b2e51838d7
Merge pull request #673 from broadinstitute/ks_md5_db_per_test_run
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Creating and MD5DB per each test, instead of overwriting in the top dir
2014-07-08 10:58:59 -04:00
2129aa05d8
Bug fix for poms missing package test artifacts.
2014-07-08 06:34:26 +08:00
e5be9c7073
Using the base directory for each test run when outputting MD5DB mismatches.
2014-07-08 06:34:25 +08:00
f084fa5ab2
Merge pull request #669 from broadinstitute/eb_improve_decomposition_of_haplotypes_PT71966916
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When converting a haplotype to a set of variants we now check for cases that are overly complex.
2014-07-02 10:08:32 -04:00
bad7865078
When converting a haplotype to a set of variants we now check for cases that are overly complex.
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In these cases, where the alignment contains multiple indels, we output a single complex
variant instead of the multiple partial indels.
We also re-enable dangling tail recovery by default.
2014-07-01 14:18:59 -04:00
297c2b0651
Merge pull request #670 from broadinstitute/rp_SBBS_min_count
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SB tables should be created even if the ref or alt columns have no count...
2014-07-01 08:34:23 -04:00
e14bff212d
SB tables should be created even if the ref or alt columns have no counts. This is so that FS/SOR will still be calculated when the variant is extremely high or low frequency.
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-- Removed long running HC integration test... sorry
2014-06-30 15:19:15 -04:00
5c45641051
Merge pull request #668 from broadinstitute/rp_AD_realigned_reads_8b9d1c1
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Reads are now realigned to the most likely haplotype before being used b...
2014-06-30 12:35:40 -04:00
0127799cba
Reads are now realigned to the most likely haplotype before being used by the annotations.
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-- AD,DP will now correspond directly to the reads that were used to construct the PLs
-- RankSumTests, etc. will use the bases from the realigned reads instead of the original alignments
-- There is now no additional runtime cost to realign the reads when using bamout or GVCF mode
-- bamout mode no longer sets the mapping quality to zero for uninformative reads, instead the read will not be given an HC tag
2014-06-30 10:35:50 -04:00
dc93507023
Merge pull request #667 from broadinstitute/ks_refactor_doc_scala_package
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Refactored DoC scala package
2014-06-25 16:05:30 -04:00
f5345e903a
Fixed minor pom.xml line that was out of place after sortpom.
2014-06-26 01:01:19 +08:00
7b5f88a49c
Refactored DoC custom Queue wrappers to a non-package object.
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Now, "mvn verify && mvn verify" should work again.
2014-06-26 00:59:18 +08:00
b935ed0df1
Merge pull request #665 from broadinstitute/ks_force_delete_bad_symlinks
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Executing a version of the delete_maven_links.sh
2014-06-25 00:13:05 -04:00
92028027c9
Merge pull request #666 from broadinstitute/pd_merge_selectvariants_test
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Removed redundant SelectVariantsIntegrationTest, merged its only test i...
2014-06-24 21:19:46 -04:00
06d619e9aa
Removed redundant SelectVariantsIntegrationTest, merged it's only test into protected version
2014-06-24 18:59:59 -04:00
45d819a00e
For now, executing the delete_maven_links.sh just ahead of creating the symbolic links during the process-test-resources phase.
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Better than running it during the "clean" phase, since these users may not run "mvn clean" before attempting to build.
2014-06-25 02:32:15 +08:00
42cfa3b53b
Merge pull request #664 from broadinstitute/ks_picard_maven_gatk_root
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Fixed gatk-root path in private/picard-maven/pom.xml
2014-06-24 18:48:40 +08:00
bffc9fbabd
Fixed gatk-root path in private/picard-maven/pom.xml
2014-06-24 18:45:51 +08:00
c191103326
Merge pull request #663 from broadinstitute/pd_jexl_user_exception
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Recast the "Invalid JEXL expression detected" error in SelectVariants fr...
2014-06-20 17:17:54 -04:00
65eeb4a7ab
Recast the "Invalid JEXL expression detected" error in SelectVariants from a RuntimeException to a UserException
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- PT 68931448
2014-06-20 00:05:23 -04:00
db7dc8ab5f
Merge pull request #660 from broadinstitute/pd_catvariants_list
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Added functionality to CatVariants to process .list files with -V
2014-06-19 23:54:03 -04:00
da5e567b73
Added functionality to CatVariants to process .list files with -V
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- Pivotal 70305712
2014-06-19 21:46:13 -04:00
da1dab6c32
Merge pull request #661 from broadinstitute/jw_allele_balance_gvcf
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Enable AB annotation in reference model pipeline. Incorporates patches f...
2014-06-19 13:10:41 -04:00
41d2a793f0
Merge pull request #662 from broadinstitute/eb_Carlos_Borroto_commits
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Eb carlos borroto commits
2014-06-19 12:49:14 -04:00
1092dd6e25
From Carlos Barroto: switch outputRoot in SplitSamFile to an empty string instead of null.
2014-06-19 11:06:55 -04:00
9212edba41
From Carlos Barroto: made 'level' in Picard's CalculateHsMetrics Scala Queue extension an argument.
2014-06-19 11:06:50 -04:00
8b75428a90
Enable AB annotation in reference model pipeline. Incorporates patches from John Wallace to public github account
2014-06-19 09:35:04 -04:00
2df2a153e6
Merge pull request #658 from broadinstitute/ldg_PbyTwithPriors
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Updated CalculateGenotypePosteriors to compute genotype posteriors using...
