kiran 23680a9a16 Replaced an expensive sort with an inexpensive direct computation. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1104 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-25 20:25:12 +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	Some changes regarding what to do when a cycle is completely busted.	2009-06-09 01:00:33 +00:00
BasecallingReadModel.java	Changed the intensities array order from cycle,channel to channel,cycle. This, I'm told, is a far more efficient allocation strategy.	2009-06-24 15:41:06 +00:00
BasecallingStats.java	Updates after seeing a certain number of reads, not a certain number of bases.	2009-06-09 01:01:36 +00:00
BasecallingTrainer.java	Wrote a public static version of loadFirstNReasonableReadsTrainingSet() so Alec can call it.	2009-06-18 20:18:17 +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	Replaced an expensive sort with an inexpensive direct computation.	2009-06-25 20:25:12 +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	Changed the intensities array order from cycle,channel to channel,cycle. This, I'm told, is a far more efficient allocation strategy.	2009-06-24 15:41:06 +00:00