zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
5,269 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

7 Commits (1129f1535d075e1b0d73d15052efef4c25cef398)

Author SHA1 Message Date
hanna 526ae92093 Getting back to '-L unmapped': 
- basic unit tests for interval sorting and merging with mix of mapped/unmapped.
- validation to ensure that locus walkers (really all non-read walkers) blow up with a user error when -L unmapped is specified.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4837 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-14 18:24:18 +00:00
depristo 44feb4a362 Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4792 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-05 18:29:39 +00:00
hanna 8e36a07bea Convert GenomeLocParser into an instance variable. This change is required 
for anything that needs to be simultaneously aware of multiple references, eg
Queue's interval sharding code, liftover support, distributed GATK etc.  

GenomeLocParser instances must now be used to create/parse GenomeLocs.
GenomeLocParser instances are available in walkers by calling either

-getToolkit().getGenomeLocParser()
or
-refContext.getGenomeLocParser()

This is an intermediate change; GenomeLocParser will eventually be merged
with the reference, but we're not clear exactly how to do that yet.  This
will become clearer when contig aliasing is implemented.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-10 17:59:50 +00:00
hanna 861ee3e37a Changing testing framework from junit -> testng, for its enhanced configurability. 
Initial test to see how Bamboo will respond.  More detailed email to follow.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4609 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-01 21:31:44 +00:00
ebanks 340bd0e2c1 Removed hard-coded pointers to references 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3934 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-04 17:59:37 +00:00
hanna 4995950d04 IndexedFastaSequenceFile is now in Picard; transitioning to that implementation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3701 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 04:40:31 +00:00
aaron 4014a8a674 A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests. 
Thanks!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-08 06:14:15 +00:00