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• 4fa5045e84 Abandoning classfileset/rootfileset approach due to difficulting managing classloading of bcel*.jar/ant-apache-bcel*.jar. Switching instead to manually specifying a minimal set of packages/classes to include in the vcf.jar via build.xml, and adding a unit test which creates a limited classloader only aware of vcf.jar and tribble.jar and tries to use it to load the core classes in the vcf jar. Matt Hanna 2011-10-06 12:49:51 -0400
• 1dbe937396 Add in argument for downsampling threshold Menachem Fromer 2011-10-06 12:00:32 -0400
• 73f9d1f217 GATK read group requirement iron hand Mark DePristo 2011-10-06 08:40:35 -0700
• 23845ac798 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-10-06 08:17:08 -0700
• 4b5b9155a9 Fixed bad expected value in PedReaderUnitTest Mark DePristo 2011-10-06 08:16:47 -0700
• daa5999489 Fixed typo in argument description Mark DePristo 2011-10-06 08:16:25 -0700
• c649759978 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-10-06 10:10:46 -0400
• 2f12bfaad5 Merged bug fix from Stable into Unstable Matt Hanna 2011-10-06 10:10:00 -0400
• efca1fdfd8 Revert change until I figure out how to use classfileset/rootfileset with a vanilla ant install. Matt Hanna 2011-10-06 10:08:48 -0400
• 8a474e38ff Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-10-06 10:08:39 -0400
• 93f7e632bd Minor fix/enhancement for VariantEval: if a vcf has symbolic alleles, program would crash ungracefully - now we'll just skip record without processing. This is a big issue since we can't process 1000G integration files with code as is. Guillermo del Angel 2011-10-06 10:07:46 -0400
• 190be4d0d1 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-10-05 21:27:11 -0700
• 8e6845806a Allowing empty samples list in LIBS Mark DePristo 2011-10-05 21:26:21 -0700
• a3c5a31686 Oops, forgot the PED test file Mark DePristo 2011-10-05 21:09:08 -0700
• 180c8f286f Merged bug fix from Stable into Unstable Matt Hanna 2011-10-05 20:37:43 -0400
• 55b9f06527 Ensure that IndelRealigner n-way out option supports MD5 generation. Matt Hanna 2011-10-05 20:36:28 -0400
• b945e97de1 Shouldn't have committed the non-fetching version by default Mark DePristo 2011-10-05 17:12:48 -0700
• b068846407 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-10-05 17:12:09 -0700
• 6d6149b9a2 Updated gsalib gsa.read.gatkreport to return all reports, even those beginning with '.'. In PreQC using geom_blank() so MEDIAN_INSERT_SIZE plot doesn't crash on facet_grid(scales='free') when data doesn't contain points for 'RF' or 'TANDEM'. Khalid Shakir 2011-10-05 18:30:40 -0400
• 982983355f Merged bug fix from Stable into Unstable Matt Hanna 2011-10-05 18:27:29 -0400
• dd780dba5f Rather than just picking a few classes to be the roots of the vcf jar and including all dependencies, use the entire codecs.vcf and variantcontext packages as roots. Matt Hanna 2011-10-05 18:25:26 -0400
• a91509e7dd Shouldn't be public Mark DePristo 2011-10-05 15:22:57 -0700
• be2d29ce69 Final PED documentation Mark DePristo 2011-10-05 15:17:41 -0700
• 3226d5dc0d Merge branch 'master' into ped Mark DePristo 2011-10-05 15:03:09 -0700
• 6a573437af Details documentation arguments for -ped Mark DePristo 2011-10-05 15:00:58 -0700
• dc6d71dec5 Merged bug fix from Stable into Unstable David Roazen 2011-10-05 16:53:32 -0400
• b732f740d2 Revert "Change vcf jar to use a classfileset to pull all dependencies. Should save" David Roazen 2011-10-05 16:51:30 -0400
• e7c80f7c45 Renaming quantitative trait to OtherPhenotype which is now a String not a double Mark DePristo 2011-10-05 12:26:33 -0700
• 51ecc20867 getFamily() and associated methods implemented and tested Mark DePristo 2011-10-05 09:55:05 -0700
• f4bac58f14 Merged bug fix from Stable into Unstable Mark DePristo 2011-10-04 21:00:34 -0700
• d1d39943d0 Updating MD5 for BAMs that I added a read group to, part 2 Mark DePristo 2011-10-04 21:00:15 -0700
• 9bd3ba4c7e Missed one MD5 Mark DePristo 2011-10-04 16:04:52 -0700
• ffdfdcde3f Updating MD5s Mark DePristo 2011-10-04 15:54:45 -0700
• a45d985818 TODO method stubs Mark DePristo 2011-10-04 15:54:09 -0700
• 463eab7604 All MD5 mismatches for test are shown Mark DePristo 2011-10-04 15:53:52 -0700
• c642a080d4 Merged bug fix from Stable into Unstable Mark DePristo 2011-10-04 14:08:41 -0700
• 941317167e Updating MD5 for BAMs that I added a read group to Mark DePristo 2011-10-04 14:08:00 -0700
• 4ebdc52b0d Merged bug fix from Stable into Unstable Matt Hanna 2011-10-04 13:16:20 -0400
