64df3950c1
Emit minimalTable that can be read into R
2011-09-12 22:03:13 -04:00
2316b6aad3
Trying to fix problems with S3 uploading behind firewalls
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-- Cannot reproduce the very long waits reported by some users.
-- Fixed problem that exception might result in an undeleted file, which is now fixed with deleteOnExit()
2011-09-12 22:02:42 -04:00
64707c33bb
Merged bug fix from Stable into Unstable
2011-09-12 21:54:11 -04:00
e63d9d8f8e
Mauricio pointed out to me that dynamic merging the unmapped regions of multiple BAMs ('-L unmapped' with a BAM list)
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was completely broken. Sorry about this! Fixed.
2011-09-12 21:50:59 -04:00
4e116760f4
Removing some old cruft from the packages dir. Updating AnalyzeCovariates to include all Covariates.
2011-09-12 15:09:25 -04:00
ec4b30de6d
Patch from Laurent: typo leads to bad error messages.
2011-09-12 14:45:53 -04:00
9d9d438bc4
New VariantAnnotatorEngine capability: an initialize() method for all annotation classes.
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All VariantAnnotator annotation classes may now have an (optional) initialize() method
that gets called by the VariantAnnotatorEngine ONCE before annotation starts.
As an example of how this can be used, the SnpEff annotation class will use the initialize()
method to check whether the SnpEff version number stored in the vcf header is a supported
version, and also to verify that its required RodBinding is present.
2011-09-12 13:00:53 -04:00
981b78ea50
Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.
2011-09-12 12:17:43 -04:00
60ebe68aff
Fixing issue in VariantEval in which insertion and deletion events weren't treated symmetrically. Added new option to require strict allele matching.
2011-09-12 09:43:23 -04:00
07d365ce39
Fixing units in queue job report Gantt plots
2011-09-12 09:01:34 -04:00
09050a01db
Adding qscript to run the HaplotypeCaller in parallel
2011-09-11 22:53:40 -04:00
30be6d8bd6
Removing the copy of the original assembler since it has been successfully assimilated
2011-09-11 21:00:27 -04:00
9344938360
Uncomment code to add deleted bases covering an indel to per-sample genotype reporting, update integration tests accordingly
2011-09-10 19:41:01 -04:00
b399424a9c
Fix integration test affected by non-calling all-zero PL samples, and add a more complicated multi-sample integration test from a phase 1 case, GBR with mixed technologies and complex input alleles
2011-09-09 20:44:47 -04:00
e95d484757
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-09 18:31:14 -04:00
a807205fc3
a) Minor optimization to softMax() computation to avoid redundant operations, results in about 5-10% increase in speed in indel calling.
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b) Added (but left commented out since it may affect integration tests and to isolate commits) fix to per-sample DP reporting, so that deletions are included in count.
c) Bug fix to avoid having non-reference genotypes assigned to samples with PL=0,0,0. Correct behavior should be to no-call these samples, and to ignore these samples when computing AC distribution since their likelihoods are not informative.
2011-09-09 18:00:23 -04:00
9e650dfc17
Fixing SelectVariants documentation
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getting rid of messages telling users to go for the YAML file. The idea is to not support these anymore.
2011-09-09 16:25:31 -04:00
72536e5d6d
Done
2011-09-09 15:44:47 -04:00
3c8445b934
Performance bugfix for GenomeLoc.hashcode
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-- old version overflowed so most GenomeLocs had 0 hashcode. Now uses or not plus to combine
2011-09-09 14:25:37 -04:00
c6436ee5f0
Whitespace cleanup
2011-09-09 14:24:29 -04:00
87dc5cfb24
Whitespace cleanup
2011-09-09 14:23:42 -04:00
7f9000382e
Making indel calls default in the MDCP
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You can turn off indel calling by using -noIndels.
2011-09-09 14:09:26 -04:00
1953edcd2d
updating Validate Variants deletion integration test
2011-09-09 13:39:08 -04:00
9ada9b3ed4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-09 13:15:36 -04:00
354529bff3
adding Validate Variants integration test with a deletion
2011-09-09 13:15:24 -04:00
91c949db74
Fixing ValidateVariants so that it validates deletion records. Fixing GATKdocs.
