d7b951b6f3Finished up my reviews for megabase chr20:10M-11M. Fixed out of order record from earlier.
Eric Banks
2012-12-01 23:35:21 -0500
2849889af5Updating md5 for UG
Mark DePristo
2012-12-01 14:23:57 -0500
d0b8cc7773Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ami Levy-Moonshine
2012-12-01 00:08:25 -0500
969c995298work under development - catVariants. Changes to AssessRRQuals based on Eric todo comments. bug fix in CombineVariants
Ami Levy-Moonshine
2012-12-01 00:08:19 -0500
3105f13df3Merge pull request #4 from jsilter/master
depristo
2012-11-30 13:24:44 -0800
1100f0733bReviews for all unique omni poly sites on chr20
Mark DePristo
2012-11-30 16:23:27 -0500
02e98fa516Remove validate, add note to put it back in when public gatk catches up
Jacob Silterra
2012-11-30 16:08:00 -0500
8020ba14dbMinor cleanup of SAMDataSource as part of my system review
Mark DePristo
2012-11-30 15:04:33 -0500
66bbe46e5bMongoDBManager prints out meaningful information with toString
Mark DePristo
2012-11-30 14:38:45 -0500
3248ca3f91Validate MongoVariantContext on creation
Mark DePristo
2012-11-30 14:37:12 -0500
79dbcc205cMinor cleanup for working version of igv
Mark DePristo
2012-11-30 14:28:02 -0500
6b6a14cc6dMoving ConsensusSummarizer to its appropriate home in core of NA12878KB
Mark DePristo
2012-11-29 16:05:16 -0500
e1b5b562ebfix TrivalTask compile issues
Douglas Voet
2012-11-30 10:48:38 -0500
db2a045321Useful walker to establish minimum depth necessary for confident calling of different types of variants
Mauricio Carneiro
2012-11-29 22:13:24 -0500
0e1287a843Adding reviews for 1st 400kb of my target megabase (10-11) on chr20
Eric Banks
2012-11-29 16:15:45 -0500
97d29f203eAdd walltime changes to LSF - Check whether the specified attribute is available - Add pipeline test (disabled due to missing attribute)
Joel Thibault
2012-10-12 17:16:56 -0400
daf6269b65Setting the walltime
Johan Dahlberg
2012-10-01 11:28:46 +0200
f837e6ced7Refactored entire NA12878KB to allow us to easily build a na12878kb.jar for IGV integration
Mark DePristo
2012-11-29 14:38:09 -0500
a6c1fcd151Removed default use of @Output syntax. If compile completes for QScripts, sending runtime errors during execute.
kshakir
2012-11-29 13:31:08 -0500
52a6df4f1aAdd SummarizeConsensus walker that spits out information about the callsets in the KB
Mark DePristo
2012-11-29 13:07:20 -0500
ed7a89c0c7Merge pull request #3 from jsilter/master
depristo
2012-11-29 08:52:38 -0800
d9e8a414efFix NA12878DBArgumentCollectionUnitTest so it uses testng, and testCompareLocalRemoteLocators compare the right things
Jacob Silterra
2012-11-29 11:03:21 -0500
df2c26b554Rename NA12878DBArgumentCollectionTest to NA12878DBArgumentCollectionUnitTest
David Roazen
2012-11-28 22:50:20 -0500
b06e71cedfUse build jars in test classpaths by default
David Roazen
2012-11-28 20:44:09 -0500
add1ab5d0eFix status of largeScaleValidationPools for NA12878-KB
Eric Banks
2012-11-28 20:34:13 -0500
b9be8850e2Bugfixes to NA12878DBArgumentCollection and JSON and the GATK argument value injection system
Mark DePristo
2012-11-28 19:02:07 -0500
7b74bf6677Excluding large scale validation callsets from KB until further reviewed, rebuilding production server now
Mark DePristo
2012-11-28 18:41:49 -0500
4729f0858dExtractConsensusSites -include and -exclude callsets now works on supporting callsets not the actual name
Mark DePristo
2012-11-28 18:41:16 -0500
65357d26bcNew walker ExtractConsensusSites that extracts a VCF from the NA12878 Knowledge Base meeting criteria
Mark DePristo
2012-11-28 18:11:09 -0500
de7049463cNew walker ExtractConsensusSites that extracts a VCF from the NA12878 Knowledge Base meeting criteria
Mark DePristo
2012-11-28 16:58:59 -0500
ff8b3904e2Added many new resources to the NA12878 KB truth set
Eric Banks
2012-11-28 17:18:24 -0500
b2e699169cUpdate GATK packaging settings to package arbitrary resources
David Roazen
2012-11-28 15:26:05 -0500
a359d43f54Merge pull request #2 from jsilter/master
droazen
2012-11-28 12:05:47 -0800
26d9c41615Allow arbitrary resources to be packaged in the GATK jar, selecting among public/private/protected appropriately
David Roazen
2012-11-28 14:06:58 -0500
c30dc3c38fMerge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Chris Hartl
2012-11-28 14:35:25 -0500
c76c808268Reads are required to be sorted - Remove the extended_only case because it's outside intervals
Joel Thibault
2012-11-28 11:09:12 -0500
198923b597Add ActiveRegionReadState handling
Joel Thibault
2012-11-26 15:01:13 -0500
f0395b457aAdding the work-in-progress, experimental RepeatLengthCovariate to the BQSR so Chris can continue the development.
