c5977e5c8f
Correct wrong left-alignment of reads in HC bamout
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Story:
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https://www.pivotaltracker.com/story/show/80684230
Changes:
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- Corrected the bug: AlignmentUtils#createReadAlignedToRef was
not realigning against the reference but the best haplotype for
the read.
Test:
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- Added integration test in HaplotypeCallerIntegrationTest to check
that the bug has been fixed.
- Fixed md5s modified by this change; these are cause due to small
changes in the state of the random-number generator and read vs
variant site overlapping.
2014-11-10 10:09:58 -05:00
31cb47b9e6
Merge pull request #763 from broadinstitute/ldg_combineGVCFsFix
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Fix bug in CombineGVCFs so now sample 2 variants occurring within sample ...
2014-11-06 12:56:15 -05:00
8ddcff159e
Merge pull request #765 from broadinstitute/rhl_improve_bad_file_err_msg
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Catch RuntimeException and add the bad file name to the newly thown exce...
2014-11-05 10:59:38 -05:00
6f78bf5041
Catch RuntimeException and add the bad file name to the newly thown exception
2014-11-05 09:14:33 -05:00
c09667a20d
Fix bug in CombineGVCFs so now sample 2 variants occuring within sample 1 deletions get merged properly.
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CombineGVCFs now outputs ref conf for the duration of deletions so that SNPs occuring in other samples aligned with those deletions will be genotyped correctly
2014-11-05 09:11:47 -05:00
c14fccb571
Merge pull request #771 from broadinstitute/ks_faster_builds
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Faster builds of GATK executables
2014-11-05 01:54:59 +08:00
0092a0b9eb
Faster builds, with updates to documentation generation.
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Reading the multiple GATKText files as a single stream, especially with new top level target executable jar files pointing to a lib folder.
Don't dirty the build with a new GATKText.properties if input files are unmodified.
Stop warning on undocumented abstract classes.
Fixed ClassNotFoundException/NoClassDefFoundError by fixing ResourceBundleExtractorDoclet artifact.
Excluding Exceptions from documentation.
Removed custom log4j dependency from ResourceBundleExtractorDoclet.
Stop generating the dependency reduced pom during shade.
Stop regenerating gsalib when the files are already up to date.
Disabled mvn site generation from external-example.
2014-11-05 00:32:23 +08:00
1cb4b99548
Added faster built executable, non-packaged jars.
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Moved top level target symlinks to package jar files to under target/package.
Executable jar files are placed under target/executable with the new target[/lib] directories.
Under top level target, symlinks to *either* the package *or* the executable jars replace what was a symlink to the package jar path.
Allow disabling of the shade package.
ant-bridge.sh by default only builds executable jars, and doesn't package by default, as did the old ant build.xml.
Added a new package_path.sh utility script for other scripts to use instead of anything in the target folder.
2014-11-05 00:30:46 +08:00
f6af776590
Merge pull request #767 from broadinstitute/gg_fix_gsalib_doc
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Updated gsalib package to match version we put in CRAN
2014-11-04 10:46:27 -05:00
65d834fece
Merge pull request #769 from broadinstitute/pd_sb_plusplus
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Added StrandAlleleCountsBySample annotation
2014-11-04 10:45:46 -05:00
10f99cbe04
Added StrandAlleleCountsBySample annotation
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This annotation outputs the number of reads supporting each allele, stratified by sample and read strand.
Addresses PT 76958712
2014-11-03 21:35:58 -05:00
20bab93634
Merge pull request #772 from broadinstitute/ks_disable_lsf_tests
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Disabling tests for Lsf706 specific functionality.
2014-11-03 16:24:57 -05:00
8b81031bf8
Disabling tests for Lsf706 specific functionality.
2014-11-04 01:31:18 +08:00
f93b5b2c39
Merge pull request #770 from broadinstitute/pd_ngs_platform
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Moved platform flow information into NGSPlatform
2014-11-03 10:15:17 -05:00
bcfd9ce19a
Moved platform flow information into NGSPlatform
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* Explicitly added a type for rarely used platforms
* PT 81767718
2014-10-31 22:27:34 -04:00
c84805c402
Merge pull request #768 from broadinstitute/pd_bcf_failures
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Fix BCF writing when FORMAT annotations contain arrays
2014-10-31 15:30:56 -04:00
eecb56e0ae
Merge pull request #766 from broadinstitute/ldg_StrandBiasForMultiallelics
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Calculate StrandBiasBySample using all alternate alleles as ref vs. any ...
2014-10-31 15:26:07 -04:00
2ff88d17ca
Merge pull request #764 from broadinstitute/ldg_fixCombineVariantsError
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Minor change to new CombineVariants error check so identical samples don...
2014-10-31 15:23:23 -04:00
2d7f906a27
Merge pull request #762 from broadinstitute/ks_refactor_mvn_packages
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Refactor maven packages
2014-11-01 02:17:01 +09:00
fc67e50faa
Revved Picard/htsjdk
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Removed inefficient array->List conversion in AlleleCountBySample
2014-10-30 21:16:25 -04:00
b3b569f43a
Picard made major changes post-v1.123. Update our tools to handle them
2014-10-30 21:16:24 -04:00
e351ca869d
Updated gsalib package to match version we put in CRAN
2014-10-30 14:26:38 -04:00
bc7202fff7
Calculate StrandBiasBySample using all alternate alleles as ref vs. any alt
2014-10-30 11:52:06 -04:00
4d3db58c71
Added a compile time script to enforce utils/engine/tools separation.
