4f4ff5c327
Merge pull request #682 from broadinstitute/ks_revert_md5_db_per_test
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Reverting md5 db per test
2014-07-11 03:42:18 +08:00
193e389b41
Merge pull request #679 from broadinstitute/eb_better_tail_merging_PT74222522
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Improved tail merging: now tails can be merged to branches that are not ...
2014-07-10 13:54:33 -04:00
598b481733
Merge pull request #671 from broadinstitute/vrr_omniploidy_assesment_na12878
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Now AssessNA12878 can handle different input ploidy for omniploidy asses...
Story:
https://www.pivotaltracker.com/story/show/74469346
2014-07-10 13:19:32 -04:00
18f6d56b4c
Revert "Using the base directory for each test run when outputting MD5DB mismatches."
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This reverts commit f192f032a153755a84b1d682f6e652a7c6787fb9.
2014-07-11 01:11:25 +08:00
cc09ef9190
Revert "Appending to md5db in the gatkdir, with additional logging."
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This reverts commit 0aa2884f7b006f5d48c325bf942b92c183e45074.
2014-07-11 01:11:20 +08:00
a105cc4c0a
Merge pull request #681 from broadinstitute/dr_md5mismatch_generator_script
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Shell script to generate md5 mismatches file from a Bamboo log of an integration test run
2014-07-10 10:40:09 -04:00
af0aab8791
Shell script to generate md5 mismatches file from a Bamboo log of an integration test run
2014-07-10 10:32:10 -04:00
1d97b4a191
Improved tail merging: now tails can be merged to branches that are not entirely reference.
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This is useful for e.g. cases where there are SNPs on insertions. Before tails were forced to be merged
(incorrectly) only to a reference node, but now they can be merged to any path in the graph from which they
directly branch.
Also, I've transferred over Ryan's code to refuse to process kmer sizes such that there are non-unique kmers
in the reference sequence with them.
2014-07-10 08:57:01 -04:00
aecd34d274
Merge pull request #677 from broadinstitute/ks_md5_db_per_test_type
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Appending to md5db in the gatkdir, with additional logging.
2014-07-10 17:53:24 +08:00
5eee065133
Merge pull request #674 from broadinstitute/rp_improve_genotyping
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Improvements to genotyping accuracy.
2014-07-09 16:03:09 -04:00
a7d1904c63
Appending to md5db in the gatkdir, with additional logging.
2014-07-10 03:58:47 +08:00
cd2c5ce1b2
Now AssessNA12878 can handle different input ploidy for omniploidy assessment where we may run HC as if it was a haploid, tetraploid (and so forth) organism.
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For example, when the input is Haploid it is considered ok to have a FN if the actual genotype is 0/1 as there is 50% chance to not call it at all.
Also it considers that the genotype call is concordant as long as the AC is as close as it can be to the 50% percent given the ploidy. So for a 0/1 true call is it ok
to have a 0 or 1 call in haploids and also 0/0/1/1 in tetraploid, and also 0/0/1 or 0/1/1 with triploid input, but it is not a 0/0/0/1 in tetraploids or 0/0/0/0/1/1 with hextaploid input.
Story:
http://www.pivotaltracker.com/story/show/72090992
Changes:
AssessNA12878 has a new argument (-ploidy / --inputPloidy) to indicate the expected ploidy of the input.
By default this is the obvious choice of 2 as NA12878 is human.
In the input has calls with a different ploidy it will complain with an user exception.
Also some refactoring has been done to make the code a bit more concise in some parts.
2014-07-09 14:42:33 -04:00
a85bc0b577
Merge pull request #678 from broadinstitute/dr_remove_junit_imports
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Remove junit imports in the test suite
2014-07-09 14:40:38 -04:00
74a7674d70
Improvements to genotyping accuracy.
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-- Global mismapping penalty was only applied to the reference haplotype. This led to problems with overlapping events, mostly STR haplotypes. Now the penalty is applied to every haplotype.
-- We subset the reads down to only those which overlap the event (after assembly based realignment) for likelihood calculations.
2014-07-09 13:11:07 -04:00
719e685759
Remove junit imports in the test suite
2014-07-09 12:09:27 -04:00
465c5ed9b0
Merge pull request #676 from broadinstitute/cww_junit_assert
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Replace improper use of org.junit imports with org.testng.
2014-07-08 16:12:34 -04:00
635b9bd1af
Replace improper use of org.junit imports with org.testng.
2014-07-08 16:07:39 -04:00
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
kshakir
Ryan Poplin
Valentin Ruano Rubio
Khalid Shakir
droazen
Eric Banks
Chris Whelan
ldgauthier
jmthibault79
Phillip Dexheimer
Nigel Delaney
Nigel Delaney