dede3a30e9
Improvements to the validation report of VariantEval
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-- If eval has genotypes and comp has genotypes, then subset the genotypes of comp down to the samples being evaluated when considering TP, FP, FN, TN status. This is important in the case where you want to use this to assess, for example, the quality of calls on NA12878 but you have a CEU trio comp VCF. The previous version was counting sites polymorphic in mom against the calls in NA12878.
-- Added testdata VCF and integrationtests to ensure this behavior continues in the future
-- TODO: actually run integration tests when I have an internet connection
2012-07-18 16:07:47 -04:00
559a4826be
Improvements to the validation report of VariantEval
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-- If eval has genotypes and comp has genotypes, then subset the genotypes of comp down to the samples being evaluated when considering TP, FP, FN, TN status. This is important in the case where you want to use this to assess, for example, the quality of calls on NA12878 but you have a CEU trio comp VCF. The previous version was counting sites polymorphic in mom against the calls in NA12878.
-- Added testdata VCF and integrationtests to ensure this behavior continues in the future
2012-07-18 16:07:46 -04:00
dc292c0317
FisherStrand now includes all reads and bases, regardless of mapping quality and base quality, just like other annotations
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-- This actually proved to be a problem with Ion Torrent data where the base quality can be quite low, and so we need to include Q15 bases for calling effectively.
2012-07-18 16:07:46 -04:00
bd799fc989
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-18 16:01:20 -04:00
2c0f073ab1
Make -qq arg hidden for now since it's still very experimental
2012-07-18 15:43:25 -04:00
b46c85e8b4
More bad BAM file catching
2012-07-18 15:26:31 -04:00
659eee13a6
Handle NPE generated in UG when non-standard reference bases are present in the fasta
2012-07-18 15:16:27 -04:00
9af2cfe283
Catch underlying file system problems that get masked as Tribble index errors. There's also a quick patch to the HMS that isn't really the ultimate fix needed; Mark and I will review at a later point.
2012-07-18 15:11:38 -04:00
4c730542f0
Handle RuntimeExceptions thrown by Picard that are really User Errors. I will add unit tests for these as best I can later.
2012-07-18 13:56:35 -04:00
ae08d35138
Catch 'too many open files' errors that show up when trying to read the bam index. All that needs to be done is to flesh out the original error message (because it will get caught later and rethrown correctly).
2012-07-18 12:57:34 -04:00
fd0c2d269e
Change committest target to allow inheritance of properties
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Needed for a fix I'm working on for the Bamboo release plan
2012-07-18 12:45:51 -04:00
f2fe59a9d4
Wow, there are a ton of errors captured having to do with being unable to merge the temp Tribble output. I'm expanding the error message a bit to help see if we can do anything going forward.
2012-07-18 12:31:59 -04:00
e4db8dde91
Enabled a whole other bunch of integration tests for BQSRv2. While I was there I also changed the default context size for indels to 3 (from 8) since that's what works best in the current implementation (as suggested by Ryan). At this point, all of the new core tools (ReduceReads, BQSRv2, HaplotypeCaller, UG extensions) have been moved over to protected and should be stable. Looks like we are pretty much ready for GATK 2.0!
2012-07-17 23:36:43 -04:00
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
Mark DePristo
Eric Banks
David Roazen
Guillermo del Angel
Laurent Francioli
Ryan Poplin
Chris Saunders