c6d8df8639
queueJobReport is a public feature of Queue
2011-08-29 17:20:54 -04:00
1e5001b447
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-29 17:04:21 -04:00
3af001fff2
Bugfix for file that must not exist on disk
2011-08-29 17:00:10 -04:00
3b09d42ed6
Now only prints 1 warning message about duplicate headers in simpleMerge
2011-08-29 14:41:29 -04:00
c2f0db969b
Don't use the default deletion value from UG if not asking to have it set
2011-08-29 13:48:10 -04:00
bb7a37e8f2
We need to allow reference calls in the input VCF for the GenotypeAndValidate walker when using the BAM as truth so that we can test supposed monomorphic calls against the truth.
2011-08-29 13:19:35 -04:00
bc252a0d62
misc minor bug fixes in assembly. Increasing the minimum number of bad variants to be used in negative model training in the VQSR
2011-08-29 08:11:31 -04:00
61633c95a8
Default jobreport is now jobPrefix, so you see logs like Q-2508.jobreport.txt
2011-08-28 19:19:45 -04:00
a5c65fc133
Debugging information to print out the Query tracks
2011-08-28 18:54:49 -04:00
b38de1fa35
Now captures the exechost in the job report
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-- Works for in process, shell, and LSF runners
-- Cleanup of debugging output
2011-08-28 12:05:56 -04:00
7bf006278d
Moved ResolveHostname to general utils as a static function
2011-08-28 12:04:16 -04:00
ccec0b4d73
AnalyzeCovariates uses the general RScript system now
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-- Convenience constructor for collection for testing
-- callRScript() now accepts Objects not Strings, for convenience
2011-08-27 12:54:13 -04:00
1ceb020fae
UnitTests for RScript
2011-08-27 10:50:05 -04:00
e37a638e09
Fix for disallowed characters in GATKReportTable
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-- Illegal characters are automatically replaced with _
2011-08-26 13:24:06 -04:00
0cb1605df0
Clean documentation for JobRunInfo
2011-08-26 09:22:58 -04:00
415d5d5301
LSF long times are in seconds, convert to milliseconds to meet standard
2011-08-26 09:18:28 -04:00
c0503283df
Spelling fix requires md5 updates
2011-08-26 07:40:44 -04:00
eef1ac415a
Merge branch 'master' into rodTesting
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
2011-08-26 00:35:41 -04:00
9b7512fd94
Just because there's a ref base doesn't mean the VC needs to be padded
2011-08-25 22:42:14 -04:00
e03dfdb0ab
Automatic iteration field addition works properly.
2011-08-25 16:59:02 -04:00
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
09a729da3a
Removing incorrect comment
2011-08-25 15:42:52 -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
0f4be2c4a4
Argument to disable queueJobReport entirely
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-- Minor improvements to RodPerformanceGoals
2011-08-25 13:32:03 -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
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
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
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
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
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
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
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
Eric Banks
Ryan Poplin
Mauricio Carneiro
Guillermo del Angel
Khalid Shakir