Changes to StingUtils command line for use in Queue, replacing Queue's use of property files.
Updates to walkers used in existing QScripts to add @Input/@Output.
RMD used in @Required/@Allows now has a new default equal to "any" type.
New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions.
Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.)
Removed dependency on BroadCore by porting LSF job submitter to scala.
Ivy now pulls down module dependencies from maven.
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features in that contig. Thanks to Mark for finding this. I'm not rev'ing the index version (which would cause all indexes to be rebuilt), since this seems like a pretty rare edge case.
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- makes writing to disk optional for indexes using the indexCreator classes (allow the user to specify the index file, if null don't write it)
- removed some system.out debugging code
- fixed version checking in interval tree
- made indexes store and return a LinkedHashSet for sequence names (to ensure they've preserved the ordering in the file)
- index creators now read the file before creating the index
- changed the Index.write() method to take a LEDataStream instead of a file
- removed the sequence dictionary code on the header
- added utils for getting LEDataStreams
- added a base Tribble exception
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an IdentityHashMap provides another 10x+ performance boost over his previous
optimization for us.
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Updated dbsnp/hapmap membership info fields to be flags now instead of ints.
While I was there, I added the change in the Annotator for Jan to force reads to be from a specific sample.
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to the vlidation directory), using the same md5sum.
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the imminent move of IlluminaUtil into picard public.
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priors were flat, but fixed nonetheless.
Also, needed to update Tribble.
Minor updates to the Beagle input maker.
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Current version only has syntatic sugar for accessing the graph via rules ex. "bam" -> "bam.bai", "samtools index ${bam}" and DOES NOT have sugar for constructing your own graph.
Usage info on the internal wiki at https://iwww.broadinstitute.org/gsa/wiki/index.php/Queue
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which improved startup time 5-10x when dynamically merging many BAMs.
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of public interfaces. This won't be the last Picard patch, but it should be the last big one.
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Picard patch, including move of some of the Picard private classes we use to Picard public.
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that bins will be present in the bin sparse array, which avoids the problem of having to hold the sparse bin array
stored in every BAM file index in memory at the same time.
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Results in drastic lowering of startup cost when multiple BAM files are
merged.
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artifact of the way we build picard-private-parts.
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WARNING: If you update frequently, you might have to rm -rf ~/.ant/cache -- this is an unfortunate side effect of the way we
distribute picard-private.jar.
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kshakir
aaron
hanna
depristo
ebanks