gatk-3.8

Author	SHA1	Message	Date
rpoplin	5ddc0e464a	Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5536 348d0f76-0448-11de-a6fe-93d51630548a	2011-03-29 21:04:09 +00:00
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

Author

SHA1

Message

Date

rpoplin

Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5536 348d0f76-0448-11de-a6fe-93d51630548a

2011-03-29 21:04:09 +00:00

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

2 Commits (e5ef8388fc494d6553e167ec8aec3fecdfffa18f)