zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/java/test/org/broadinstitute/sting/gatk/datasources/providers
History
hanna 5c3198520c A few minor modifications masquerading as significant changes according to 
svn's logs:
- Copied BAM indexing engine from Picard back into the GATK anticipating
  shard merging algorithm.  Tried to leave most of the building blocks in
  Picard.  If this turns into a logistical nightmare, I'll merge the building
  blocks into the GATK as well.
- Reorganized the org.broadinstitute.sting.gatk.datasources package, giving
  better separation of query and management functionality for reads, ref, rmd,
  and samples.  
- Merged Shard building blocks into org.broadinstitute.sting.gatk.datasources.
  reads package, indicating it's current strong relationship with the reads,
  rather than the general unifying element I wish this would be.
- Collapsed BAMFormatAwareShard into Shard.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5184 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-02-03 17:59:19 +00:00
..
AllLocusViewUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
CoveredLocusViewUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
LocusReferenceViewUnitTest.java A few minor modifications masquerading as significant changes according to 2011-02-03 17:59:19 +00:00
LocusViewTemplate.java A few minor modifications masquerading as significant changes according to 2011-02-03 17:59:19 +00:00
ReadBasedReferenceOrderedViewUnitTest.java Oops...forgot to commit the changes that allow primitive VCF streaming. 2011-01-12 21:54:51 +00:00
ReadReferenceViewUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
ReferenceOrderedViewUnitTest.java A few minor modifications masquerading as significant changes according to 2011-02-03 17:59:19 +00:00
ReferenceViewTemplate.java 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. 2010-12-05 18:29:39 +00:00
ShardDataProviderUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00