aab417c94d
Fix missing argument in unittest
2012-08-12 13:58:14 -04:00
f032e0aba4
A bit better output for ContextCovariate context size logging
2012-08-12 13:45:52 -04:00
243af0adb1
Expanded the BQSR reporting script
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-- Includes header page
-- Table of arguments (Arguments)
-- Summary of counts (RecalData0)
-- Summary of counts by qual (RecalData1)
-- Fixed bug in output that resulted in covariates list always being null (updated md5s accordingly)
-- BQSR.R loads all relevant libaries now, include gplots, grid, and gsalib to run correctly
2012-08-12 13:45:14 -04:00
458bbdee8f
Add useful logger.info telling us the mismatch and indel context sizes
2012-08-12 10:27:05 -04:00
6fefdaf428
"update integration tests in CombineVariantsIntegrationTest"
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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-10 17:00:35 -04:00
4968daf0a5
update integration tests at CombineVariantsIntegrationTest
2012-08-10 16:58:05 -04:00
1a87f67258
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-10 15:11:12 -04:00
40f0320a1c
When adding a unit test to LIBS for X and = CIGAR operators, I uncovered a bug with the implementation of the ReadBackedPileup.depthOfCoverage() method.
2012-08-10 14:58:29 -04:00
eca9613356
Adding support of X and = CIGAR operators to the GATK
2012-08-10 14:54:07 -04:00
949ed207ca
capMaxAllelesForIndels -> capMaxAltAllelesForIndels
2012-08-10 14:25:13 -04:00
b17edaad66
Change memoryValues to List[Double]
2012-08-10 14:25:12 -04:00
32a66b5ae4
Add -nt parameter
2012-08-10 14:25:12 -04:00
2a113977a9
Resolving merge conflicts with the new MD5s
2012-08-10 11:47:00 -04:00
5f82ffd5d8
Adding LowQual filter to the output of the HaplotypeCaller.
2012-08-10 11:25:14 -04:00
d7d7ccf789
Revert unintentional license change
2012-08-09 17:10:47 -04:00
d56a4631dc
Update cofoja version in build.xml
2012-08-09 17:08:43 -04:00
68fb04b8f7
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable into testing
2012-08-09 16:48:22 -04:00
3362584014
Updating cofoja to the latest version
2012-08-09 16:36:18 -04:00
06258c8a01
BCF2 optimizations
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-- Added Write method to BCF2 types that directly converts int value to byte stream. Deleted writeRawBytes(int)
-- encodeTypeDescriptor semi-inlined into encodeType so that the tests for overflow are done in just one place
-- Faster implementation of determineIntegerType for int[] values
2012-08-09 16:36:18 -04:00
c6bd9b15ff
BCF2 optimizations
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-- BCF2Type enum has an overloaded method to read the type as an int from an input stream. This gets rid of a case statement and replaces it with just minimum tiny methods that should be better optimized. As side effect of this optimization is an overall cleaner code organization
2012-08-09 16:36:18 -04:00
9a0dda71d4
BCF2 optimizations
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-- All low-level reads throw IOException instead of catching it directly. This allows us to not try/catch in readByte, improving performance by 5% or so
-- Optimize encodeTypeDescriptor with final variables. Avoid using Math.min instead do inline comparison
-- Inlined willOverflow directly in its single use
2012-08-09 16:36:18 -04:00
9887bc4410
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-09 16:31:06 -04:00
f4c72a26d5
A few quick, minor findbugs fixes.
2012-08-09 16:30:58 -04:00
c7f22e410f
A few quick, minor findbugs fixes.
2012-08-09 16:22:08 -04:00
abb168e1ba
Merged bug fix from Stable into Unstable
2012-08-09 16:09:58 -04:00
67d4148b32
Fixing but reported by Thomas in the forum where reads were soft-clipped beyond the limits of the contig and ReduceReads was failing with a NoSuchElement exception. Now we hard clip anything that goes beyond the boundaries of the contig.
