9fe68776c0
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-16 09:22:55 -04:00
eacf205f40
Tests needed to be updated to reflect the code reorg of tribble.
2011-07-16 09:22:34 -04:00
7524b00cbc
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-16 09:12:13 -04:00
6e8ec206c8
Now with clean output. Ready to go live in crontab.
2011-07-16 09:11:49 -04:00
e106a5e734
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-16 08:52:18 -04:00
5e7bc862a3
Rev tribble to include new equal() method that prints out details of why two indices are not the same.
2011-07-16 08:51:21 -04:00
5cb5a4ec75
Merged bug fix from Stable into Unstable
2011-07-16 00:23:59 -04:00
dd92a14b40
Made extra indel VCF optional but DBSNP mandatory.
2011-07-16 00:23:35 -04:00
2fa5dbb0fe
Merged bug fix from Stable into Unstable
2011-07-16 00:15:19 -04:00
ed55182a4c
Removing Broad specific paths from parameters and making them required. This should make it unambiguous for people inside and outside the Broad to use the DataProcessingPipeline (as per request in the GetSatisfaction)
2011-07-16 00:09:00 -04:00
43bd45fcad
Merged bug fix from Stable into Unstable
2011-07-15 19:40:02 -04:00
fd1df31ef0
changing the output directory names for Analyze Covariates
2011-07-15 19:39:42 -04:00
0cac5e9ebe
Merged bug fix from Stable into Unstable
2011-07-15 19:38:20 -04:00
1e4798d5d0
Added targets to build.xml to re-run only tests that have failed (integration, unit, performance or pipeline tests).
...
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
dc6edf56f3
Walker to use RBP and trio to determine source of de novo het SNPs
2011-07-15 18:34:22 -04:00
dc7d1d2f08
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-15 17:49:13 -04:00
9bdf36bb69
Refactoring to enable object-oriented version of haplotype calculation
2011-07-15 17:48:42 -04:00
72f4cf9c0e
Walker to perform deterministic annotation of phasing by transmission (to be compatible with RBP's definition of consecutive pairwise phasing)
2011-07-15 17:44:31 -04:00
93ec4763ee
Adding hard filters and making it the default test mode of the ReducedBAM evaluation script
2011-07-15 17:34:33 -04:00
af6c4e30c7
Deleting some useless Queue scripts
...
Restoring two useful scripts to private repository:
manySampleUGPerformance.scala [calculates performance of UG and other tools as a function of the number of samples]
PostCallingQC.scala [VariantEval of a call set + R scripts to create pretty pictures. For the pipeline team to eventually own]
2011-07-15 16:51:05 -04:00
3193a3a992
Moving the PostCallingQC script to archive.
2011-07-15 16:25:01 -04:00
aa30f416a3
Resolving conflicts
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Conflicts:
private/scala/qscript/depristo/ExomePostQCEval.scala
private/scala/qscript/depristo/PostCallingQC.scala
private/scala/qscript/org/broadinstitute/sting/queue/qscripts/archive/ExomePostQCEval.scala
2011-07-15 16:21:42 -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.
...
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.
...
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
ce4d702e25
No-calls and filtered genotypes are now properly considered missing
2011-07-15 14:36:37 -04:00
7b7d40d5d9
A better name for the qscript utilities. Throw here every method you find yourself repeatedly implementing in your qscripts!
...
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
c2c8df49e1
Can specify the phasing/child sample on the command-line.
2011-07-15 13:46:24 -04:00
9283ac906e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-14 19:16:46 -04:00
6620ebd8d8
Changes to indel VQSR consensus creation script
2011-07-14 19:16:14 -04:00
f19862a643
Fixing conflicts.
2011-07-14 17:13:31 -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
4f8230c750
Merged bug fix from Stable into Unstable
2011-07-14 16:44:57 -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
c0bbeb23ba
Now providing more information when the index on the fly isn't equal to the one created by reading the file from disk.
2011-07-14 15:12:28 -04:00
5ffeddd3b1
better to use _ instead of ., as this is a special case later.
2011-07-14 14:45:16 -04:00
9540df6998
Oops, forgot to update unit test
2011-07-14 14:00:19 -04:00
ed6beae1f3
Adding headers to diffable reading for VCFs
2011-07-14 13:55:35 -04:00
57a90173f3
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-14 11:56:20 -04:00
66c652d687
Added some extra error checks in the VCF codec. Now that we've moved this back into the GATK, changed some of the standard exceptions to be USerErrors (instead of TribbleExceptions).
2011-07-14 11:56:10 -04:00
ad373ffa7e
Broke down and implemented parallel get. Now running 10x parallel no problems on gsa1.
2011-07-14 09:12:43 -04:00
Mark DePristo
Mauricio Carneiro
Menachem Fromer
Guillermo del Angel
Eric Banks