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
very hard to validate and still very hard to use (requires core hacking to
support additional tags).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5038 348d0f76-0448-11de-a6fe-93d51630548a
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
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
This will allow other programs like Queue to reuse the functionality.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4351 348d0f76-0448-11de-a6fe-93d51630548a
(-B:name,type file) as well as the old syntax. Also, a bonus feature: BAMs can now be tagged at the
command-line, which should allow us to get rid of some of the hackier calls in GenomeAnalysisEngine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4105 348d0f76-0448-11de-a6fe-93d51630548a
- Eliminate reduncancy of filter application.
- Track filter metrics per-shard to facitate per merging.
- Flatten counting iterator hierarchy for easier debugging.
- Rename Reads class to ReadProperties and track it outside of the Sting iterators.
Note: because shards are currently tied so closely to reads and not the merged triplet of <reads,ref,RODs>, the metrics
classes are managed by the SAMDataSource when they should be managed by something more general. For now, we're hacking
the reads data source to manage the metrics; in the future, something more general should manage the metrics classes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4015 348d0f76-0448-11de-a6fe-93d51630548a
are gone where I could identify them, but hierarchies that split to support two sharding systems have
not yet been taken apart.
@Eric: ~4k lines.
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unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
infrastructure can be torn down:
1) New sharding system emulates old MonolithicSharding mechanism.
2) Better awareness of differences between fasta and BAM files when creating
shards.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2948 348d0f76-0448-11de-a6fe-93d51630548a
simplification of some of the locus traversal code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2886 348d0f76-0448-11de-a6fe-93d51630548a
the pathway from command line to traversal engine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@727 348d0f76-0448-11de-a6fe-93d51630548a
hanna
depristo
kshakir
aaron