fe9e52c47e
allow on fly sorting AND validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@86 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 15:50:17 +00:00
1aa3958644
Added ability to sort reads on the fly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@83 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 20:29:09 +00:00
58aa2aab43
Rough draft of patch to use bam indices when available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@81 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 16:39:03 +00:00
478425b3d8
Better error messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@79 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 15:37:02 +00:00
0fd55d91d2
Fixed bug in unsafe mode
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@78 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 15:28:04 +00:00
9ae551e858
Lots of error checking added, fixed bugs associated with reading files out of order, added support for U (unsafe) flag for processing reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@75 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 23:22:04 +00:00
3b5003bd11
Added support for accessing the reference in read traversal
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@60 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 14:46:19 +00:00
c9cb7a3596
Renaming of ATK to GATK, the genome analysis TK.
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Also added several more layers of error checking
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@53 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-15 22:21:48 +00:00
ebanks
hanna
depristo