Ryan Poplin
2012-11-28 13:56:32 -0500
3463774f2aMerged bug fix from Stable into Unstable
Eric Banks
2012-11-28 13:26:52 -0500
6030605242Added quick check for creation of bad BAQ values associated with badly encoded base qualities; hopefully this can help us debug the non-reproducible issue seen by many users.
Eric Banks
2012-11-28 13:26:31 -0500
c676853731Merged bug fix from Stable into Unstable. Updating md5s
Mark DePristo
2012-11-28 12:54:36 -0500
a1d6461121Critical bugfix to AFCalcResult affecting UG/HC quality score emission thresholds
Mark DePristo
2012-11-28 11:35:41 -0500
cf56ca3bc9Call at known sites (initially from 1000G) at end of fastq2bam. DEV-272 #resolve #time 2m
Guillermo del Angel
2012-11-28 11:15:16 -0500
f95803ee05Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Chris Hartl
2012-11-28 10:49:16 -0500
fb1e525e0fMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Mark DePristo
2012-11-28 07:57:05 -0500
9fd1a3cb9cRemove echo from startNA12878kbServer.csh
Mark DePristo
2012-11-28 07:56:50 -0500
79bc878e6aAllow debugging to be set from the command line
Menachem Fromer
2012-11-27 22:37:41 -0500
1cc0b48caaAbstract connection to MongoDB so we can specify it through JSON file. Include 2 JSON spec files in GenomeAnalysisTK.jar
Jacob Silterra
2012-11-27 17:44:35 -0500
31069ffcedAdd HC pruning parameter option, as per Ryan's advice
Menachem Fromer
2012-11-27 17:21:22 -0500
c0a1d2fe31Rolling back merge changes that undid Doug's commits.
Mauricio Carneiro
2012-11-27 16:01:03 -0500
6f1eb65ec8Merge pull request #1 from jsilter/master
depristo
2012-11-27 12:35:18 -0800
b15edd9eb3Modifications so these classes can more easily be used as a library. In particular:
Jacob Silterra
2012-11-27 14:42:55 -0500
d10b858e0bFinalizing setupNA12878kb script for use in cron
Mark DePristo
2012-11-27 14:43:43 -0500
b40d3eb8aaMerged bug fix from Stable into Unstable
Eric Banks
2012-11-27 14:41:07 -0500
01abcc3e0fTests didn't like my note to Geraldine in the output logs; apparently it's tested in integration tests
Eric Banks
2012-11-27 14:40:49 -0500
ffb232bdf0NA12878 Knowledge Base modules use DEV by default if they modify the database, while accessors use PRODUCTION
Mark DePristo
2012-11-27 14:25:51 -0500
7e4b9c9e6eFix failing unit tests for VariantContextUtilsUnitTest
Mark DePristo
2012-11-27 10:12:39 -0500
4281498c2cImprovements to NA12878KnowledgeBase system
Mark DePristo
2012-11-26 15:31:26 -0500
9bfe39411eEqual overlap should match right/later region
Joel Thibault
2012-11-26 14:29:22 -0500
d83ad906efAdd profile range contract
Joel Thibault
2012-11-26 13:44:13 -0500
cc550b4145Add a read and interval on a different contig
Joel Thibault
2012-11-26 11:48:05 -0500
37eb6c92bfMerge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Chris Hartl
2012-11-27 12:39:50 -0500
9531e58445Merged bug fix from Stable into Unstable
Eric Banks
2012-11-27 11:00:50 -0500
4543ece088Fixing parsing of genomelocs that contain colons in the contig names (which is allowed by the spec) as reported on the forum. Added unit test for this case.
Eric Banks
2012-11-27 11:00:33 -0500
a82ec7ad80Merged bug fix from Stable into Unstable
Eric Banks
2012-11-27 10:27:08 -0500
e199562c25I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever).