2012-08-09 15:58:18 -04:00
58420098ac
Merged bug fix from Stable into Unstable
2012-08-09 13:02:23 -04:00
c6132ebe26
Fixed divide by zero bug when downsampler goes over regions where reads are all filtered out. Added Guillermo's bug report as an integration test
2012-08-09 13:02:11 -04:00
def077c4e5
There's actually a subtle but important difference between foo++ and ++foo
2012-08-09 12:42:50 -04:00
e48727dae3
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-09 10:31:10 -04:00
5be7e0621d
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-09 09:58:34 -04:00
71ee8d87b3
Rename per-sample ML allelic fractions and counts so that they don't have the same name as the per-site INFO fields, and clarify wording in VCF header
2012-08-09 09:58:20 -04:00
6230b49a86
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-08 21:44:43 -04:00
35cec8530c
Make coverage threshold in FindCoveredIntervals a command-line argument
2012-08-08 21:44:24 -04:00
250ffd2ad7
Merged bug fix from Stable into Unstable
2012-08-08 15:50:07 -04:00
78c1556186
Fixing ReduceReads downsampling bug -- downsampled reads were not being excluded from the read window, causing them to trail back and get caught by the sliding window exception
2012-08-08 15:49:31 -04:00
1223d77546
Removing argument from HaplotypeCaller that was made unneccesary by recent improvements to triggering around large events
2012-08-08 15:13:20 -04:00
0a2a646a52
Other random FindBugs fixes
2012-08-08 14:56:27 -04:00
f652d7806e
FindBugs found an infinite loop in the code
2012-08-08 14:44:49 -04:00
4c84cc9486
Quick pass of FindBugs 'should be static inner class' fixes.
2012-08-08 14:42:06 -04:00
a0196c9f5b
Quick pass of FindBugs 'method invokes inefficient Number constructor' fixes.
2012-08-08 14:34:16 -04:00
4b2e3cec0b
Quick pass of FindBugs 'inefficient use of keySet iterator instead of entrySet iterator' fixes for core tools.
2012-08-08 14:29:41 -04:00
3e2752667c
Intermediate checkin for ReducedReads with HaplotypeCaller - change min read count over k-mer to average count over k-mer when doing assembly of a reduced read (not optimal, currently trying max and then will decide on best approach), fix merge conflicts
2012-08-08 12:07:33 -04:00
a7811d673f
Update URL for phone home / GATK key documentation output by the GATK upon error
2012-08-08 09:29:54 -04:00
cda8d944b7
Bugfixes for BCF with VQSR
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-- Old version converted doubles directly from strings. New version uses VariantContext getAttributeAsDouble() that looks at the values directly to determine how to convert from Object to Double (via Double.valueOf, (Double), or (Double)(Integer)).
-- getAttributeAsDouble() is now smart in converting integers to doubles as needed
-- Removed unnecessary logging info in BCF2Codec
-- Added integration tests to ensure that VQSR works end-to-end with BCF2 using sites version of the file khalid sent to me
-- Added vqsr.bcf_test.snps.unfiltered.bcf file for this integration test
2012-08-07 17:22:39 -04:00
80b94a4f9a
AdaptiveContexts implement pruning to a given chi2 p value
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-- Added bonferroni corrected p-value pruning, so you tell it how significant of a different you are willing to collapse in the tree, and it prunes the tree down to this maximum threshold
-- Penalty is now a phred-scaled p-value not the raw chi2 value
-- Split command line arguments in VisualizeContextTree into separate arguments for each type of pruning
2012-08-07 17:22:39 -04:00
982c735c76
VisualizeAdaptiveTree now considers only leaf nodes when computing max/min penalty
2012-08-07 17:22:39 -04:00
15085bf03e
The UnifiedGenotyper now makes use of base insertion and base deletion quality scores if they exist in the reads.
2012-08-07 13:58:22 -04:00
2c76f71a03
Update -maxAlleles argument in integration tests
2012-08-06 22:48:04 -04:00
c66a896b8e
Fix UG integration test broken by new -maxAltAlleles nomenclature
2012-08-06 21:29:21 -04:00
Mark DePristo
Ami Levy Moonshine
Eric Banks
Joel Thibault
Ryan Poplin
David Roazen
Mauricio Carneiro
Guillermo del Angel