zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
5,785 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

12 Commits (0095aa2627bbfca377925de71df9dbf16fa6dd6b)

Author SHA1 Message Date
ebanks d89e17ec8c Fare thee well, UGv1. Here come the days UGv2. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4747 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-29 21:51:19 +00:00
hanna 9f356b6cd0 Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4702 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-18 02:33:45 +00:00
hanna 6ebca5d219 Enhancements to build external projects for walker sharing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4348 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-24 21:17:16 +00:00
ebanks 4979dcc9a7 Finishing up the playground cleanup (for now) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4135 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 01:19:37 +00:00
ebanks 0452b1ab68 archiving, removing, or promoting to core from playground 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4134 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 01:07:42 +00:00
hanna c177801d81 Add deprecated command-line arguments, and switched over UG to output to 
-o/--out instead of -varout.  Let's watch as our intrepid support engineer
gracefully responds to all the incoming questions of the form: "the GATK told
me to use -o instead of -varout.  What do I do?"


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4078 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-22 21:01:44 +00:00
hanna b80cf7d1d9 Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4077 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-22 14:27:05 +00:00
hanna c7e006a996 Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes 
basic tests for small and large intervals and intervals that cross bin boundaries.  Currently works
only with a single BAM file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2800 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 21:47:54 +00:00
ebanks 45199136f0 Completed my documentation responsibilities - based on Mark's reasonable assignment and not the one Matt made up while on Meth. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2342 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-13 04:13:30 +00:00
ebanks b979bd2ced - Optimized implementation of -byReadGroup in DoCWalker 
- Added implementation of -bySample in DoCWalker
- Removed CoverageBySample and added a watered down version to the examples directory



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2209 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 03:39:24 +00:00
hanna 21d1eba502 Cleaned division of responsibilities between arguments to map function. Reference has been changed 
from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-04 21:01:37 +00:00
hanna e93f751bd7 First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-30 21:59:54 +00:00