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8 Commits (fe9e52c47e53a6504d51c1fa5f586b3a5e5f355f)

Author SHA1 Message Date
hanna bb94c853f8 Added WalkerManager -- a class that dynamically loads available walkers 
from the jar file.  For now, added placeholder Walker interface so that
WalkerManager could work with classes of type Walker rather than classes 
of type Object.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@85 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-17 23:22:37 +00:00
ebanks 28cc670a92 Walker to print out a histogram of aligned reads per mismatches allowed 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@76 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-17 14:05:29 +00:00
depristo 9ae551e858 Lots of error checking added, fixed bugs associated with reading files out of order, added support for U (unsafe) flag for processing reads 
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
andrewk 685fc8bd61 Partial implementation of single sample allele calling 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@64 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-16 19:30:42 +00:00
depristo 8ccbcc4101 Mismatch counter 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@62 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-16 15:51:48 +00:00
depristo 69aa669928 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@56 348d0f76-0448-11de-a6fe-93d51630548a 2009-03-15 22:42:24 +00:00
depristo 24ae381c97 Renaming of ATK to GATK, the genome analysis TK. 
Also added several more layers of error checking 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@54 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-15 22:23:25 +00:00
depristo c9cb7a3596 Renaming of ATK to GATK, the genome analysis TK. 
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