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AlignmentUtils.java
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count X/N/etc. as mismatches for the NM attribute in the BAMs
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2009-06-30 16:08:55 +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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IndelInspectorMain.java
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Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.
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2009-06-22 14:39:41 +00:00 |
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IndelRecordPileCollector.java
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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)
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2009-05-06 21:59:33 +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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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
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2009-04-16 03:56:47 +00:00 |
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PileBuilder.java
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new optional arg added that allows to specify a separate bam file to send all piles that fail to realign to; plus minor fixes
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2009-05-13 20:24:23 +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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Make sure indel position from SW alignment is leftmost possible
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2009-06-05 15:36:10 +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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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...
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2009-05-28 20:13:01 +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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