08fb21f127
Removing hostname
2011-08-24 16:45:50 -04:00
d50474f14c
Merged bug fix from Stable into Unstable
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resolved conflicts by maintaining all the changes in UNSTABLE where this bug had already been fixed.
Conflicts:
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
2011-08-24 16:06:36 -04:00
dc8398e165
fixing bai output for indel cleaning.
2011-08-24 15:58:34 -04:00
da5e6b52e7
Refactoring the smith-waterman and genotyping-related pieces into their own engine
2011-08-24 15:54:17 -04:00
06e30a81d1
Fixes throughout for getting job information
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-- no more hostname -- it's just not going to be important
2011-08-24 15:30:09 -04:00
29c7b10f7b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-24 15:18:58 -04:00
e5008aba00
Output the top two haplotypes as a variant call by running smith-waterman alignment against the reference and calling any difference as variation. This is the first verion that runs end-to-end by taking in reads as bam file and writing out variant calls in VCF.
2011-08-24 15:18:44 -04:00
4918519a58
No more NPE in getRuntime() when you cntr-c out of Queue
2011-08-24 14:14:01 -04:00
16d8360592
QJobReport is now the official capability name
2011-08-24 13:59:14 -04:00
d047c19ad1
Writes output to file
2011-08-24 13:52:05 -04:00
61f5968807
Change indel/snp selection to new arguments
2011-08-24 13:42:23 -04:00
3ae68e2397
JobLogging trait now writes out GATKReport log of jobs
2011-08-24 13:36:39 -04:00
e618cb1e79
a) Renamed/expanded SelectVariants arguments that choose particular kinds of variants and particular allelic types, now instead of -Indels or -SNPs we can specify for example -selectType [MIXED|INDEL|SNP|MNP|SYMBOLIC]. To select biallelic, multiallelic variants, use -restrictAllelesTo [BIALLELIC|MULTIALLELIC]. Corresponding gatkdocs changes.
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b) More useful AC,AF logging in VariantsToTable with multiallelic sites: instead of logging comma-separated values, log max value by default. Hidden, experimental argument -logACSum to log sum of ACs instead. This is due to extreme slowness of R in parsing strings to tokens and computing max/sum itself (~100x slower than gatk).
c) Added integrationtest for new SelectVariants commands
2011-08-24 12:25:50 -04:00
cd12f7f286
Fixed list dependency
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Instead of creating a bam list file, I dynamically create a scala list and pass as parameters. This way the intermediate bam files don't get deleted before they should.
2011-08-24 11:12:46 -04:00
219252a566
Adapting to the new RodBinding framework
2011-08-24 11:12:46 -04:00
28ee6dac41
Fixed spelling mistake
2011-08-24 10:14:45 -04:00
f37875600a
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-24 09:02:44 -04:00
1ecbf05aae
Avoid segfaults due to out of date and possibly abandonded LSF DRMAA implementation when use'ing LSF instead of .combined_LSF_SGE
2011-08-23 23:49:36 -04:00
b8bc03bb42
JobRunInfo improvements
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-- dry-run now adds some info, for testing
-- InProcessRunner adds some, but not all, of the information we want
2011-08-23 17:11:22 -04:00
569e1a1089
Walker.isDone() aborts execution early
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-- Useful if you want to have a parameter like MAX_RECORDS that wants the walker to stop after some number of map calls without having to resort to the old System.exit() call directly.
2011-08-23 16:53:06 -04:00
31ec6e316c
First implementation of JobRunInfo
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-- onExecutionDone(Map(QFunction, JobRunInfo)) is the new signature, so that you can walk over your jobs and inspect their success/failure and runtime characteristics
2011-08-23 16:51:54 -04:00
7d653c48b1
Consensus Reads call close() when crossing a gap
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addToAlignment returns a collection of SAMRecords
Not fully working yet
2011-08-23 16:07:10 -04:00
08e5503a60
Likelihood engine now gives non-zero likelihoods. Using HMM function that can handle context specific gap open and gap continuation penalties
2011-08-23 13:43:43 -04:00
a1a1fac9e4
Likelihood engine now gives non-zero likelihoods. Using HMM function that can handle context specific gap open and gap continuation penalties
2011-08-23 13:43:07 -04:00
3c37d841db
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-23 13:05:12 -04:00
6e2552a9ef
Merge fix
2011-08-23 12:40:43 -04:00
8b7a0b3b62
Two new arguments to SelectVariants to exclude either multiallelic or biallelic sites from input vcf
2011-08-23 12:40:01 -04:00
ac36271457
Fixed extra reads showing up in Variable Sites
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Reads that were not hard clipped for the variable site no longer show up in output file
Walker now uses unclippedStart of Read to determine position in the sliding Window
2011-08-23 11:26:00 -04:00
6d6feb5540
Better error message when you cannot determine a ROD type because the file doesn't exist or cannot be read
2011-08-23 10:56:37 -04:00
bcc0cae89e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-23 10:51:24 -04:00
bd26de9741
Resurrect IndelCountCovariates walker, update to new rod system. IndelCountCovariate (singular) seems broken, not to be used for now (but it's not very useful anyway)
2011-08-23 10:50:55 -04:00
a9ba945595
onExecutionDone(jobs, successFlag) added to QScript.
