a8d08ea18d
As a user pointed out, it is not valid for a GenomeLoc to have a start or stop equal to 0.
2012-07-17 22:18:43 -04:00
7e2c830636
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 21:54:56 -04:00
a9f27e5b02
Updated md5s for DPP test
2012-07-17 21:54:46 -04:00
29273abab7
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 16:58:12 -04:00
731bbba2e6
Bug fixes for integration test, use correct new UG syntax
2012-07-17 16:57:59 -04:00
33be41ecf5
Cleaning up integration test
2012-07-17 16:06:04 -04:00
8dbc9cb29c
Add the ability to emit the original quals in the OQ tag
2012-07-17 15:52:56 -04:00
4e3780fd4f
Updated md5 for PBPP
2012-07-17 15:47:43 -04:00
40b8c7172c
Pool Caller refactoring in preparation of GATK 2.0: a) PoolCallerUnifiedArgumentCollection disappeared, and arguments moved to UnifiedArgumentCollection. b) PoolCallerWalker is no longer needed and redundant, all functionality subsumed by UG. UG now checks if GATK is lite - if so, don't allow ploidy > 2. c) Moved pool classes from private to protected. d) Changed the way to specify ploidy. Instead of specifying samples per pool and having ploidy = 2*samplesPerPool, have user specify ploidy directly, which is cleaner. Update tests accordingly. We can now call triploid seedless grape genotypes correctly in theory. e) Renamed argument -reference to -reference_sample_calls since the former is ambiguous and it's not clear what it refers to.
2012-07-17 15:27:04 -04:00
68d0e4dd6d
- Multi-allelic sites are now correctly ignored - Reporting of mendelian violations enhanced - Corrected TP overflow by caping it to Bye.MAX_VALUE
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-Updated integrationtests to reflect changes in MVF file output
Signed-off-by: Eric Banks <ebanks@broadinstitute.org>
2012-07-17 15:21:10 -04:00
863eb5b5c0
Use Context not Dinuc covariate
2012-07-17 15:18:11 -04:00
b0d99fd10d
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 15:12:28 -04:00
305db8c0d1
Total rewrite of the isGATKLite() functionality with help of Khalid/David. PluginManager was not working for us.
2012-07-17 15:11:03 -04:00
bf2d5efe4d
Moving HaplotypeCaller integration and unit tests over to protected as well.
2012-07-17 14:51:26 -04:00
c55934043e
Moving HaplotypeCaller from private to protected
2012-07-17 14:41:19 -04:00
6efbcd99f1
HaplotypeCaller is now an AnnotatorCompatibleWalker with all the rights and privileges pertaining thereto. Enabling the ClippingRankSumTest after showing it was useful for 1000 Genomes calling.
2012-07-17 14:38:36 -04:00
110886e8b9
Oops, got the logic wrong.
2012-07-17 13:37:11 -04:00
836f882c30
Forgot to escape fallback text in email script; fixed TERRIBLE sed-related bug
2012-07-17 13:18:08 -04:00
a963b37424
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 13:15:37 -04:00
17d627b86d
Update the DPP and PBPP to use the BQSRv2 walkers
2012-07-17 13:15:32 -04:00
3a64398d07
Cleaned up the isGATKLite check
2012-07-17 12:46:16 -04:00
62c5228048
1) Revert previous change - indel recalibration is turned on by default and users of the Lite version will need to turn it off to avoid a User Error. 2) Implemented the engine.isGATKLite() method.
2012-07-17 12:23:40 -04:00
1913d1bbd0
Put RunReport S3 upload on timeout thread
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Move the RunReport S3 upload process onto a separate thread with a timeout allowing the parent to continue.
Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
2012-07-17 12:19:39 -04:00
beacdf66c5
Bringing the git email scripts under version control
2012-07-17 11:24:30 -04:00
d4f55f5376
Revert "Email script test: test "no net change" detection"
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This reverts commit 556dafc697753d1129dc2fccd5994aead3e3144b.
2012-07-17 11:16:42 -04:00
a5548d1592
Email script test: test "no net change" detection
2012-07-17 11:16:23 -04:00
251f141e22
Revert "Email script test: added an under-limit file"
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This reverts commit b2af5a88c0b0c63ae5eb69b7ae730aaa53a7be7e.