2014-10-29 05:14:26 +08:00
7bae70ec1a
Minor change to new CombineVariants error check so identical samples don't need genotypeMergeOption
2014-10-28 08:17:49 -04:00
5c9fe1a06d
Split all imports of tools|engine from utils, and all tools from engine.
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Second of two commits, modifying actual files.
2014-10-24 20:59:46 +08:00
bb7151192a
Split all imports of tools|engine from utils, and all tools from engine.
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First of two commits, renaming files only.
2014-10-24 20:59:45 +08:00
b69b256003
Update pom versions to mark the start of GATK 3.4 development
2014-10-23 22:31:44 -04:00
eee94ec81f
Update pom versions for the 3.3 release
2014-10-23 22:25:17 -04:00
a5aa4d5822
Merge remote-tracking branch 'unstable/master'
2014-10-23 22:23:22 -04:00
22230cc820
Merge pull request #761 from broadinstitute/ks_junction_plugin_local_repo
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Adding sysinternals:junction:1.04:exe to local repo.
2014-10-23 19:12:41 -04:00
75c17bbd6f
Adding sysinternals:junction:1.04:exe to local repo.
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With Geraldine's blessing, works around issue where the repo for this exe keeps going down.
2014-10-24 05:33:47 +08:00
37464c38f2
Merge pull request #760 from broadinstitute/ks_queue_patches
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Queue patches
2014-10-23 14:52:26 -04:00
ac33eda231
Queue patches.
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Fixed Queue bug with bad localhost addresses.
Spaces in job names, while fine in GridEngine 6, break in (Son of) GE8.
2014-10-23 22:59:19 +08:00
7dc8638ca4
Merge pull request #759 from broadinstitute/gg_minor_docfixes
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Minor documentation clarifications in HC and a typo fix in SelectVariants
2014-10-22 22:20:26 -04:00
3ba94b987c
Minor documentation clarifications
2014-10-22 17:54:11 -04:00
0f89d1a362
Merge pull request #755 from broadinstitute/sc_Annotation_Docs_73647570
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Improvements to documentation of variant annotations
2014-10-22 13:41:00 -04:00
f093950bf9
Merge pull request #740 from broadinstitute/rp_ROC_curve_total_sensitivity
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Adding total sensitivity option to ROCCurveNA12878 to help with Mauricio...
2014-10-22 11:33:16 -04:00
e2fec7582e
Merge pull request #756 from broadinstitute/gg_fixGenotypeAndValidate
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Fix GenotypeAndValidate
2014-10-22 09:43:42 -04:00
be4cbf7035
Merge pull request #757 from broadinstitute/ks_smowton_scatter_contigs_fix
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Improved scatter contigs algorithm to be fairer when splitting many contigs into few parts.
2014-10-22 19:27:02 +08:00
26ba4c11aa
Minor fixups for previous commit once tests (only runnable at Broad) were run.
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Fixed off by one error in size calculation IntervalUtils.scatterContigIntervals().
In test for fewer files than intervals, adjusted expected intervals.
In test for more files than intervals, adjusted expected exception.
2014-10-22 17:37:37 +08:00
a62dc84795
Improved scatter contigs algorithm to be fairer when splitting a large number of contigs into a small number of parts.
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See also: http://gatkforums.broadinstitute.org/discussion/comment/16010
Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
2014-10-22 16:26:17 +08:00
b3c5ed4414
Improvements to documentation of variant annotations
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- Added or modified explanations for majority of variant annotations
- Generalized NBaseCount to include all tech platforms (not just SOLiD)
2014-10-21 18:20:04 -04:00
895b8c5931
Minor fix for missing INFO key definition in VCF header
2014-10-21 16:50:37 -04:00
edaa78dea1
Merge pull request #743 from broadinstitute/gg_gsaweb_switchover
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Switch GATKDocs publishing to new gsaweb VM
2014-10-21 12:27:51 -04:00
c4fcd70a88
Merge pull request #754 from broadinstitute/rhl_variant_array_exception
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Do not process a variant if it is too large (> readLength), and log an e...
2014-10-21 12:01:52 -04:00
bcf6be0b08
Merge pull request #753 from broadinstitute/ldg_HCzeroDepth
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Fix GenotypeGVCF bugs in -allSites mode
2014-10-21 12:00:04 -04:00
7ec38bf2a2
Merge pull request #752 from broadinstitute/pd_cran_license
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Changed license of gsalib R package from BSD to MIT
2014-10-21 11:51:24 -04:00
312a833db3
Merge pull request #751 from broadinstitute/pd_bamout_ref_regions
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Added -disableOptimizations argument to HaplotypeCaller.
2014-10-21 11:50:46 -04:00
2b848ad859
Variants that become hom-ref after regenotyping in GenotypeGVCFs are now getting output in -allSites mode.
2014-10-21 08:21:53 -04:00
Valentin Ruano-Rubio
rpoplin
jmthibault79
Ron Levine
Laura Gauthier
kshakir
Khalid Shakir
Phillip Dexheimer
droazen
Geraldine Van der Auwera
Chris Smowton
Sheila Chandran