Eric Banks
2012-11-27 10:26:17 -0500
b1969a66bdUpdate docs
Eric Banks
2012-11-27 08:24:41 -0500
cc72aaefebMinor efficiency: use >= instead of > in test
Eric Banks
2012-11-27 01:11:23 -0500
405f3c675dFix for GSA-649: GenomeLocSortedSet.overlaps is crazy slow. Also improved GenomeLocSortedSet.sizeBeforeLoc.
Eric Banks
2012-11-27 01:07:00 -0500
e27d677c13Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Ryan Poplin
2012-11-26 12:20:32 -0500
59cef880d1Updating HC integration tests because experimental, HC-specific annotations have been removed.
Ryan Poplin
2012-11-26 12:20:07 -0500
c3b7dd1374Misc cleanup in the HaplotypeCaller. Cleaning up unused arguments after recent changes to HC-GenotypingEngine
Ryan Poplin
2012-11-26 12:19:11 -0500
dcc339b35cMerge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
Chris Hartl
2012-11-26 11:39:01 -0500
4f7fa3009aI forget why I thought that the VariantAnnotator couldn't run multi-threaded because it works just fine. Now you can specify -nt with VA.
Eric Banks
2012-11-26 11:34:59 -0500
c0261f75ceMerging master and develop together
Mauricio Carneiro
2012-11-26 11:31:47 -0500
b15b62157aUse correct path in imports
Eric Banks
2012-11-26 10:09:13 -0500
3784bb5258Fixes to process all SNPs and indels simultaneously (even those at same site)
Menachem Fromer
2012-11-26 03:59:36 -0500
fedc4fde6cMerged bug fix from Stable into Unstable
Ryan Poplin
2012-11-25 21:55:55 -0500
d978cfe835Soft clipped bases shouldn't be counted in the delocalized BQSR.
Ryan Poplin
2012-11-25 21:55:29 -0500
9719ba7adcRemove -number example from the docs since it's no longer supported.
Eric Banks
2012-11-22 21:53:42 -0500
2306518ab6Fix to deal with 'proper' options of casting
Menachem Fromer
2012-11-22 01:45:18 -0500
d33a412b5fMerge branch 'master' of github.com:broadinstitute/gsa-unstable
Menachem Fromer
2012-11-22 01:42:29 -0500
48f271c5bdAdding 80% support for multi-allelic variants
Mark DePristo
2012-11-21 17:23:41 -0500
e14bfa9f5cUpdate reviews.vcf to have genotypes, and downstreams changes to tools to support this
Mark DePristo
2012-11-21 14:45:03 -0500
5d2ee32936Documentation and validation for NA12878 KB tools
Mark DePristo
2012-11-21 13:42:35 -0500
c68bc95db6Initial read mapping tests
Joel Thibault
2012-11-21 16:22:57 -0500
3ad9128800Add some reads - Move intervals and reads to init - Update intervals and reads
Joel Thibault
2012-11-20 13:11:24 -0500
3fa3b00f4aAdd ActiveRegion tests and refactor
Joel Thibault
2012-11-19 14:45:19 -0500
e8defcb20dTest multiple bases and intervals
Joel Thibault
2012-11-19 14:44:00 -0500
c08b782743Count isActive calls directly
Joel Thibault
2012-11-19 14:39:06 -0500
7580a487f3Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Eric Banks
2012-11-21 16:20:49 -0500
4f2229d399As per the TODO message, I removed a check that was no longer necessary. Now ID is an allowable INFO field key.
Eric Banks
2012-11-21 16:01:26 -0500
a8c7edca05Fixed fragment handling in DepthOfCoverage
Menachem Fromer
2012-11-21 16:01:10 -0500
06261b58c2Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Menachem Fromer
2012-11-21 15:57:08 -0500
ed50814ccbFinally found a case where user errors were being masked behind other errors and could debug. It turns out that the checkForMaskedUserErrors() method needs to run recursively over all levels (calling exception.getCause()) to check for the original cause.
Eric Banks
2012-11-21 15:57:05 -0500
c8be7c3102Keep SNPs and indels separately for batch merging; Add options to DepthOfCoverage to count fragments (to not double-count overlapping reads of same fragment); DepthOfCoverage should now support ReducedReads; Replace recusrion with loop in DoC/package.scala (for lists longer than 5000 elements)
Menachem Fromer
2012-11-21 15:56:53 -0500
Eric Banks
Mark DePristo
Ami Levy-Moonshine
Jacob Silterra
Douglas Voet
Mauricio Carneiro
Joel Thibault
Johan Dahlberg
kshakir
David Roazen
Chris Hartl
Ryan Poplin
Guillermo del Angel
Menachem Fromer