2012-07-17 11:12:56 -04:00
7cfc6968fc
Email script test: added an under-limit file
2012-07-17 11:11:12 -04:00
159439aa7d
Revert "Email script test: added a file with a number of lines equal to the line limit"
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This reverts commit ebc469e94a92729a6d364c300080e6df8551b59b.
2012-07-17 11:08:52 -04:00
207e42a5a3
Email script test: added a file with a number of lines equal to the line limit
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Should show diff for this one.
2012-07-17 11:06:00 -04:00
385fff595c
Revert "Email script test: added a file over the new line limit"
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This reverts commit 71d70cea3420aa8d634ab5c7144469a91ce6ff6a.
2012-07-17 11:04:17 -04:00
b4afa60d7f
Email script test: added a file over the new line limit
2012-07-17 11:02:17 -04:00
40618ac471
A bunch of BQSR changes: 1) by default we do not emit indel quals, but they can be turned on with --enable_indel_quals. 2) We check whether or not we are running in Lite mode (not done yet) and if so and the user is trying to recalibrate indels, we throw a User Error (not supported). 3) Like v1 we now allow the user to set the qual value below which we don't recalibrate (this was the remaining source of differences in the v1 vs. v2 plots).
2012-07-17 10:52:43 -04:00
d5b3a2eabf
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 00:32:53 -04:00
f657b8bda8
Complete overhaul of the BQSRv2 integration tests. Much more comprehensive. Still need to deal with a few tests that need some modifications before I'm done, but I'll take care of that sometime tomorrow.
2012-07-17 00:32:34 -04:00
a003148d50
Move AnalyzeCovariates over too.
2012-07-16 16:11:56 -04:00
0a89adbcdb
Add utility decorators so that classes can tell you which package source they come from if they want to (suggested by Khalid). Using those decorators, we can easily pull out the BQSR updateDataForPileupElement() method into a standard RecalibrationEngine and an AdvancedRecalibrationEngine and use the protected one (AdvancedRE) if available (otherwise, the public one).
2012-07-16 15:34:50 -04:00
52baac1e16
Move BQSRv2 into public and v1 into the archive.
2012-07-16 14:23:38 -04:00
6c6a324583
Loosen a restriction on isOriginalRead()
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* no longer needs to satisfy ReadAndIntervalOverlap.OVERLAP_CONTAINED
2012-07-16 14:07:10 -04:00
07822d6c0f
Fixed input annotations for master/test files on DiffObjectsWalker.
2012-07-16 13:33:11 -04:00
2a830939df
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-14 23:49:59 -04:00
f29cadd7e2
By default, don't quantize quals in BQSRv2
2012-07-14 23:49:48 -04:00
75543a3f22
ReadClipper.clipRead's claim that it doesn't modify the original read was false. Ultimately, GATKSAMRecord.clone (as documented) creates a soft copy of the read - so modifying e.g. the bases of the cloned read means that you modify the bases of the original read too. Because of this, when the BQSRv2 Context covariate was writing Ns over the low quality tails of the reads they got propagated out to the output BAM file (very bad). I've updated the ReadClipper docs and cleaned up the code (no reason to use a clone of the read anymore given that we are already modifying the original). For now, the simplest thing is to have the Context covariate store the original bases, overwrite low quality Ns, compute covariates, and rewrite the original bases; we can update later if needed.
2012-07-13 18:50:27 -04:00
44c532531b
VC priority list needs to be updated after removing unassembled haplotypes.
2012-07-13 16:50:08 -04:00
443f02ffc2
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-13 16:09:24 -04:00
c978e37e5c
updating HC integration tests for all these changes
2012-07-13 16:09:11 -04:00
6dfcc486e8
In ApplyRecalibration marking filter as PASS instead of '.' when the site passes by calling .passFilters().
2012-07-13 15:40:56 -04:00
d553905d79
Don't try to genotype both an unassembled symbolic allele and a fully assembled insertion if they both start at the same location. Bug fix for the case of multiple indels that when all combined together make an MNP.
2012-07-13 15:22:22 -04:00
3ab5e2c64b
Don't try to combine together unassembled, symbolic alleles.
2012-07-12 21:20:14 -04:00
d70bb59182
HaplotypeCaller now calls insertion events that aren't fully assembled as symbolic alleles.
2012-07-10 14:22:23 -06:00
Eric Banks
Guillermo del Angel
Laurent Francioli
Ryan Poplin
David Roazen
Chris Saunders
Joel Thibault
Khalid Shakir