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gatk-3.8/java/src/org/broadinstitute/sting/secondarybase
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hanna 5e8c08ee63 Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-05-28 20:13:01 +00:00
..
AbstractFirecrestFileParser.java Documentation. 2009-05-14 18:58:43 +00:00
AddFourProbsToSAM.java Added loads of documentation. 2009-05-21 19:40:47 +00:00
AnnotateSecondaryBase.java Added the ability to specify the sorted, unaligned bam and/or the sorted, aligned bam such that broken computations can be restarted. 2009-05-22 19:33:34 +00:00
BasecallingBaseModel.java Added loads of documentation. 2009-05-21 19:40:47 +00:00
BasecallingReadModel.java Added loads of documentation. 2009-05-21 19:40:47 +00:00
BasecallingStats.java Added loads of documentation. 2009-05-21 19:40:47 +00:00
BasecallingTrainer.java Replaced dumb training function with a version that creates a training set slightly more sensibly. 2009-05-22 19:34:33 +00:00
CombineSamAndFourProbs.java Documentation. 2009-05-14 18:58:43 +00:00
FirecrestFileParser.java Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard... 2009-05-28 20:13:01 +00:00
FirecrestFilenameComparator.java Moved secondary base stuff out of playground for the purpose of making it a core utility. Modified package names and imports such that things would build properly. 2009-05-12 20:24:18 +00:00
FirecrestReadData.java Moved secondary base stuff out of playground for the purpose of making it a core utility. Modified package names and imports such that things would build properly. 2009-05-12 20:24:18 +00:00
FourBaseRecaller.java Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard... 2009-05-28 20:13:01 +00:00
FourIntensity.java Documentation. 2009-05-14 18:58:43 +00:00
FourProb.java Added loads of documentation. 2009-05-21 19:40:47 +00:00
FourProbRead.java Added loads of documentation. 2009-05-21 19:40:47 +00:00
IlluminaParser.java Added loads of documentation. 2009-05-21 19:40:47 +00:00
MatchSQTagToStrand.java Documentation. 2009-05-14 18:58:43 +00:00
RawRead.java Added loads of documentation. 2009-05-21 19:40:47 +00:00