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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d4d3af20f2
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made a fake fasta generator, so we can now generate a complete bam / fasta combo of made up data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1150 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-01 21:35:34 +00:00 |
depristo
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5289230eb8
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Version 0.2.1 (released) of the TableRecalibrator
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 22:50:55 +00:00 |
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aaron
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4e04370f14
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forgot a file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1096 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 17:56:17 +00:00 |
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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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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195b4ea7b4
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a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@984 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-11 17:46:06 +00:00 |