1e4798d5d0
Added targets to build.xml to re-run only tests that have failed (integration, unit, performance or pipeline tests).
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This is very useful and easy. After running any test (for example ant integrationtest) and seeing failures, you can rerun ONLY THE TESTS THAT FAILED by using one of the following commands:
ant failed-integration
ant failed-pipeline
ant failed-test
ant failed-performance
obviously matching whatever tests you were running and got failures on.
This should run only the failed tests, and you can keep using this command until you have fixed everything.
(Thanks to David Roazen for major help with ANT)
2011-07-15 19:34:14 -04:00
210368c128
new annotations package for menachem's script.
2011-07-15 16:11:46 -04:00
44dedf3912
moving khalid's oneoff scripts.
2011-07-15 16:08:38 -04:00
a40de4d123
No more packages with user names.
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All STABLE/PRIVATE (oneoffs) scripts that didn't get moved by their authors were put in :
org/broadinstitute/sting/queue/qscripts/archive
if you find any of these scripts that are dear to you, please move it to the appropriate package within qscripts, or create a new package that best describes what your script does.
2011-07-15 16:07:41 -04:00
e017e2bacd
Moving the mendelian violation (perhaps more than one-off) script to the appropriate package.
2011-07-15 15:51:06 -04:00
b745405195
Moving downsampling script to the calling package.
2011-07-15 15:44:25 -04:00
32a5e60e54
Removing MY old oneoff scripts.
2011-07-15 15:40:16 -04:00
9d5b560013
1. moving everyone's oneoff scala script to the appropriate package.
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2. updating pipeline tests to the new directories
2011-07-15 15:38:25 -04:00
224d373997
No need to double overload the file constructor
2011-07-15 15:19:10 -04:00
633b764877
Fixed pipeline tests accordingly.
2011-07-15 14:58:29 -04:00
63262c1440
Moving the pipeline queue scripts into a new 'pipeline' package in the org.broadinstitute.sting.queue.qscripts structure.
2011-07-15 14:56:23 -04:00
7b7d40d5d9
A better name for the qscript utilities. Throw here every method you find yourself repeatedly implementing in your qscripts!
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Refactoring appropriately.
2011-07-15 14:34:50 -04:00
a670d6420a
Refactoring Qscript utils into queue general utils package.
2011-07-15 14:31:43 -04:00
43c6a8565b
looks better now.
2011-07-14 17:10:44 -04:00
09ffe277ae
Added a qscripts util package with some utility functions commonly shared across queue scripts. Refactored some of my public scripts to use it in an effort to make queue scripts more reusable and "supportable".
2011-07-14 17:09:35 -04:00
9f5180ab05
Recalibrates a list of bam files allowing multiple bams to be recalibrated out of a single 'mother' queue job.
2011-07-14 16:42:17 -04:00
ff4e31c554
Changing the file names as per Kris request.
2011-07-13 12:59:18 -04:00
fa3ff53508
Filters should only be applied to the new VC if the old VC had filters applied
2011-07-13 11:58:16 -04:00
73735863b0
Fix for the case of requesting genotype for a sample that doesn't exist in a VariantContext
2011-07-12 13:55:21 -04:00
cfe43e3971
Bug fix for Genotype given alleles: if we are in INDEL mode ignore SNPs and MNPs instead of emitting an empty site with alleles but no annotations
2011-07-12 13:43:46 -04:00
8a78414432
Removed TileCovariate as a dependency for AnalyzeCovariates.jar
2011-07-11 12:10:11 -04:00
7fbc5987d0
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-08 21:17:32 -04:00
a3c9d9c3ff
Fixing Contracts for Java, and enabling contracts by default for unit/integration tests.
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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
2011-07-08 15:34:39 -04:00
224574424e
Bug fix: if we're genotyping a very long indel (>100 bp) fail gracefully instead of with an array out of bounds exception
2011-07-08 12:48:49 -04:00
5ed7243b64
Removing old oneoffs walkers as I threatened
2011-07-07 23:02:41 -04:00
4cfe0dd857
Test for bad alleles so that we don't generate IndexOutOfBoundsExceptions
2011-07-07 23:01:03 -04:00
ce5a1c2cbe
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-07 16:21:27 -04:00
1a42a5b4ec
Refactored oneoffs to properly be in the private package
2011-07-07 16:16:12 -04:00
13519c2c3d
Moved PhaseByTransmission per Eric's request
2011-07-07 16:14:14 -04:00
06f12eca56
Move from qscript/delangel to qscripts/calling
2011-07-07 15:39:48 -04:00
8a571e3488
Move IndelCountCovariates package to gatk.walkers
2011-07-07 15:25:37 -04:00
50111db2b7
Fixing non-determinism in single-threaded VQSR by moving references to cern.Normal over to the static random generator available in GenomeAnalysisEngine
2011-07-07 15:02:48 -04:00
54121eb082
Catch malformed bams that cause the writer to run in infinite loops
2011-07-06 16:05:08 -04:00
14fee4ccbd
Patch from Bob to deal with symbolic alleles: these weren't getting padded but they should be.
2011-07-06 12:51:44 -04:00
0b86958a56
Merge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-06 11:33:15 -04:00
c93d0b37a8
Fixed namespace of the pipeline classes.
2011-07-06 11:32:46 -04:00
e8ed6b7f0f
Adding more comments to main VQSR walker. Fixing copyright lines. Bug fix for default paths to now point to public/R/ instead of R/ Bug fix in VQSR for the path to the R scripts not ending in a slash.
2011-07-06 10:01:14 -04:00
81a4d18468
Mark several indel-related arguments as @Hidden
2011-07-06 09:56:38 -04:00
5298e3a942
Making the outputDir optional. Default = ./
2011-07-05 16:30:41 -04:00
7d3dfdfdf2
Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter.
2011-07-05 16:30:10 -04:00
cd53e5a131
Removing the ReduceReads files and package from the stable repo. It should only exist in private/unstable.
2011-07-05 13:22:55 -04:00
b38529309c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-05 01:03:36 -04:00
e7e7cc390f
fixing a wrong refactor
2011-07-05 01:02:54 -04:00
8f5773fc5c
preparing the classes for future functionalities
2011-07-05 00:19:38 -04:00
514b9c1751
UnifiedGenotyper already has @input/@output annotations
2011-07-04 19:23:05 -04:00
3206c581ce
Cleaning up the gatk jar argument, as queue now uses the queue's classpath.
2011-07-04 19:10:54 -04:00
980580287a
Fixing with the new variantcontext location
2011-07-04 19:06:06 -04:00
14eb7873a0
Reorganizing private oneoff qscripts
2011-07-02 17:41:19 -04:00
14375c3ba9
Moving my very first walkers into the archive.
2011-07-02 10:45:12 -04:00
5faf40b79d
Moving AnalyzeAnnotations into the archive because it has outlived its usefulness.
2011-07-02 10:39:53 -04:00
Mauricio Carneiro
Menachem Fromer
Ryan Poplin
Guillermo del Angel
David Roazen
Eric Banks
Kiran V Garimella
Khalid Shakir