92c7cfa1c8
BWA bindings and tests moved to public (was required for ValidationAmplicons)
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Integration tests for ValidationAmplicons. New argument to disable BWA, lowercase letters only for repetitiveness instead.
2011-07-19 20:11:31 -04:00
07e716d23a
PickSequenomProbes2 expanded functionality: lowercasing based on sequence uniqueness, preserving reference base prior to indel (not a part of the VC as I thought it was), masking deletion bases with 'N's, flanking insertion with 'N's, output is a fasta formatted file. Renamed to ValidationAmplicons since this is really not for picking sequenom probes, but for generating amplicon sequence from which other applications (like sequenom) can choose PCR primers. Moved from private to public.
2011-07-19 15:21:47 -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
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
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
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
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
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
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
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
86890c6357
N and K (in binomial probability) got switched in RFA Walker with the last commit. No longer will NaNs be produced.
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Added: TableToVCF. Kind of a longer-term project, but there are lots of variant calls available in a weird tabular format. I used this to convert Ju Et Al small indels to VCF. I'll check against the 1000G ASN superpopulation calls to see if we see a good amount of recapitulation, and if so, i'll put them in unvalidated comparisons. Minor chances to the TableCodec and TableFeatures to allow for this (the codec can sometimes drop a column, and the feature now allows you to grab on to its header).
2011-07-11 16:16:15 -04:00
b327fa3779
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 15:20:45 -04:00
41db509a17
A simple python program for downloading S3 logs in the cron script.
2011-07-11 15:20:01 -04:00
a18380ab96
Merged bug fix from Stable into Unstable
2011-07-11 12:16:50 -04:00
8a78414432
Removed TileCovariate as a dependency for AnalyzeCovariates.jar
2011-07-11 12:10:11 -04:00
6e7b5e1e7a
Merged bug fix from Stable into Unstable
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Merge branch 'master' into unstable
2011-07-08 21:19:45 -04:00
7fbc5987d0
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-08 21:17:32 -04:00
68e19edf59
Merged bug fix from Stable into Unstable, and resolved merge conflicts.
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Conflicts:
build.xml
settings/ivysettings.xml
2011-07-08 15:50:31 -04:00
a3c9d9c3ff
Fixing Contracts for Java, and enabling contracts by default for unit/integration tests.
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The NullPointerException we were seeing when trying to run with contracts enabled was being caused
by an outdated version of the asm library.
To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant.
Also did some minor unrelated cleanup in build.xml
2011-07-08 15:34:39 -04:00
bd29236684
Merge branch 'master' into diffengine
2011-07-08 14:08:17 -04:00
8de82f3974
Updated names to be more reflective of the fact that this works for exomes and WG now.
2011-07-08 14:07:28 -04:00
ae02eabc93
Since it now works with all classes of variants, should really be renamed
2011-07-08 14:04:59 -04:00
2ea36b06cc
Really works now with files where (1) there's no functional annotation and (2) there's no indel calls.
2011-07-08 14:04:00 -04:00
38d9b9b568
A printf from debugging made it in in some prior commit.
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The read transform adding the AI tag can cause an exception for widowed reads -- added a check for this case, preventing blowup.
2011-07-08 13:13:58 -04:00
51338cbe07
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-08 12:49:00 -04:00
224574424e
Bug fix: if we're genotyping a very long indel (>100 bp) fail gracefully instead of with an array out of bounds exception
2011-07-08 12:48:49 -04:00
2a4b3ae4a2
Cleaning up / removing most of the monkeying around with annotation values that happens in VariantDataManager
2011-07-08 12:48:33 -04:00
Christopher Hartl
Mauricio Carneiro
Ryan Poplin
Mark DePristo
Roger Zurawicki
Eric Banks
Guillermo del Angel
Khalid Shakir
David Roazen