db92671b7f
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-15 13:32:07 -04:00
7599f94296
Updating large-scale validation script to new UG syntax
2012-08-15 13:31:45 -04:00
87e41c83c5
In AlleleCount stratification, check to make sure the AC (or MLEAC) is valid (i.e. not higher than number of chromosomes) and throw a User Error if it isn't. Added a test for bad AC.
2012-08-14 15:02:30 -04:00
8e3774fb0e
Fixing behavior of the --regenotype argument in SelectVariants to properly run in GenotypeGivenAlleles mode. Added integration tests to cover recent SV changes.
2012-08-14 14:21:42 -04:00
34b62fa092
Two changes to SelectVariants: 1) don't add DP INFO annotation if DP wasn't used in the input VCF (it was adding DP=0 previously). 2) If MLEAC or MLEAF is present in the original VCF and the number of samples decreases, remove those annotations from the VC.
2012-08-14 12:54:31 -04:00
cfb994abd2
Trivial removal of ununsed variable (mentioned in resolved JIRA entry)
2012-08-13 22:55:02 -04:00
f809f24afb
Removed SelectHeader's --include_reference_name option since the reference is always included.
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In SelectHeaders instead of including the path to the file, only include the name of the reference since dbGaP does not like paths in headers.
2012-08-13 16:49:27 -04:00
22b4466cf5
Added setupRetry() to modify jobs when Queue is run with '-retry' and jobs are about to restart after an error.
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Implemented a mixin called "RetryMemoryLimit" which will by default double the memory.
GridEngine memory request parameter can be selected on the command line via '-resMemReqParam mem_free' or '-resMemReqParam virtual_free'.
Java optimizations now enabled by default:
- Only 4 GC threads instead of each job using java's default O(number of cores) GC threads. Previously on a machine with N cores if you have N jobs running and java allocates N GC threads by default, then the machines are using up to N^2 threads if all jobs are in heavy GC (thanks elauzier).
- Exit if GC spends more than 50% of time in GC (thanks ktibbett).
- Exit if GC reclaims lest than 10% of max heap (thanks ktibbett).
Added a -noGCOpt command line option to disable new java optimizations.
2012-08-13 15:43:05 -04:00
6ad75d2f5c
Reverting changes to BCF2 ranges
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-- The previously expanded ones are actually the missing values in the range. The previous ranges were correct. Removed the TODO to confirm them, as they are now officially confirmed
2012-08-13 15:06:28 -04:00
4d3fad38e9
Increase allowable range for BCF2 by -1 on low-end
2012-08-13 14:20:26 -04:00
4cbd11faf5
Fixed spelling error in BQSR.R
2012-08-13 10:01:33 -04:00
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
Guillermo del Angel
Eric Banks
Khalid Shakir
Mark DePristo
Ami Levy Moonshine
Joel Thibault
Ryan Poplin
David Roazen
Mauricio Carneiro