kiran e48078b476 Updated to reflect change to BasecallingReadModel constructor. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@760 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-20 15:43:26 +00:00
..
AbstractFirecrestFileParser.java	Documentation.	2009-05-14 18:58:43 +00:00
AddFourProbsToSAM.java	Documentation.	2009-05-14 18:58:43 +00:00
AnnotateSecondaryBase.java	Forgot to say that the mate is unmapped too. This is necessary to prevent SAM-JDK from yelling at me about an invalid SAM file.	2009-05-20 15:38:51 +00:00
BasecallingBaseModel.java	Documentation.	2009-05-14 18:58:43 +00:00
BasecallingReadModel.java	Now basecalls an entire read (both ends of the pair, barcode... everything) at once. After, RawRead and FourProbRead can be asked to return a specified subset (corresponding to the ranges specified for each end of the read.	2009-05-20 00:09:20 +00:00
BasecallingStats.java	Aesthetic cleanup.	2009-05-17 04:09:23 +00:00
BasecallingTrainer.java	Renamed to BasecallingTrainer.	2009-05-20 00:03:46 +00:00
CombineSamAndFourProbs.java	Documentation.	2009-05-14 18:58:43 +00:00
FirecrestFileParser.java	Documentation.	2009-05-14 18:58:43 +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	Updated to reflect change to BasecallingReadModel constructor.	2009-05-20 15:43:26 +00:00
FourIntensity.java	Documentation.	2009-05-14 18:58:43 +00:00
FourProb.java	Documentation.	2009-05-14 18:58:43 +00:00
FourProbRead.java	Now basecalls an entire read (both ends of the pair, barcode... everything) at once. After, RawRead and FourProbRead can be asked to return a specified subset (corresponding to the ranges specified for each end of the read.	2009-05-20 00:09:20 +00:00
IlluminaParser.java	Now basecalls an entire read (both ends of the pair, barcode... everything) at once. After, RawRead and FourProbRead can be asked to return a specified subset (corresponding to the ranges specified for each end of the read.	2009-05-20 00:09:20 +00:00
MatchSQTagToStrand.java	Documentation.	2009-05-14 18:58:43 +00:00
RawRead.java	Now basecalls an entire read (both ends of the pair, barcode... everything) at once. After, RawRead and FourProbRead can be asked to return a specified subset (corresponding to the ranges specified for each end of the read.	2009-05-20 00:09:20 +00:00