7457fc2c6d
Switched svn up invocation from buildnumber-maven-plugin to maven-antrun-plugin, due to mixed revisions by running svn up <dir> instead of just svn up.
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Removed unused scm element that was required by buildnumber.
2014-02-13 09:07:11 +08:00
1c3c20ece3
Merge pull request #514 from broadinstitute/dr_update_nightly_build_script_for_maven
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Update nightly build script for maven
2014-02-12 17:43:40 -05:00
0d07121a8d
Update nightly build script for maven
2014-02-12 17:14:26 -05:00
a1f191ce45
Merge pull request #507 from jsilter/master
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Add ability to read dbSpec over http
2014-02-12 16:15:09 -05:00
400800e676
Add ability to read dbSpec over http
2014-02-12 16:02:31 -05:00
10716ca17b
Merge pull request #510 from broadinstitute/dr_phone_home_script_updates
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Bring live versions of phone home scripts under version control
2014-02-12 15:40:41 -05:00
5bde7fbf37
Merge pull request #511 from broadinstitute/dr_enable_exclusions_in_maven_package_tests
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Exclude all transitive dependencies in maven package-tests
2014-02-12 15:38:39 -05:00
b8db5a9502
Merge pull request #512 from broadinstitute/jt_multi_allele_fix
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Fix the broken AD field for multi-allelic variants
2014-02-12 15:38:02 -05:00
bc3d1addee
Merge pull request #508 from broadinstitute/rp_ROCCurveNA12878_plot_filtered_status
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Adding the filter field to the output of ROCCurveNA12878
2014-02-12 15:33:15 -05:00
ef87b051b0
Rev Picard to 1.107.1683 (4 jars)
2014-02-12 15:25:50 -05:00
6f12c8b0dc
Exclude all transitive dependencies in maven package-tests
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This change should allow us to test that the GATK jar has been
correctly packaged at release time, by ensuring that only the
packaged jar + a few test-related dependencies are on the classpath
when tests are run.
Note that we still need to actually test that this works as intended
before we can make this live in the Bamboo release plan.
2014-02-12 14:59:05 -05:00
3b8670490d
Use s3funnel instead of s3cmd for listing/downloading/deleting
2014-02-12 14:35:24 -05:00
9ef3f5663f
Phone home script updates
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-Add support for multiple S3 accounts
-Add chunking for downloads so that we never try to store/process
too many files at once
-Process chunks asynchronously in parallel to greatly speed up
downloading/parsing of phone home reports
2014-02-12 14:35:06 -05:00
cc9477aedb
Minimal test for the multi-allelic reordering bug
2014-02-12 13:38:32 -05:00
1fcca8c5c0
Adding the filter field to the output of ROCCurveNA12878
2014-02-12 12:46:30 -05:00
6facf695ab
Merge pull request #506 from broadinstitute/eb_quick_fixes_to_single_sample_pipeline
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Several improvements to the single sample combining steps.
2014-02-12 11:30:48 -05:00
300b474c96
Several improvements to the single sample combining steps.
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1. updated QualByDepth not to use AD-restricted depth if it is zero.
Added unit test this change.
2. Fixed small bug in CombineGVCFs where spanning deletions were not being treated consistently throughout.
Added test for this situation.
3. Make sure GenotypeGVCFs puts in the required headers.
Updated test files to make sure this is covered.
4. Have GenotypeGVCFs propagate up the MLEAC/AF (which were getting clobbered out).
Tests updated to account for this.
2014-02-12 10:15:12 -05:00
ff8c9575b0
Merge pull request #505 from broadinstitute/ks_build_na12878kb-utils
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Ported na12878kb.jar assembly from Ant's build.xml to Maven
2014-02-12 10:10:52 -05:00
403ce7bfb7
Ported na12878kb.jar assembly from Ant's build.xml to Maven at request of jsilter
2014-02-12 06:01:32 +08:00
3cfcfa4fa0
Merge pull request #504 from broadinstitute/dr_enable_kb_tests_in_maven
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Add ability to run *KnowledgeBaseTests to maven
2014-02-11 15:32:24 -05:00
95e1402d21
Add ability to run *KnowledgeBaseTests to maven
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Run with: mvn verify -Dsting.knowledgebasetests.skipped=false
2014-02-11 14:08:24 -05:00
cc9a3b68fc
Merge pull request #503 from broadinstitute/ks_maven_gatkdocs_patch
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Patched PluginManager to ignore null classes
2014-02-11 13:28:24 -05:00
96e29d3d94
Merge pull request #500 from broadinstitute/eb_make_qd_more_robust
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Adding smarts to the QD annotation
2014-02-11 12:57:50 -05:00
303a60c8c6
Adding smarts to the QD annotation:
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when the AD annotation is present for a given genotype then we only use its depth for QD if the variant depth > 1.
Added new unit tests for QualByDepth.
2014-02-11 12:56:49 -05:00
1666bb7e3a
Patched PluginManager to ignore null classes, that will allow gatkdocs to build successfully when running from the source root directory, due to its hardcoded paths.
2014-02-12 00:48:58 +08:00
b33d9d9105
Merge pull request #502 from broadinstitute/eb_make_combine_gvcfs_faster
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Refactoring of CombineGVCFs to make it run a lot faster.
2014-02-11 09:03:16 -05:00
2e36dd9001
Refactoring of CombineGVCFs to make it run a lot faster.
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Creating new VariantContexts each time we broke up a block was very expensive because we break up
blocks so often. Also, calling into GATKVariantContextUtils.simpleMerge was really hurting performance.
