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.
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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
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!
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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
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
1390f354dc
Giving up on parallel s3 fetching. The solution here is to do incremental processing, and not try to download 1.5M records at once, but obtain the ~10K per day that are appearing.
2011-07-13 23:12:19 -04:00
ae044af678
Forgot to comment out a debug
2011-07-13 22:39:58 -04:00
caa3629467
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-13 22:38:27 -04:00
d6c1540e57
Parallel version.
2011-07-13 22:37:49 -04:00
63c58c5f7e
Log file no longer optional.
2011-07-13 21:41:15 -04:00
d163a2106a
Now uses the log file to determine which files exist locally, avoiding the potentially expensive check on disk
2011-07-13 21:36:02 -04:00
a4ab19d040
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-13 15:14:06 -04:00
0c54c796ed
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-13 14:57:33 -04:00
bb0e3a26fc
Added integration test for VCF writing. Also, bug fix for writing the GT-free records.
2011-07-13 14:57:21 -04:00
df996a1a73
more progress report for the Data Processing Pipeline.
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Bam lists can now have empty lines, comments and whitespaces anywhere.
2011-07-13 14:53:58 -04:00
6a431da554
Don't output source and ref header lines anymore. Short-term motivation for this is that I'd like this tool when run on a VCF to emit the exact same VCF. Long-term motivation is that these tags should be output by the VCF writer itself for all tools.
2011-07-13 14:40:01 -04:00
e2f2917bd2
Merged bug fix from Stable into Unstable
2011-07-13 13:00:55 -04:00
ff4e31c554
Changing the file names as per Kris request.
2011-07-13 12:59:18 -04:00
74aa49e423
Merged bug fix from Stable into Unstable
2011-07-13 12:12:42 -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
e86113e537
Minor fixes for logging. Now logs even if you don't need to download the file (it's a complete log now).
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Bug fix for del logging.
2011-07-13 10:27:24 -04:00
b04b8b20a5
Added support for -p log so that we can track progress without trying to ls a directory with 1.5M entries in it.
2011-07-13 10:22:32 -04:00
6450b48951
manageGATKS3Logs now downloads and deletes files in groups of 100 files by default. This should significantly improve the performance of the S3 log synchronization.
2011-07-13 10:14:38 -04:00
969227c657
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-13 10:01:28 -04:00
797c50e689
Fixing integration tests I broke yesterday; removing batch merging test since we don't support that anymore.
2011-07-13 10:01:23 -04:00
6007eea3ff
Allowing VCF records without GTs in vf4.1
2011-07-13 09:56:08 -04:00
Mauricio Carneiro
Menachem Fromer
Guillermo del Angel
Mark DePristo
Eric Banks