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.
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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
05212aea62
reader now takes an argument for the maximum number of elements to read from the file.
2011-07-12 08:53:19 -04:00
8056a3fe89
getElement() now uses O(1) get from hash instead of linear O(n) search. Enables us to read large files easily.
2011-07-12 08:52:31 -04:00
f313e14e4e
Now deletes the dump directory on ant clean
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Moving diffengine tests from private to public
2011-07-12 08:50:58 -04:00
b0127f6578
Merge branch 'laptop'
2011-07-12 01:32:16 -04:00
23f2c5fabc
Fixed a bug where the first variant in a haplotype was not getting phased properly.
2011-07-12 01:31:58 -04:00
d7d15019dd
Adding support for other simple header line types (e.g. ALT) and cleaning up the interface a bit.
2011-07-12 01:16:21 -04:00
89792ee0f7
Prototype for incorporating RBP information into trio-phased data
2011-07-12 00:03:12 -04:00
400b0d4422
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 23:38:57 -04:00
d5056ad899
Merge branch 'master' into diffit
2011-07-11 23:16:15 -04:00
893cc2e103
Making the package public, so there's no dependances from public -> private
2011-07-11 23:15:08 -04:00
5e593793af
DiffEngine utility function simpleDiffFiles
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printSummaryReport now uses GATKReport for nice formating
Moved print formatting arguments into inner class provided to printing functions themselves, not the class
BAMDiffableReader only reads 1000 entries to avoid performance issue. Work around for BAM files with non-unique names
Uncommented all of the incorrectly commented out CombineVariants integrationtests
BaseTest now uses DiffEngine to provide inline differences to VCF and BAM files
2011-07-11 23:10:27 -04:00
39bd90a8e3
Merge branch 'laptop'
2011-07-11 22:46:35 -04:00
7d579a5b95
PhaseByTransmission now sort the samples in the VCF
2011-07-11 22:45:57 -04:00
6368d5bfad
Attempting to resolve changes to ComputeSwitchErrorRate
2011-07-11 20:53:36 -04:00
e0c03c2c06
Fixed imports
2011-07-11 20:48:17 -04:00
48e5078497
Restored ComputeSwitchErrorRate.java from old SVN repo
2011-07-11 20:40:26 -04:00
2d12976254
Restored ComputeSwitchErrorRate from old SVN repo
2011-07-11 19:44:15 -04:00
d11155ce2e
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 19:19:54 -04:00
e93052a51e
When generating the QGraph, don't regenerate if there aren't scatter/gather jobs.
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Fixed a display issue with the number of milliseconds that Queue has tried to contact LSF.
2011-07-11 19:17:58 -04:00
e3748675db
Support for VCF 4.1 header counts
2011-07-11 17:40:45 -04:00
7a89275458
Count the number of phase error, phase correct, and total phaseable sites
2011-07-11 17:25:02 -04:00
f5a1d8a40f
Count the number of phase error, phase correct, and total phaseable sites
2011-07-11 17:19:40 -04:00
d6517adb42
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 16:16:37 -04:00
Mark DePristo
Eric Banks
Christopher Hartl
Mauricio Carneiro
Ryan Poplin
Roger Zurawicki
Guillermo del Angel
Kiran V Garimella
Khalid Shakir