2011-09-09 12:57:14 -04:00
06cb20f2a5
Intermediate commit cleaning up scatter intervals
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-- Adding unit tests to ensure uniformity of intervals
2011-09-09 12:56:45 -04:00
6bd8a53efd
Fix nasty bug involving the build report generation when multiple test targets are specified on the same command line.
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Ant immutable properties: sometimes your friend, often your enemy.
2011-09-09 12:13:10 -04:00
60a3618845
Added "alltests" build targets.
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To run the same set of tests as the bamboo "All Tests" plan (unit tests,
integration tests, and pipeline tests):
ant alltests
To do the same as above on only the public portion of the codebase:
ant alltests.public
2011-09-09 12:13:10 -04:00
51eb95d638
Missed these tests before
2011-09-09 11:46:37 -04:00
b318fcba35
Added ability to profile the VCF output system too. Also, don't make the index test required.
2011-09-09 11:13:11 -04:00
6ad8943ca0
CompOverlap no longer keeps track of the number of comp sites since it wasn't (and cannot) keeping track of them correctly.
2011-09-09 09:45:24 -04:00
510d5e7730
Merged bug fix from Stable into Unstable
2011-09-09 01:34:55 -04:00
367bbee25a
Fixed typo when printing the contents or last N lines of a file. Thanks to larryns.
2011-09-09 01:33:25 -04:00
507574b1c8
Merge branch 'cancer'
2011-09-08 16:10:02 -04:00
61bccb71c6
Improvements to AssignSomaticStatus
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-- Added SOMATIC_AC_TAG_NAME, SOMATIC_NONREF_TAG_NAME tags
-- Added minimalVCF option for testing output
2011-09-08 16:09:33 -04:00
388c9a9c55
Enable public-only tests.
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Public-only tests will allow us to check for runtime public -> private
dependencies when bamboo updates the github repository (currently, we
only check for *compile-time* public -> private dependencies).
To compile/run only public tests, append ".public" to the name of an existing
test target:
ant test.public
ant integrationtest.public
ant performancetest.public
ant pipelinetest.public
ant pipelinetestrun.public
2011-09-08 15:58:42 -04:00
48461b34af
Added TYPE argument to print out VariantType
2011-09-08 15:01:13 -04:00
eaaba6eb51
Confirming that when stratifying by sample in VE the monomorphic sites for a given sample are not counted for the relevant metrics. Adding integration test to cover it.
2011-09-08 13:17:34 -04:00
c204a08319
Merge branch 'cancer'
2011-09-08 13:10:37 -04:00
beabb67669
Working version of AssignSomaticStatus
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-- Called 2400 somatic mutations (~ right number) when calling NA12878 vs. her parents.
-- Now ready for testing in the 100 T/N pairs
2011-09-08 13:09:26 -04:00
5edc8f8578
Moved to private package (intended home)
2011-09-08 11:54:55 -04:00
7557f4a03a
AssignSomaticStatus, now with the correct mathematical model
2011-09-08 11:54:14 -04:00
2636d216de
Adding indel vqsr integration test
2011-09-08 10:38:13 -04:00
9cba1019c8
Another fix for genotype given alleles for indels. Expanding the indel integration tests to include multiallelics and indel records that overlap
2011-09-08 09:25:13 -04:00
e0020b2b29
Fixing PrintRODs. Now has input and only prints out one copy of each record
2011-09-08 08:58:37 -04:00
6e6bf796d5
first version of somatic detector
2011-09-08 08:48:02 -04:00
29c968ab60
clean up
2011-09-08 08:42:43 -04:00
59841f8232
Fixing genotype given alleles for indels. Only take the records that start at this locus.
2011-09-08 08:41:16 -04:00
7f9047aec1
updating parameters in assembler to decrease runtime
2011-09-07 20:35:08 -04:00
Mark DePristo
Matt Hanna
Eric Banks
David Roazen
Ryan Poplin
Guillermo del Angel
Mauricio Carneiro
Khalid Shakir