MD5 changes because we no longer propogate any INFO fields (except for END) for reference blocks; the tests
have the now unused BLOCK_SIZE field that now get dropped.
2014-02-11 03:18:52 -05:00
b81494b704
Merge pull request #499 from broadinstitute/eb_fix_ad_updates
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Fixed bug in generating AD values when new alleles are present for genot...
2014-02-09 17:55:00 -05:00
abb67cfa5e
Fixed bug in generating AD values when new alleles are present for genotpying GVCFs.
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This was a dumb mistake that wasn't well tested (but is now).
2014-02-09 15:15:19 -05:00
c2a2484a18
Merge pull request #498 from broadinstitute/ks_delete_pricard_private
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Removed use of picard private.
2014-02-09 10:27:48 -05:00
12bb6fd361
Removed use of picard private.
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Updated picard-maven script to tag locally modified builds with -SNAPSHOT.
Removed old picard jars.
2014-02-09 17:08:52 +08:00
597cc88f33
Merge pull request #497 from broadinstitute/eb_remove_ac0_alleles_PT65118652
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Removing parameters that were incorrectly copied over from RegenotypeVariants
2014-02-08 23:46:23 -05:00
abef6cfcb6
Removing parameters that were incorrectly copied over from RegenotypeVariants.
2014-02-08 23:44:32 -05:00
e9189cd471
Merge pull request #496 from broadinstitute/eb_remove_test_for_blocksize
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Removing the test for BLOCK_SIZE since we no longer emit it
2014-02-08 21:29:02 -05:00
659a9f0e79
Removing the test for BLOCK_SIZE since we no longer emit it
2014-02-08 21:28:07 -05:00
a33d7ace11
Merge pull request #495 from broadinstitute/ks_increase_scala_memory
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Made scala.maxmemory an argument, and defaulted it to 1g.
2014-02-08 21:13:26 -05:00
4decb49ecb
Merge pull request #494 from broadinstitute/vrr_reference_model_nocall_bugfix
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Fixed nocall (./.) without PLs bug in GVCF output
2014-02-08 21:12:45 -05:00
4e0f7521f2
Made scala.maxmemory an argument, and defaulted it to 1g.
2014-02-09 09:24:44 +08:00
bf630abe88
Fixed nocall (./.) without PLs bug in GVCF output
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Story:
https://www.pivotaltracker.com/story/show/65388246
Additional changes and notes:
1. The fix consist in forcing the output of all PLs by setting the standard flag for that '-allSitePLs'.
2. BP_RESOLUTION was handled differently to GVCF in some aspect that should be common. That has been fixed.
2014-02-07 19:30:26 -05:00
8c922be684
Merge pull request #491 from broadinstitute/eb_get_AD_back_from_gvcfs
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Fixed up some of the genotype-level annotations being propogated in the ...
2014-02-07 12:50:01 -05:00
d689f61005
Fixed up some of the genotype-level annotations being propogated in the single sample HC pipeline.
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1. AD values now propogate up (they weren't before).
2. MIN_DP gets transferred over to DP and removed.
3. SB gets removed after FS is calculated.
Also, added a bunch of new integration tests for GenotypeGVCFs.
2014-02-07 12:47:54 -05:00
0a1385a4d9
Merge pull request #493 from broadinstitute/eb_fix_failing_merge_for_tim
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The UG engine can return a null VC if there are tons of alt alleles, cau...
2014-02-07 12:43:40 -05:00
67ed0d2403
The UG engine can return a null VC if there are tons of alt alleles, causing Tim's merge jobs to fail.
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Pushing the null check up so that it doesn't error out in such cases.
2014-02-07 12:41:20 -05:00
335483bb53
Merge pull request #492 from broadinstitute/eb_fix_failing_unit_tests
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Fixing failing unit tests
2014-02-07 12:25:10 -05:00
db68d3fa10
Fixing failing unit tests
2014-02-07 12:24:14 -05:00
8e87e083ff
Merge pull request #490 from broadinstitute/vrr_reference_model_unsorted_records_bugfix
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Fixed out of order non-variant gVCF entries when trimming is active.
2014-02-07 12:21:12 -05:00
4a3c8e68fa
Fixed out of order non-variant gVCF entries when trimming is active.
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Story:
https://www.pivotaltracker.com/story/show/65319564
2014-02-07 11:03:26 -05:00
369fbd4439
Merge pull request #489 from broadinstitute/eb_hierarchical_gvcf_merger
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Eb hierarchical gvcf merger
2014-02-07 08:50:39 -05:00
eb463b505d
Remove a whole bunch of unused annotations from gVCF output.
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AC,AF,AN,FS,QD - they'll all be recomputed later.
BLOCK_SIZE and MIN_GQ were not necessary.
I also made the StrandBiasBySample annotation forced on when in gVCF mode.
It turns out that its output wasn't compatible with BCF so I patched it (and the variant jar too).
2014-02-07 08:49:36 -05:00
2648219c42
Implementation of a hierarchical merger for gVCFs, called CombineGVCFs.
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This tool will take any number of gVCFs and create a merged gVCF (as opposed to
GenotypeGVCFs which produces a standard VCF).
Added unit/integration tests and fixed up GATK docs.
2014-02-07 08:49:18 -05:00
Khalid Shakir
droazen
Eric Banks
Jacob Silterra
Joel Thibault
Ryan Poplin
Valentin Ruano-Rubio