11:45 +00:00
CommandLineGATK.java Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils. 2009-07-21 22:23:28 +00:00
GATKArgumentCollection.java Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very* 2009-07-29 16:11:45 +00:00
GenomeAnalysisEngine.java A bit of reorganization to help with more flexible output streams. Pushed construction of data 2009-07-29 23:00:15 +00:00
OutputTracker.java Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very* 2009-07-29 16:11:45 +00:00
Reads.java Better support for specifying read filters to apply directly from the walkers. 2009-07-09 23:59:53 +00:00
WalkerManager.java Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils. 2009-07-21 22:23:28 +00:00
package.html More package-level documentation. 2009-06-17 16:28:45 +00:00