4d3db58c71
Added a compile time script to enforce utils/engine/tools separation.
2014-10-29 05:14:26 +08:00
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
5465e4484e
For GenotypeGVCFs -allSites mode, make genotypes no-call if depth is zero.
2014-10-21 08:21:43 -04:00
239151ac7b
Do not process a variant if it is too large (> readLength), and log an error
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remove final keyword before refMap and altMap, constructHaplotype() changes their values
return ArtificialHaplotype from constructHaplotype instaed of passing as an argument
Add logic so arraycopy does not throw an IndexOutOfBoundsException, add test for a long insert
2014-10-20 15:51:32 -04:00
f766608b4e
Changed license of gsalib R package from BSD to MIT
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- PT 75827540
2014-10-16 21:37:07 -04:00
b348ce8f25
Added -disableOptimizations argument to HaplotypeCaller.
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* This argument is intended to be used in conjunction with -bamout, and disable early-exit optimizations to allow reference regions to be contained in the output bam
* Also forcibly includes the reference haplotype in the set of haplotypes given to the BAMWriter
* Made -dontTrimActiveRegions visible, as it is likely also desirable in this use case
* Addresses PT 77731660
2014-10-16 21:11:20 -04:00
5fa5724e4a
Merge pull request #750 from broadinstitute/ldg_uniqueSamplesInCombineVariants
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Throw UserException if input VCFs have duplicate samples but no genotype...
2014-10-16 07:57:27 -04:00
0f08065ebc
Throw UserException if input VCFs have duplicate samples but no genotypemergeoption is specified
2014-10-15 16:03:10 -04:00
286f4cc8a8
Merge pull request #749 from broadinstitute/ldg_CGPfasterTests
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Decrease interval on CGP integration test to reduce test execution time
2014-10-15 15:53:48 -04:00
2b67e46e29
Adding total sensitivity option to ROCCurveNA12878 to help with Mauricio's analyses.
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-- We now keep a tally of uncalled sites so that they can be factored into the denominator of the sensitivity/specificity metric
2014-10-15 12:48:42 -04:00
81482138ca
Decrease interval on CGP integration test to reduce test execution time
2014-10-15 11:28:27 -04:00
0ad9daeac1
Merge pull request #747 from broadinstitute/gg_fixLicenseOmission
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Updated license files and text
2014-10-15 11:26:42 -04:00
e7e8052f84
Updated license information
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- Updated license files (private/protected) for version, address and a couple of legal clauses
- Updated license snippet throught the codebase
2014-10-14 17:10:12 -04:00
32bf46d8bf
Merge pull request #748 from broadinstitute/rp_roc_curve_qual_field
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In ROCCurveNA12878, if VQSLOD value is not present default to using the ...
2014-10-14 14:30:52 -04:00
9680511cc3
In ROCCurveNA12878, if VQSLOD value is not present default to using the QUAL field instead to rank the variants.
2014-10-14 12:15:23 -04:00
426907ddd0
Merge pull request #744 from broadinstitute/gg_gatkdocs_annots_and_GSON
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Output JSON version of docs for Galaxy
2014-10-14 11:41:16 -04:00
d259f3c84f
Merge pull request #745 from broadinstitute/ldg_VariantAnnotatorDocs
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Added docs to VariantFiltration is accordance with new htsjdk changes. ...
2014-10-10 14:11:24 -04:00
22a3c6e556
Merge pull request #742 from broadinstitute/rhl_prob_thresh_param_arg
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Rhl prob thresh param arg
2014-10-10 12:55:01 -04:00
0ecb85d321
Added docs to VariantFiltration is accordance with new htsjdk changes. Fixed typo in VariantAnnotator docs.
2014-10-10 11:54:24 -04:00
36c27155af
Made the threshold for the probability of a state being active a command line argument
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remove TODO comment after activeProbThreshold
recover static ACTIVE_PROB_THRESHOLD for unit tests
Add min/max values for active_probability_threshold parameter
Move activeProbThreshold parameter to GATKArguemtnCollection
define ACTIVE_PROB_THRESHOLD in unit tests
add construction of argCollection in in ctor
Move arguments from GATKArgumentCollection to ActiveRegionWalker
Throw exception if threshold < 0 or > 1 in ActivityProfile ctor
max propogation distance parameter to ActiveRegionWalker for AcrtivityProfile
Use polymorphic getMaxProbPropagationDistance() so BandPassActivityProfile computes the crrect region size cutoff
Get the maxProbPropagationDistance from the super class's method, instead of directly, this is safer
Removed extraneous command line imports and make maxProbPropagationDistance a hidden argument
remove limit check for activeProbThreshold, not necessary because the check is made when imput as a command line arg
Remove extra 'region' in the doxygen param description for maxProbPropagationDistance
2014-10-10 10:36:02 -04:00
4e099c1f44
Merge pull request #741 from broadinstitute/rhl_activiteregion_read_limits_args
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Changed hardcoded downsampling max/min coverage values to parameters
2014-10-09 18:49:22 -04:00
645d418015
Changed hardcoded downsampling max/min coverage values to parameters
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Rename parameters using camel case and add to integration test
Correct documentation for maxReadsInRegionPerSample and minReadsPerAlignmentStart
Change the argument--minReadsPerAlignmentStart in the integration test from 50 to 5
'each genomic location' only pertains to minReadsPerAlignmentStart, not maxReadsInRegionPerSample
2014-10-09 17:09:26 -04:00
3f21f63161
Output JSON version of docs for Galaxy
2014-10-09 06:42:25 -04:00
58ca51e255
Switch GATKDocs publishing to new gsaweb VM
2014-10-08 21:07:58 -04:00
1cbf37c539
Merge pull request #739 from broadinstitute/rp_KB_reviews
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Adding manual review.
2014-10-01 09:53:08 -04:00
b0481ced87
Merge pull request #738 from broadinstitute/vrr_slow_integration_test_due_to_general_ploidy_exact_af_calculator
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Reduce execution time of various integration tests
2014-10-01 09:52:04 -04:00
Khalid Shakir
Geraldine Van der Auwera
droazen
rpoplin
kshakir
Chris Smowton
Sheila Chandran
Laura Gauthier
Ron Levine
Phillip Dexheimer
jmthibault79
Ron Levine