2014-06-18 15:04:39 -04:00
9640d5d745
Merge pull request #649 from broadinstitute/pd_genotypegvcf_args
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Refactored StandardCallerArgumentCollection to expose args to GenotypeGVCFs
2014-06-18 11:36:13 -04:00
2356d5d63f
Updated CalculateGenotypePosteriors to compute genotype posteriors using likelihoods from all members of the trio.
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(Right now it only works if all members of the trio are called.)
Takes posteriors as input, defaulting to PLs
Added annotations for possible de novos for us in full genotype refinement pipeline
Added family priors to CGP integration test.
Changed CGP to use PP tag instead of GP tag because posteriors are Phred-scaled. Updated CGP integration test md5s to reflect change.
2014-06-18 11:17:15 -04:00
7570666f2a
Merge pull request #655 from broadinstitute/nfd_mathutil_opts
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Optimization of function to calculate the logged sum of exponentiated values
2014-06-17 17:07:42 -04:00
5e258bfeff
Minor optimization to function to calculate the log of exponentials.
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* Avoids calling Math.Pow whenever possible (skips -Inf and 0 values),
leads to better performance.
2014-06-17 15:26:10 -04:00
0ce28b78e0
Merge pull request #657 from broadinstitute/rp_ref_model_pipeline_noMQ_indels
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Using MQRanksum for indels was a bad idea according to the knowledgebase...
2014-06-16 11:29:11 -04:00
9390c56d52
Using MQRanksum for indels was a bad idea according to the knowledgebase. Removing from the ref model pipeline. Indels create mapping quality biases that aren't indicitive of error.
2014-06-16 11:28:33 -04:00
2e78815055
Added missing arguments to GenotypeGVCFs
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- New arguments are nda, hets, indelHeterozygosity, stand_call_conf, stand_emit_conf, ploidy, and maxAltAlleles
- Addresses PT 70110918
- To do this, moved those arguments out of the StandardCallerArgumentCollection into a new GenotypeCalculationArgumentCollection, which is now included as a member of SCAC
2014-06-16 08:10:54 -04:00
838304cc89
Merge pull request #656 from broadinstitute/cww_fastSiblingIBD
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Added licenses to siblingibd classes
2014-06-13 11:37:31 -04:00
01380d20a5
Added licenses to siblingibd classes
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touch files to add licenses
2014-06-13 10:11:42 -04:00
164d270447
Merge pull request #651 from broadinstitute/cww_fastSiblingIBD
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Created a new tool, SiblingIBD, which finds Identical-By-Descent regions...
2014-06-13 09:51:33 -04:00
ba1d23e535
Created a new tool, SiblingIBD, which finds Identical-By-Descent regions in two siblings.
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-When parental genotypes are available, implements an HMM on genotype observations in the quartet.
-Outputs IBD regions as well as per-site posterior probabilities of being in each IBD state.
-Includes an experimental heuristic based mode for when parental genotypes are not available.
-Made a method in MendelianViolation public static to reuse code.
-Added the mockito library to private/gatk-tools-private/pom.xml
2014-06-13 09:41:37 -04:00
fbc75c8e14
Merge pull request #654 from broadinstitute/rp_gvcf_indexing_strategy
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Adding the required GVCF indexing strategy arguments.
2014-06-12 10:45:25 -04:00
b61b16ac6d
Adding the required GVCF indexing strategy arguments.
2014-06-12 10:41:36 -04:00
5493126034
Merge pull request #653 from broadinstitute/rp_updated_ref_model_qscript
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Updating the ref model pipeline qscript.
2014-06-12 09:52:17 -04:00
58e9e7df95
Updating the ref model pipeline qscript.
2014-06-12 09:51:33 -04:00
3079755b4c
Merge pull request #646 from broadinstitute/ks_disable_distribution_with_private
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Add maven -Pgsadev flag to build private jars only
2014-06-11 11:00:31 -04:00
f082572593
If passed -Pgsadev, don't build the distribution package.
2014-06-10 23:33:33 -04:00
a20da6b9aa
Merge pull request #650 from broadinstitute/xhmm_Qscript
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For XHMM and Depth-of-Coverage Qscripts, add ability for user to input s...
2014-06-10 10:20:21 -04:00
a1868e8b82
For XHMM and Depth-of-Coverage Qscripts, add ability for user to input sample renaming file at the GATK level using existing GATK flag (--sample_rename_mapping_file) and custom pre-processing code. For XHMM Qscript, add scatter-gather for Discovery and Genotype stages.
2014-06-09 23:49:54 -04:00
ea98a59c78
Stop downloading GATK reports from legacy AWS account
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Our old AWS account is due to be deactivated today. Starting tonight,
we'll no longer attempt to download GATK reports from it.
2014-06-06 15:19:28 -04:00
4ea53f7132
Merge pull request #647 from broadinstitute/pd_output_dir_check
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Ensure that output files are specified in a writeable location
2014-06-03 10:07:24 -04:00
4eb9858461
Ensure that output files are specified in a writeable location
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-PT 69579780
2014-06-02 21:13:59 -04:00
droazen
Khalid Shakir
Ryan Poplin
Eric Banks
ldgauthier
jmthibault79
Phillip Dexheimer
kshakir
Nigel Delaney
Nigel Delaney
Chris Whelan
Menachem Fromer