Now uses GATKDoc class to organize documentation for arguments.
Arguments now listed by feature (required, optional, hidden, etc) and link to detailed information about the argument in the html
Lots of code moving between Class and ClassDoc objects. Should be refactored into a single static utility class.
The NullPointerException we were seeing when trying to run with contracts enabled was being caused
by an outdated version of the asm library.
To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant.
Also did some minor unrelated cleanup in build.xml
Temporarily disabled contracts in integrationtests until we can find the cause
of the new error that's cropping up for Ryan.
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only download that test configuration when running unit/integration tests.
This means that the build will (hopefully) never break because it can't
fetch a file that isn't required for the GATK to run.
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though sonatype is back up). This will tide us over until I figure out how
to add caliper to test configuration, so that it's only swapped in when we
actually run our unit / performance tests.
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but I'm still not sure that GC is a good long-term solution.
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- bsub command line is no longer fully printed out.
- extraBsubArgs hack is now a callback function updateJobRun.
Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q.
Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits.
Updated VE packages that live in oneoffs to compile to oneoffs.
Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac.
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Shell invoking scripts so that even really long shell scripts make it through LSF.
Using the truncated (up to 1000 characters) of the command line for the job name for use with bjobs.
Switched the default from re-running everything to re-running only files that need to be regenerated. --skip_up_to_date replaced with --start_clean for those who want to regenerate everything.
Updated logging to let users know when the scatter gather generator is running, which still takes a while but is orders of magnatudes faster for large lists of functions. (40s for a 100 function graph exploding to a 2500 function graph)
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removed the auto-deletion of the reflections jar, and removed the very old OmniPlan document we had checked-in.
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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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codebase to a dependency on a jar file compiled from my private picard branch.
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Hopefully this is a temporary solution and these classes will be migrated
into picard-public.
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Just stomped on the existing md5s because that's what Eric told me to do.
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Revert until we find out whether the cause is legit.
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Integration tests were validated against svn rev 1861, before the wonder
twins committed their changes.
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inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.
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Produces sane looking output on region of 1kG pilot1:
CALL NA12813.SRP000031.2009_02.bam CC 0.609084 0.609084
CALL NA12003.SRP000031.2009_02.bam CC 2.114234 2.114234 CCCCC
CALL NA06994.SRP000031.2009_02.bam CC 0.910114 0.910114 C
CALL NA18940.SRP000031.2009_02.bam CT 2.589749 0.910114 T
CALL NA18555.SRP000031.2009_02.bam CC 0.609084 0.609084
Next up, eval vs. Baseline pilot1 calls and pilot3 deep-coverage truth.
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Mark DePristo
David Roazen
Khalid Shakir
Matt Hanna
droazen
hanna
depristo
kshakir
aaron
ebanks
alecw
jmaguire