c0286853b7
Merge pull request #584 from broadinstitute/dr_update_queue_test_script_for_naming_change
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Update queue test runner script for upcoming naming changes
2014-04-01 11:52:22 -04:00
ef8f91a5be
Update queue test runner script for upcoming naming changes
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Use both the old and new names for now, until the transition
is complete.
2014-04-01 11:49:55 -04:00
8703bd7ad4
Merge pull request #583 from broadinstitute/jt_tabix
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Create Tabix indices for block-compressed VCFs
2014-03-31 16:17:25 -04:00
70fe7f72f1
Return a TabixIndexCreator for appropriate file types
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[Fixes #68291082 ]
2014-03-31 16:15:34 -04:00
ab5634cbac
Test that a Tabix index is created for block-compressed output formats
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- Replace .idx and .tbi with appropriate constants
2014-03-31 14:36:48 -04:00
a2d40c84ba
Keep the list of zipped suffixes in sync with Variant
2014-03-31 14:36:41 -04:00
a2cd9703fa
Rev Picard 1.110.1773
2014-03-31 14:15:06 -04:00
821fbe7260
Merge pull request #582 from broadinstitute/vrr_hc_bugfixes_dangling_heads
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Fix loss of key alternative haplotypes due to a change on threading star...
2014-03-31 10:42:08 -04:00
313d20d849
Merge pull request #581 from broadinstitute/jt_picard
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Rev Picard because it's needed by another branch
2014-03-30 11:05:50 -04:00
2049eb1658
Rev Picard 1.110.1763
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- SamPairUtils migrated in Picard r1737
- Revert IndelRealigner changes made in commit 4f4b85
-- Those changes were based on Picard revision 1722 to net/sf/picard/sam/SamPairUtil.java
-- Picard revision 1723 reverts these changes, so we also revert to match
2014-03-30 09:33:57 -04:00
258b2bce28
Fix loss of key alternative haplotypes due to a change on threading start policy required when recovering dangling heads.
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Story:
- https://www.pivotaltracker.com/story/show/67601310
Change:
- Unless recover-danging-heads is active, the threading starting location policy is the original one. i.e. just at already existing unique kmer vertices.
Tests:
- HaplotypeCallerIntegrationTest#testMissingKeyAlternativeHaplotypesBugFix
2014-03-29 22:40:26 -04:00
5abb7ea2db
Merge pull request #579 from broadinstitute/rp_fix_DP_annotation
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Fix for dropping of reference sample depth in the DP annotation.
2014-03-24 15:49:20 -04:00
6566dd6ca9
Fix for dropping of reference sample depth in the DP annotation.
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-- In the case of hierarchical merge we can't assume that we have only one genotype.
-- Removed use of deprecated VC annotation access functions.
2014-03-24 14:01:50 -04:00
c61a791914
Merge pull request #578 from broadinstitute/eb_trivial_fix_to_IR
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Fix for reads that are all insertions (e.g. 50I) and causing the IndelRe...
2014-03-21 15:24:58 -04:00
b8581d7d3a
Merge pull request #576 from broadinstitute/rp_fix_AssessNA12878_dropping_contigs
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Bug fix in AssessNA12878 when working with more than one contig.
2014-03-21 15:23:59 -04:00
32a96e3ab3
Fix for reads that are all insertions (e.g. 50I) and causing the IndelRealigner to error out.
2014-03-21 15:01:34 -04:00
dd1b0a48db
Bug fix in AssessNA12878 when working with more than one contig.
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-- SmartSiteIterator needs to know to span across Chunks when iterating by polling the Chunk list
-- Added KB test to test for this case
-- Removed the maxSites argument in ExtractConsensusSites because it is counterintuitive and not useful.
2014-03-21 14:52:10 -04:00
69eaf7c82d
Merge pull request #577 from broadinstitute/eb_minor_fixes_for_fragment_utils
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Fixed docs for method and fixed the edge case optimization to properly u...
2014-03-21 14:01:44 -04:00
ce39fcd8a3
Merge pull request #575 from broadinstitute/eb_various_fixes_for_gvcfs
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Eb various fixes for gvcfs
2014-03-21 09:47:08 -04:00
0d82a70633
Fixed docs for method and fixed the edge case optimization to properly use equals() on Integers.
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Shouldn't affect actual results at all.
2014-03-20 15:55:09 -04:00
7c8ce3cd6a
Several improvements to GenotypeGVCFs: --includeNonVariantSites now actually works and we propagate AD to hom ref samples
2014-03-20 00:35:54 -04:00
824983af1d
Enable CombineGVCFs to process gVCFs that were created with basepair resolution.
2014-03-19 19:23:05 -04:00
3b1c337401
Have CombineVariants throw a UserError when trying to combine GVCFs from the HaplotypeCaller.
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Was previously throwing an IllegalArgumentException (in the wrong place in the code).
Error message tells users to use CombineGVCFs.
2014-03-19 19:11:40 -04:00
7117bebb5e
Merge pull request #572 from broadinstitute/rp_fix_manual_reviews_fix
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Forgot to change the padding ref base as well.
