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
5b56c83401
Don't output variants that on the edges of the haplotype, far away from the original interval.
2011-08-29 11:15:07 -04:00
661d658a0e
Updating smith-waterman parameters for the general case of aligning both with indels and snps simultaneously
2011-08-29 09:49:34 -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
f9afc5876a
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-29 08:04:39 -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
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
...
-- 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
77426d0fe1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-28 09:31:15 -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.
...
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.
...
This is a replacement for an ancient Perl script that will soon be retired.
2011-08-26 14:48:38 -04:00
dd2cf7d81e
Evaluating the likelihood of a haplotype should only use the passing reads
2011-08-26 14:36:28 -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
...
-- 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
...
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
Eric Banks
Ryan Poplin
Mark DePristo
David Roazen
Menachem Fromer
Guillermo del Angel