1c387848de
No more use of -D in the integration tests but instead stick with VCFs only. Since all of these tests were duplicated (one each for dbSNP format and for VCF), we don't actually lose coverage in the integration tests.
2011-08-02 10:39:50 -04:00
2c5e526eb7
Don't use the mismatch fraction by default in the RealignerTargetCreator (since it's only useful when using SW in the indel realigner). Also, no more use of -D but instead move over to using VCFs. One integration test is temporarily commented out while I wait for a VCF file to get fixed.
2011-08-02 10:34:46 -04:00
5626199bb6
The Unified Genotyper now does NOT emit SLOD/SB by default; to compute SB use --computeSLOD
2011-08-02 10:14:21 -04:00
33b32c4211
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-28 13:57:22 -04:00
7a2a65155f
Merged bug fix from Stable into Unstable
2011-07-28 13:56:43 -04:00
1afc49a297
There are some really 'interesting' (but apparently valid) records in the Mus musculus dbSNP file. Generalized the handling of complex cases in the dbSNP adaptor to handle it all. I just grabbed the actual Mus musculus dbSNP file as a test, ran it whole genome, and confirmed that we finally produce a valid VCF on it. Should be the last commit needed on this adaptor.
2011-07-28 13:55:58 -04:00
1865211b6d
Merged bug fix from Stable into Unstable
2011-07-27 22:52:06 -04:00
6230315ff2
Along with my half-written commit message from earlier, I also forgot to commit the integration test updates. This is what happens when you try to do things 30 seconds before you leave for the day. To finish up from before: complex events weren't being padded with the reference base as per the VCF spec. They are now.
2011-07-27 22:51:21 -04:00
ff31fa7990
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-27 16:15:23 -04:00
405e521d44
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-26 17:56:48 -04:00
92a11ed8dc
Updated MD5 for PhaseByTransmissionIntegrationTest
2011-07-26 17:52:25 -04:00
f6a5e0e36a
Go for global integrationtest path first, if possible.
2011-07-26 17:35:30 -04:00
a53aeb75ab
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 15:10:35 -04:00
a29554e565
Removing the Genomic Annotator and its supporting classes
2011-07-25 15:10:25 -04:00
3afcb3415d
Max of 1000 records will be loaded and compared to avoid heap size problem.
2011-07-25 14:58:31 -04:00
bbb8473f03
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 10:59:00 -04:00
1d3bcce2c4
Merge branch 'master' into NoDistributedGATK
2011-07-23 20:04:50 -04:00
0b36b6540f
Merge branch 'laptop'
2011-07-23 01:44:54 -04:00
e23cb27451
Modified MD5 to account for the triple hets that shouldn't be phased
2011-07-23 01:44:44 -04:00
f366124778
Merge branch 'laptop'
2011-07-23 01:25:36 -04:00
45f2ca8d99
Changed MD5 to reflect latest changes to PhaseByTransmission.
2011-07-23 01:21:07 -04:00
b5deff48e6
Merge branch 'laptop'
2011-07-23 00:56:50 -04:00
5638017137
Removed the nofilters argument specification in the integrationtest
2011-07-23 00:56:23 -04:00
ffa361f57f
Merge branch 'laptop'
2011-07-23 00:50:38 -04:00
9417ba8c2c
Modified to accept multi-sample VCFs, removed the application of filters, and changed transmission probability field to be a genotype field rather than an INFO field.
2011-07-23 00:48:26 -04:00
f50145b872
Reinitialize random seed in the bwa bindings from the fixed seed stored in the
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BWA support files every time the support files are loaded.
2011-07-22 13:41:53 -04:00
172b35372b
Moved all of the distributed GATK code to archive.
2011-07-22 09:20:32 -04:00
8b8f121cfb
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-21 23:01:11 -04:00
59eb1f4663
Memory limits changed from Int to Double.
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Updated LSF calls to read memory units from config along with tweaks to select hosts.
Moved some common code from GridEngine and LSF to super classes.
2011-07-21 22:57:18 -04:00
7054c5342f
When using the BWA bindings, you have to explicitly call close() to get the
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bindings to release memory.
It may or may not be possible to implicitly close triggered by the GC; I'll add a JIRA.
2011-07-21 12:13:29 -04:00
15610ce0c3
Per Matt's request, disabling BWA-based integration tests so he can assess bamboo memory usage.
2011-07-21 11:04:22 -04:00
d31b176e15
Removed GATK use of distributed parallelism framework.
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Moved distributed GATK prototype code into distributedutils, separating from threading package
2011-07-20 16:26:09 -04:00
5d706c9e92
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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Removing PSP and CSM
Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
2011-07-19 20:25:33 -04:00
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
baae381acb
Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable"
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This reverts commit 039a6bb01f345322ce2be50ae3634308bb24e77e, reversing
changes made to b9c9973d1c638dfc9f8c19b5eb845e99844f9d29.
2011-07-19 18:38:53 -04:00
8f0badc52b
Updating md5s, as the diffobjects walker now emits the summary in reverse order.
2011-07-18 15:44:21 -04:00
83ba2c066a
Making it deterministic
2011-07-18 13:59:02 -04:00
80b5c5261a
CombineVariants no longer combines records of different types. So now when combining SNP and indel callsets, overlapping calls get their own records. Useful for Khalid in the pipeline. For those interested, it turns out the previous behavior was doing the wrong thing occasionally (and this was even captured in the integration tests).
2011-07-18 13:42:45 -04:00
51b0dd01c3
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 10:47:29 -04:00
d6e2e89f99
Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.
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System has the concept of a local and a global MD5 db. The local one is like it operated previously. The global one lives in /humgen/gsa-hpprojects/GATK/data/integrationtests. If the system can find this directory then MD5s will also be read / written to this location. This means that gsabamboo will print differences as appropriate. And all users will in effect have access to a complete history of MD5 file results.
A few minor code reshuffles changed VariantRecalibration and VCFHeader test files.
2011-07-18 10:46:01 -04:00
6f26c07b85
Removed the SpecificDifference class. Now Difference classes always have the option to remember specific master and test values. This means that all summarized differences carry with them specific examples of their differences. Consequently, now even summarized differences give at least one example of the specific difference, even when the count of the difference is > 1. Unit tests updated. Added DiffObjects integrationtest. VCFDiffableReader now specifically reads the first line of the VCF file to capture the version number.
2011-07-18 10:42:35 -04:00
ac9c66138d
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 00:20:33 -04:00
824100e57f
Corrected typo in MergeAndMatchHaplotypes integration test
2011-07-17 22:50:54 -04:00
8167aba601
Moved (poorly named) MergeAndMatchHaplotypes to public. Added integration test
2011-07-17 22:47:32 -04:00
afb506e128
Added MD5s for PhaseByTransmission integration tests
2011-07-17 21:55:33 -04:00
558e197989
Integration test for PhaseByTransmission
2011-07-17 21:25:08 -04:00
9ca9cf52ac
Uncommenting a stray commented test.
2011-07-17 15:38:33 -04:00
4db2b13e9e
Rev tribble.
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Just added more documentation for diffEngine and pointer to new wiki:
http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
2011-07-17 13:05:04 -04:00
eacf205f40
Tests needed to be updated to reflect the code reorg of tribble.
2011-07-16 09:22:34 -04:00
c0bbeb23ba
Now providing more information when the index on the fly isn't equal to the one created by reading the file from disk.
2011-07-14 15:12:28 -04:00
Eric Banks
Kiran V Garimella
Mark DePristo
Matt Hanna
Khalid Shakir
Christopher Hartl
David Roazen