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-- This function is called when the Qscript ends, so scripts can overload this function if they want to run some code after all of the jobs have completed
2011-08-23 10:09:51 -04:00
9597d6edad
Commented out debug info
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Bases of incoming reads no longer print on screen
2011-08-23 10:04:11 -04:00
feeab6075f
Merging ReduceReads development with unstable repo
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It is time to bring the ReadClipper class to the main repo. Read Clipper has tested functionality for soft and hard clipping reads. I will prepare thorough documentation for it as it will be very useful for the assembler and the GATK in general.
2011-08-22 23:03:03 -04:00
af4db34407
Apparently git can't deal with renaming a file that only changes capitalization?
2011-08-22 22:00:04 -04:00
ee68713267
Further Bug fixes to CountVariants: stratifications were wrong in case genotypes had no-calls, for example if we stratified by sample and a sample had a no-call, this no-call was considered a true variant and counts were incorrectly increased
2011-08-22 20:42:47 -04:00
c270384b2e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-22 20:39:32 -04:00
8ae24912f4
a) Misc fixes in Phase1 indel vqsr script,
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b) More R-friendly VariantsToTable printing of AC in case of multiple alt alleles
c) Rename FixPLOrderingWalker to FixGenotypesWalker and rewrote: no longer need older code, replaced with code to replace genotypes with all-zero PL's with a no-call.
2011-08-22 20:39:06 -04:00
136f0eb685
Creating sample-bam list instead of joining
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This should save us at least one day in the trio decoy processing.
2011-08-22 18:03:39 -04:00
04d8bcaf19
Fixed bai removal on picard tools
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BAM index files were not being deleted because picard replaces the name of the file with bai instead of appending to it.
2011-08-22 18:03:39 -04:00
8aed151a71
Created RevertSam queue class
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Class for the picard tool RevertSam with all the options for queue scripts.
2011-08-22 18:03:39 -04:00
caebc88e9a
Consensus mode and new RodBinding framework.
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The DPP was not using the parameter correctly. It didn't matter for the default option (which is the only one we have been testing) but it would not work for knowns only or smith waterman. It is fixed now.
It now complies with the new rod binding framework.
2011-08-22 18:03:39 -04:00
85c5a6f890
Merge branch 'rodTesting'
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Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/performance/ProfileRodSystem.java
2011-08-22 17:43:47 -04:00
e728e407d9
First pass Queue script to test progress on ROD refactoring towards Eric+Mark goals
2011-08-22 17:40:35 -04:00
fe7d3ee236
A bit of refinement of the modes
2011-08-22 17:40:02 -04:00
649f134536
Added mode argument that lets you test separately tribble IO and GATK
2011-08-22 17:33:41 -04:00
1eab9be35d
Now with accurate javadoc
2011-08-22 17:25:15 -04:00
3612a3501d
info, not warn, about dynamic type determination
2011-08-22 17:24:51 -04:00
9fb208c8f0
First Working Implementation
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Used ReadClipper to hardClip to VariableRegion
Runs 9,000,000-9,050,000
close() not tested
Does not use toSAMRecord() method
*Commented out debug info
2011-08-22 16:46:24 -04:00
dc42571dd9
Only create the genotype map when necessary
2011-08-22 15:40:36 -04:00
Mark DePristo
Mauricio Carneiro
Ryan Poplin
Guillermo del Angel
Khalid Shakir
Roger Zurawicki
Eric Banks