e01273ca7c
Queue now writes out queueJobReport.pdf
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-- General purpose RScript executor in java (please use when invoking RScripts)
-- Removed groupName. This is now analysisName
-- Explicitly added capability to enable/disable individual QFunction
2011-08-25 16:57:11 -04:00
e132c97098
*Glitch at Low Coverage Gap
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Around 19193000 a consensus read is correctly made but it is off by almost 100 bp
Otherwise, working
2011-08-25 16:56:36 -04:00
09a729da3a
Removing incorrect comment
2011-08-25 15:42:52 -04:00
3eed5af2f7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-25 15:37:35 -04:00
8bbef79fc2
Create clipped alleles during allele parsing instead of creating a full VC, clipping alleles, and regenerating the VC from scratch.
2011-08-25 15:37:26 -04:00
c34b4b20aa
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-25 14:58:15 -04:00
6347317ba8
Too fast to commit last time
2011-08-25 14:58:10 -04:00
0f4be2c4a4
Argument to disable queueJobReport entirely
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-- Minor improvements to RodPerformanceGoals
2011-08-25 13:32:03 -04:00
999dff1252
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-25 13:28:23 -04:00
1bf0fcd7a4
Obvious bug fix in HSP script: not enough to fix test yet, though
2011-08-25 13:27:55 -04:00
d81122cf5f
Fixed up so that all modes can go through multiple iterations
2011-08-25 13:22:39 -04:00
d65faf509c
Default output name for Queue JobReport is queue_jobreport.gatkreport.txt
2011-08-25 13:15:20 -04:00
a7d6946b22
Refactored QJobReport and QFunction, which is now automatically tracked
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-- All QFunctions, including sg ones, are tracked
-- Removed memory information
2011-08-25 13:13:55 -04:00
08f6c3eea9
companion gantt charts for Q runtimes
2011-08-25 12:59:59 -04:00
e5ca61e371
Bug fix for multiallelic events in haplotype caller
2011-08-25 11:09:39 -04:00
5e0660e27d
Adding debug option to output all possible haplotypes in fasta format for use with bwa
2011-08-25 10:31:10 -04:00
16caca0822
BLASR BAMs and new BWA parameters
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*Added the functions to turn a BLASR generated BAM file into a usable BAM file.
*Modified the bwa parameters according to test results from NA12878 pb2k dataset.
2011-08-24 17:04:07 -04:00
e3f5d7067a
Added ReorderSam queue binding
2011-08-24 17:03:11 -04:00
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
Mark DePristo
Roger Zurawicki
Eric Banks
Ryan Poplin
Guillermo del Angel
Mauricio Carneiro
Khalid Shakir