hanna
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433ad1f060
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Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-08 18:49:08 +00:00 |
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hanna
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d8fbb2b62c
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Refactoring; make a better home for the MalformedReadFilteringIterator.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1194 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-08 16:54:20 +00:00 |
aaron
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f6a273a537
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other fixes for some broken unit tests
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1181 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-07 05:53:13 +00:00 |
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aaron
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033bafe7a1
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fixed sam by reads test for the new filtering code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1180 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-07 05:45:50 +00:00 |
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aaron
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0a16519aa2
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a couple of additions to the tests, plus a change to the artificial resource pool to support the queryContained flag
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1099 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 18:30:32 +00:00 |
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aaron
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5b1c23a7f2
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changes to fix and test the interval based traversals
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1095 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 17:54:15 +00:00 |
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hanna
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ef546868bf
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Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude.
Desperately needs cleanup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1080 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-23 23:48:06 +00:00 |
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aaron
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bcb64d92e9
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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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-22 14:39:41 +00:00 |
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aaron
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6ee64c7e43
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added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1021 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-16 22:15:56 +00:00 |
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hanna
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71e3825fa1
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First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@989 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-11 20:18:13 +00:00 |
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aaron
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63b5c12cbd
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Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-11 18:13:22 +00:00 |