ebanks
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758db73b98
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Fixed SLOWNESS issue.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@469 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-17 20:10:34 +00:00 |
asivache
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baae98c6d5
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and don't allocate new 200M string every time please, just pass byte array!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@417 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 21:55:33 +00:00 |
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asivache
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9d56355abe
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bug fixed when reference name was passed as a string instead of actual reference bases
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@416 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 21:46:27 +00:00 |
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ebanks
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647827b18c
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Transitioned indel code to use GATK and Walkers
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@410 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 19:14:15 +00:00 |
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asivache
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f47a214f96
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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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@197 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-26 02:26:17 +00:00 |
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asivache
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40f45c2333
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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 |