ad3a3aa350
First pass at passing lists of files / lists of interval arguments work. Note that the interval
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ROD system will throw up its hands and not deal with intervals at all if multiple interval files
are passed in (see JIRA GSA-95).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1105 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:44:23 +00:00
bcb64d92e9
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 14:39:41 +00:00
dde52e33eb
Cleanup of the cleaned read injector based on Eric's feedback.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1062 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 22:04:47 +00:00
71e3825fa1
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@989 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:18:13 +00:00
hanna
aaron