aaron 2e4949c4d6 Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1751 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-30 20:37:59 +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	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +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
FourIntensity.java	Documentation.	2009-05-14 18:58:43 +00:00
FourProb.java	I committed this too soon... reverting...	2009-06-25 20:49:12 +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
SecondaryBaseAnnotator.java	A single class that can be handed reads for training and basecalling. When in training mode, we accumulate no more than 10000 reads and always replace the lowest-quality reads with superior quality reads. Thus, the training set always contains 10000 of the best reads available. After training is complete, the class can be interrogated to return the SQ tag for a given RawRead object.	2009-06-30 16:03:15 +00:00