2014-03-19 13:58:58 -04:00
a3aa68e626
Forgot to change the padding ref base as well.
2014-03-19 13:58:21 -04:00
c737b8ed1e
Merge pull request #571 from broadinstitute/rp_fix_manual_reviews
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Fixing the reference base in one of the manual review files.
2014-03-19 13:49:51 -04:00
523fd40a07
Fixing the reference base in one of the manual review files.
2014-03-19 11:08:06 -04:00
3f326b14be
Merge pull request #570 from broadinstitute/rp_assessNA12878_arg_docs_fix
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Small argument docs fix in AssessNA12878.
2014-03-19 09:01:23 -04:00
7b38019199
Merge pull request #569 from broadinstitute/vrr_speedup_integration_test
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Reduce runtime of very long integration test
2014-03-18 23:39:16 -04:00
905b6066b2
Reduce runtime of very long integration test
2014-03-18 21:48:13 -04:00
14eb0a8a30
Merge pull request #566 from jsilter/master
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Improvements to na12878kb
2014-03-18 15:16:20 -04:00
cec4ff3a2a
Merge pull request #568 from broadinstitute/dr_fix_UtilsUnitTest
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Fix typo in UtilsUnitTest data provider name
2014-03-18 14:31:14 -04:00
e549f4a9d2
Fix typo in UtilsUnitTest data provider name
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This is currently my leading suspect for the cause of the
intermittent NoSuchElementException errors on master, since
the maven surefire plugin seems unable to handle errors in
TestNG DataProviders without blowing up.
2014-03-18 11:52:29 -04:00
a02383fc6a
Small argument docs fix in AssessNA12878.
2014-03-18 10:07:14 -04:00
4ba72d43cf
Re-enable GATKRunReportUnitTest
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This test is not, as I had initially thought, the cause of the
maven errors. Our master branch is failing intermittently
regardless of whether this test is enabled or disabled.
This reverts commit 45fc9ff515eec8d676b64a04fb34fb357492ff84.
2014-03-18 09:53:41 -04:00
3cd8158bed
Merged bug fix from Stable into Unstable
2014-03-18 03:01:28 -04:00
cfc45fdc0b
Disable GATKRunReportUnitTest
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These tests pass individually and as part of complete test suite runs,
but cause an intermittent NoSuchElementException in maven when the
unit tests are run on their own. Disabling these tests until the
cause of this can be identified.
2014-03-18 02:57:19 -04:00
afa6abe554
Temporarily disable GATKRunReportUnitTest in unstable while maven issues are worked out
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This test passes when run individually, as part of the commit tests, or as
part of the package tests. However, when running the unit tests in isolation
it causes maven/surefire to throw a NoSuchElementException.
This is clearly a maven/surefire bug or configuration issue. I will re-enable
this test on a branch as Khalid and I try to work through it.
2014-03-18 01:28:28 -04:00
2d8653f493
Update pom versions to mark the start of GATK 3.2 development
2014-03-18 01:18:59 -04:00
72492bb875
Merge remote-tracking branch 'unstable/master'
2014-03-18 01:11:23 -04:00
a6a41c777c
Update pom versions for 3.1
2014-03-18 01:09:29 -04:00
975b3f321e
Merge pull request #567 from broadinstitute/dr_public_GATKRunReport_tests
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Move GATKRunReport tests from private to public
2014-03-17 18:33:26 -04:00
d5e38ec39b
Move GATKRunReport tests from private to public
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-Hide AWS downloader credentials in a private properties file
-Remove references to private ActiveRegion walker
Allows phone home functionality to be tested at release time
when we are running tests on the release jar.
2014-03-17 18:29:40 -04:00
6b3320f067
Merge pull request #561 from broadinstitute/ks_package_classpath
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Updated package-tests classpath, and allowing javac -cp <package>.jar.
2014-03-17 17:38:24 -04:00
0715a9fd7d
Make sure to follow HTTP redirects when loading dbSpec
2014-03-17 16:31:14 -04:00
cfc4f708dc
Load dbSpec into string before parsing it as JSON
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This is to make the causes of errors more obvious; if there is an error parsing the json string the entire received message is included in the error message
2014-03-17 16:30:26 -04:00
2e34ff7692
Merge pull request #563 from broadinstitute/aw_refactor_tribble
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GATK changes to conform to Tribble refactoring as part improving Tabix s...
2014-03-17 13:35:46 -04:00
2115195d18
Merge pull request #565 from broadinstitute/eb_remove_one_more_reference_to_rr
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Remove unused and unnecessary argument
2014-03-17 12:29:26 -04:00
dabdd0a0fd
Remove unused and unnecessary argument
2014-03-17 12:28:27 -04:00
759c4c8c5a
Merge pull request #564 from broadinstitute/eb_rename_truth_set
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Mark had mis-named this input callset to the knowledgebase. It's the pi...
2014-03-17 12:15:57 -04:00
droazen
jmthibault79
Eric Banks
Valentin Ruano-Rubio
MauricioCarneiro
Ryan Poplin
Jacob Silterra