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
af9b7f27eb
Readded ComputeSwitchErrorRate
2011-07-13 23:04:23 -04:00
db7a23d896
Added check to only evaluate phased genotypes, in case I ever want to use this program on another file that's not guaranteed to have every genotype phased.
2011-07-13 22:58:04 -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
1e81d521c0
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 20:12:29 -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
d4c6caaed8
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 16:06:47 -04:00
f68064eb95
Change MBRC parameter to CS
2011-07-12 16:06:36 -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.
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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.
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Added a size() function that calculates the number of elements tree from a DiffElement.
2011-07-12 15:20:28 -04:00
c504a42137
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 15:02:44 -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
17c3999428
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 13:46:08 -04:00
c4c145afb9
Merged bug fix from Stable into Unstable
2011-07-12 13:44:48 -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
a0d074a71c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 12:37:43 -04:00
40622e55d4
Further changes to project consensus indel script
2011-07-12 12:37:28 -04:00
bfbca8b194
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 12:11:58 -04:00
Mark DePristo
Kiran V Garimella
Mauricio Carneiro
Eric Banks
Menachem Fromer
Guillermo del Angel
Christopher Hartl
Roger Zurawicki
Ryan Poplin