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.
...
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
95040d95b9
Adding in check for filtered site (Sorry Mark, looks like it wasn't checking the validated rod, only the mask). Also by allowing user to lowercase SNPs, could miss 'SNP_TOO_NEAR_PROBE', now we properly check for that.
2011-07-12 19:21:26 -04:00
61dad4f090
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 18:33:30 -04:00
30768eccbb
Big change to PSP2: Amplicon sequence no longer lower-cased for repetitiveness, but instead for non-uniqueness via alignment by bwa. Performance heavily dependent on length of sequence (duh), with size=30 a good balance, but default is 20 because that's the default length of a sequenom primer. Indentation changes to other stuff.
2011-07-12 18:33:12 -04:00
60870b360a
Fixed the calculation of the allele count prior, it was using ac instead of maxAlleleCount.
2011-07-12 17:18:52 -04:00
d21388f0cb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 15:56:38 -04:00
775d2c2598
Added VQSR to the ReducedBAM evaluation script. Our tests need to address the annotations used by VQSR so we can actually measure the impact of changing the parameters in the ReduceReads walker (especially context size).
2011-07-12 15:56:24 -04:00
c944019678
Adding dev qscript I used to perform the exome t2d+1kg calling experiment
2011-07-12 15:44:45 -04:00
837fb8f689
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 15:39:26 -04:00
5077c94d85
Adding MappingQualityUnavailableReadFilter to the SNP and indel CountCovariates
2011-07-12 15:39:07 -04:00
2092fb439c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 15:29:52 -04:00
6ee8a86197
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 15:26:13 -04:00
7991d69ba4
I added experimental function in the ReducedBAMEvaluation.
...
At the beginning of the scrpit you can specify a list of values to test and it will process the ReduceReadsWalker for your parameter.
I also added a method to convert the number when naming files to be sort-friendly.
2011-07-12 15:25:43 -04:00
01fd6a6949
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 15:20:44 -04:00
ccedd6ff4c
Difference is now the general form -- used to be SummarizedDifference. The old Difference class is now a subclass of Difference that includes pointers to specific the master and test DiffElements.
...
Added a size() function that calculates the number of elements tree from a DiffElement.
2011-07-12 15:20:28 -04:00
a2597e7f00
This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.
2011-07-12 14:11:53 -04:00
329c3d8050
Merged bug fix from Stable into Unstable
2011-07-12 13:55:51 -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
Mauricio Carneiro
Mark DePristo
Eric Banks
Menachem Fromer
Christopher Hartl
Ryan Poplin
Roger Zurawicki