a5c65fc133
Debugging information to print out the Query tracks
2011-08-28 18:54:49 -04:00
d1b2b4ece9
Simple R script to analyse node performance
2011-08-28 16:40:38 -04:00
796ba34f6d
Simple script that can be used to access farm node performance
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-- spawns bundle dbsnp countrod that takes ~15 minutes to complete in general
-- import cleanup for RodPerformanceGoals
2011-08-28 15:09:50 -04:00
7542d29507
Oops, enabling default displays again
2011-08-28 12:07:38 -04:00
84704aaee3
Support for exechosts. Only displays by default in the gantt chart as jobname @ exechosts.
2011-08-28 12:06:41 -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
810a71c631
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-27 10:50:15 -04:00
1ceb020fae
UnitTests for RScript
2011-08-27 10:50:05 -04:00
ede4b0a116
Now includes the standard deviation in the average parameter results
2011-08-27 09:57:10 -04:00
50908fe285
Enable conditional inclusion of documentation for hidden features in GATKDocs.
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To include documentation for hidden features in the generated GATKDocs,
run with -Dgatkdocs.include.hidden=true
I will enable this flag when bamboo generates GATKDocs for unstable.
2011-08-27 03:38:01 -04:00
ccfed5d64d
Enable Contracts for Java by default for test targets.
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Contracts remain disabled for non-test build targets. To enable for
non-test targets, run with -Duse.contracts=true. To disable for test
targets, run with -Duse.contracts=false.
2011-08-27 02:45:47 -04:00
beb947d3cc
Standalone program to create an XML index of the GSA pipeline directory suitable for loading in IGV.
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This is a replacement for an ancient Perl script that will soon be retired.
2011-08-26 14:48:38 -04:00
5a6ae954bf
Added VCF streaming to tribbleVsGATK
2011-08-26 14:04:48 -04:00
bd92a1b220
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-26 13:24:26 -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
6e66f1c243
Removing code that cleans up the assembly graph for purposes of display. There seems to be bugs
2011-08-26 12:36:12 -04:00
8f150c6764
Assembly debug mode now uses smith-waterman to locally align all haplotypes and outputs to a bam file instead of first writing a fasta file and using bwa-sw outside of the GATK.
2011-08-26 10:43:40 -04:00
8f90a22555
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-26 10:16:56 -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
c11ddf3da3
Enchancements to queueJobReport
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-- Runtimes are in seconds, not milliseconds
-- Job names are shown in the gantt chart
-- axis names are clearer
-- documentation for all of the function
2011-08-26 09:17:09 -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
6bd3959ff2
Now shows job scheduling over time
2011-08-26 00:19:50 -04:00
34fb6ef798
SitesVsGenotypes should only be on chr1
2011-08-26 00:18:09 -04:00
c0e55c5ca4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-25 22:42:27 -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
6d8851eb63
Added option to control memory usage of DoC merging step
2011-08-25 22:12:54 -04:00
03a655023c
Must explicitly enable multithreaded tests
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-- Avoids sending nt 8 jobs to the unsuspecting farm
2011-08-25 19:41:08 -04:00
1a50a251d8
Draft version of report
2011-08-25 17:03:50 -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
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
Mark DePristo
David Roazen
Ryan Poplin
Eric Banks
Menachem Fromer
Guillermo del Angel
Mauricio Carneiro