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AlignmentUtils.java
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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
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2009-03-26 02:26:17 +00:00 |
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ConsensusSequence.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@184 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-25 05:48:10 +00:00 |
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DiscardingPileReceiver.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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DiscardingReceiver.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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Indel.java
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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
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2009-03-26 02:26:17 +00:00 |
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IndelInspector.java
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added MAX_READ_LENGTH - now we can ignore long reads (454?); a bad idea in general, but the performance hit is to hard to take, at least for preliminary testing runs...
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2009-04-13 16:53:12 +00:00 |
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IndelRecordPileCollector.java
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a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg
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2009-04-13 04:49:19 +00:00 |
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IndexedSequence.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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IntervalComparator.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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KmerCodeIterator.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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MSAColumn.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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Matrix.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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MultipleAlignment.java
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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
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2009-03-26 02:26:17 +00:00 |
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PairwiseAlignment.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@184 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-25 05:48:10 +00:00 |
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PassThroughWriter.java
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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
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2009-03-26 02:26:17 +00:00 |
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PileBuilder.java
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there are really cases when we can not merge until we get just two pilesant now we do not crash in those cases but print a warning and just show the resulting n piles even when n>2
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2009-04-14 00:45:47 +00:00 |
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RecordPileReceiver.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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RecordReceiver.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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SWPairwiseAlignment.java
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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
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2009-03-26 02:26:17 +00:00 |
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SequencePile.java
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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
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2009-03-26 02:26:17 +00:00 |
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ShowMSA.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@167 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 14:06:44 +00:00 |
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StrictlyUpperTriangularMatrix.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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SymmetricMatrix.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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