ebanks d044681fbe change paths to new ones ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1308 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-24 07:28:43 +00:00
..
ConsensusSequence.java	git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@184 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-25 05:48:10 +00:00
DiscardingPileReceiver.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
DiscardingReceiver.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
Indel.java	massive changes everywhere; lots of bugs fixed; methods moved around; computation and printout of overall stats added; now decides whether to accept or reject 'improvement'; writes alignments into two output sam files (unmodified reads/failed piles into one, realigned piles into the other); special treat for paranoids: writes third sam file with all the analyzed reads, unmodified	2009-03-26 02:26:17 +00:00
IndelInspectorMain.java	change paths to new ones	2009-07-24 07:28:43 +00:00
IndelRecordPileCollector.java	added COUNT_CUTOFF arg: it is nor possible to tell the code to try to realign all read piles over trains of nearby indels with at least one indel observed in COUNT_CUTOFF or more different alignments (set the arg to 1 to realign around all indels); also, some diagnostic printouts added to the output (time spent on loading the reference, time spent on scrolling through the input bam file, counts of discarded reads)	2009-05-06 21:59:33 +00:00
IndexedSequence.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
IntervalComparator.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
KmerCodeIterator.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
MSAColumn.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
Matrix.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
MultipleAlignment.java	massive changes everywhere; lots of bugs fixed; methods moved around; computation and printout of overall stats added; now decides whether to accept or reject 'improvement'; writes alignments into two output sam files (unmodified reads/failed piles into one, realigned piles into the other); special treat for paranoids: writes third sam file with all the analyzed reads, unmodified	2009-03-26 02:26:17 +00:00
PairwiseAlignment.java	git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@184 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-25 05:48:10 +00:00
PassThroughWriter.java	fix a few related issues when not all the reads were written into the output files. now cleaned output still contains all reads either with modified alignments or untouched	2009-04-16 03:56:47 +00:00
PileBuilder.java	change paths to new ones	2009-07-24 07:28:43 +00:00
RecordPileReceiver.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
RecordReceiver.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
SequencePile.java	massive changes everywhere; lots of bugs fixed; methods moved around; computation and printout of overall stats added; now decides whether to accept or reject 'improvement'; writes alignments into two output sam files (unmodified reads/failed piles into one, realigned piles into the other); special treat for paranoids: writes third sam file with all the analyzed reads, unmodified	2009-03-26 02:26:17 +00:00
ShowMSA.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
StrictlyUpperTriangularMatrix.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
SymmetricMatrix.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00