intervals -- altered the validation methods to not throw an error for
unmapped intervals.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5700 348d0f76-0448-11de-a6fe-93d51630548a
to the same standard as GATK format intervals. Full validation against contig
bounds is now performed for all intervals, regardless of their source. Also
fixed a few tests for validation exclusions that were backwards.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5698 348d0f76-0448-11de-a6fe-93d51630548a
Feeding FCP UG the bam list instead of individual bams to cut scatter gather time from O(m^100) as measured by Chris to O(m^1).
Fixed NPE when eval values aren't found in PipelineTests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5694 348d0f76-0448-11de-a6fe-93d51630548a
ByteBuffer.allocateDirect() behaves like Java NIO MappedByteBuffers in that
it consumes address space, which counts against our virtual memory allocation;
but cannot be destroyed or otherwise freed. This was definitely contributing
to the LSF failures that I was seeing, but I'm not yet convinced that it's the
sole source of these virtual memory 'leaks'. More tomorrow as the results of
my whole exome tests start to roll in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5693 348d0f76-0448-11de-a6fe-93d51630548a
Scattering non-contig interval lists by number of loci in the intervals instead of just number of intervals.
Queue caches the list of locs and how to split them up instead of reloading them from disk repeatedly.
TODO: general purpose function to divide data evenly.
Skip over comments when parsing picard analysis files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5687 348d0f76-0448-11de-a6fe-93d51630548a
Added the ability to add a file path to a package.
Checking for missing files when packaging.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5685 348d0f76-0448-11de-a6fe-93d51630548a
but I'm still not sure that GC is a good long-term solution.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5683 348d0f76-0448-11de-a6fe-93d51630548a
Added a rudimentary GATKReportParser for parsing VE3 results.
Re-enabled the FCPTest using VE3, the GATKRP, and the PicardAggregationUtils.
The tag type for .rod files is DBSNP, not ROD.
More explicit return types on implicit methods.
Added null checks for implicit string to/from file conversions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5668 348d0f76-0448-11de-a6fe-93d51630548a
See https://www.broadinstitute.org/gsa/wiki/index.php/GATK_resource_bundle
Which live locally in /humgen/gsa-hpprojects/GATK/bundle/current
You use this following command to create the bundle:
java -Djava.io.tmpdir=/broad/shptmp/depristo/tmp -jar dist/Queue.jar -S scala/qscript/core/GATKResourcesBundle.scala --gatkjarfile dist/GenomeAnalysisTK.jar -bsub -jobQueue gsa -svn 5660 $*
Annoyingly, it must be run in the trunk directory, and requires an explicit svn version number to create the directory. It also must be run in two stages manually. First, the local bundle is created, and then with the -phase2 argument all of the files in the local bundle are compressed and pushed to the FTP server. I'm likely going to shift most of my processes over to using this location for data file access, especially for b37 data sets.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5665 348d0f76-0448-11de-a6fe-93d51630548a
a progress message, then aggregate metrics. Makes the overhead of
printProgress in RealignerTargetCreator go from >20% to ~3%.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5663 348d0f76-0448-11de-a6fe-93d51630548a
- fixing a bug on single ended BWA option of the data processing pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5662 348d0f76-0448-11de-a6fe-93d51630548a
interface between SAMDataSource and IntervalSharder that needs to stay around
until the original BAM sharder is retired. Will add a JIRA to fix design
flaw.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5661 348d0f76-0448-11de-a6fe-93d51630548a
After viewing results on real case/control data from RAW -- it's really working quite well. ReadIndels, however, needs to use a T-test rather than a U-test, especially in deep coverage (at indel sites, the reads with indels will have mostly the same number of CIGAR indel elements -- one -- which doesn't really play nicely with the UTest when sample sets are large). Modified ReadsLargeInsertSize to be a two-way test (e.g. ReadsLarge and ReadsSmall). BaseQualityScore also suffers from the same issue as read indels, so switching over to a T-test in that case as well.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5653 348d0f76-0448-11de-a6fe-93d51630548a
rpoplin
droazen
hanna
kshakir
chartl
ebanks
delangel
corin
depristo
carneiro