asivache
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de0cce87ea
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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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@691 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-13 20:24:23 +00:00 |
ebanks
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7de5da7065
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Start getting the cleaner working in Walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@561 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-29 14:59:53 +00:00 |
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asivache
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240eb18564
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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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@444 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-16 03:56:47 +00:00 |
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asivache
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bc43c0eefc
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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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@390 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 00:45:47 +00:00 |
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asivache
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c6d9848d08
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synchronizing latest changes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@212 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-27 14:15:44 +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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4c29dca70d
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@186 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-25 09:23:42 +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 |
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asivache
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3d1e0bf079
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@166 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 14:06:24 +00:00 |
hanna
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63cd1fe201
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Push core / playground lower into the tree.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-23 23:19:54 +00:00 |