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7 Commits (760f06cf8c6f3bbde2c28b4c3b40b8b675e39b39)

Author SHA1 Message Date
hanna c1e53d407d The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 
unicode quote characters embedded in it.  These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset.  Fixed.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 15:26:32 +00:00
hanna 1bc26f69e9 An attempt to cleanup the Utils directory. Email to follow. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 23:00:08 +00:00
asivache 0721c450c2 Bug fix: single unmapped read now keeps mapping qual 0 after remapping, not 37! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1557 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 15:29:34 +00:00
asivache 5202d959bf NM attribute changed in sam jdk (?) from Integer to Short, or maybe it is presented differently by the reader depending on whether SAM or BAM is processed; in any case, both Integer and Short are safe now 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1522 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-03 19:03:32 +00:00
asivache e4acd14675 Now GenomicMap maps (and RemapAlignment outputs) regions between intervals on the master reference as 'N' cigar elements, not 'D'. 'D' is now used only for bona fide deletions. 
Also: do not die if alignment record does not have NM tags (but mapping quality will not be recomputed after remapping/reducing for the lack of required data)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1411 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 21:10:17 +00:00
asivache 36312ae4b2 tiny cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1401 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-10 20:26:52 +00:00
asivache 921d4f4e95 RemapAlignments is a standalone picard-level tool that does not use gatk engine; moved to 'tools' 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1396 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-10 15:41:07 +00:00