• 88c2fad64f Change vcf jar to use a classfileset to pull all dependencies. Should save Jim Robinson some detective work in the long run. Matt Hanna 2011-10-04 13:14:39 -0400
• e1d6c7a50a Updating MD5 that have changed due to sample ordering differences Mark DePristo 2011-10-04 09:33:23 -0700
• 343a7b6b2f Updating UG integration tests for arbitrary impact of sample order changes on downsampling Mark DePristo 2011-10-04 08:14:00 -0700
• fee89e47ff Only throws an error when there are no samples but there are reads Mark DePristo 2011-10-04 06:50:54 -0700
• f552aede42 Only provide the sample names in the BAM file for efficiency Mark DePristo 2011-10-04 06:50:12 -0700
• a27641e1fc Cleaned up imports Mark DePristo 2011-10-04 06:28:36 -0700
• 8b4a27092d Merge branch 'master' into rr Mauricio Carneiro 2011-10-03 19:46:04 -0700
• 6ca162ae9a Not pre-sorted. Mauricio Carneiro 2011-10-03 19:45:46 -0700
• b20689ff55 No longer supports extraProperties Mark DePristo 2011-10-03 19:20:33 -0700
• 867a7476c1 Systematic unit tests for the sample object Mark DePristo 2011-10-03 19:09:02 -0700
• 3837aa45b4 Fixing conflicts Mauricio Carneiro 2011-10-03 19:07:59 -0700
• 2e3dc52088 Minor function renaming Mark DePristo 2011-10-03 14:41:13 -0700
• dd71884b0c On path to SampleDB engine integration Mark DePristo 2011-10-03 12:08:07 -0700
• c3eff7451a Found a small inefficiency while profiling: we were still using String.split instead of ParsingUtils.split to break up array values in the INFO field. There was a noticeable (albeit not big) difference in the change when reading sites only files. Eric Banks 2011-10-03 14:20:39 -0400
• 8ee0f91904 Remove residual processing tracker arguments Mark DePristo 2011-10-03 09:50:01 -0700
• 89ac50e86e SampleDataSource -> SampleDB Mark DePristo 2011-10-03 09:33:30 -0700
• 93fba06cb5 Support for whitespace only lines Mark DePristo 2011-10-03 09:30:10 -0700
• 0604ce55d1 PedReader support for ; separated lines, not only newline Mark DePristo 2011-10-03 09:19:58 -0700
• 52f670c8b8 100% version of PedReader Mark DePristo 2011-10-03 06:12:58 -0700
• bf6a3a6532 Added framework to do batch CigarClip Testing Roger Zurawicki 2011-10-02 22:33:46 -0400
• dd75ad9f49 95% PedReader Mark DePristo 2011-09-30 18:03:34 -0400
• c7898a9be7 inconsequential change in string constants printed into the vcf which noone uses anyway... Andrey Sivachenko 2011-09-30 16:40:21 -0400
• 010899f886 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-09-30 15:51:09 -0400
• 84160bd83f Reorganization of Sample Mark DePristo 2011-09-30 15:50:54 -0400
• 05fba6f23a Clipping ends inside deletion and before insertion Mauricio Carneiro 2011-09-30 15:44:30 -0400
• e0b771c233 Pre-sorting output Mauricio Carneiro 2011-09-30 14:11:42 -0400
• b5bdea1cb9 Fix: hardclip first interval overlap but overlap subsequent intervals Mauricio Carneiro 2011-09-30 13:25:05 -0400
• d211b3b7f0 Fixing interval overlap logic Mauricio Carneiro 2011-09-30 10:53:59 -0400
• c1cf6bc45a PEDReader should be in samples Mark DePristo 2011-09-30 14:22:19 -0400
• 56f10b40a8 Fixing test bugs for WindowMaker that required empty sample list Mark DePristo 2011-09-30 14:18:27 -0400
• 73577b72cf Misc minor updates in HaplotypeCaller Ryan Poplin 2011-09-30 13:41:24 -0400
• af6c053435 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-09-30 13:33:31 -0400
• 810e8ad011 Removed getXByReaders() function from the engine Mark DePristo 2011-09-30 10:43:51 -0400
• f75573dd54 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-09-30 10:35:26 -0400
• 6637cd9dd5 Fixes to CalibrateGenotypeLikelihoods: a) Fix up the walker itself which was broken since the new rod binding system, b) added ability to do indels and to optionally test banded implementation, c) experimental ability to do multiple samples (may need more work) Guillermo del Angel 2011-09-30 10:35:10 -0400
• 178ba24c27 Move getSamplesForSamFile to SampleUtils Mark DePristo 2011-09-30 10:28:18 -0400
• 30d23942b1 Renamed ReadBackedPileup getXSampleName() functions to getXSample Mark DePristo 2011-09-30 10:02:57 -0400
• 3289a325fc Removed final use of Sample in RBP Mark DePristo 2011-09-30 09:57:39 -0400
• a69a4dda2f SamplesDB no longer has null sample Mark DePristo 2011-09-30 09:56:23 -0400
• e055a78f6e LIBS now requires at least one sample be present Mark DePristo 2011-09-30 09:49:35 -0400
• 9860a2c989 Merge branch 'master' into ped Mark DePristo 2011-09-30 09:28:18 -0400
• a881d6f145 Now only generates the poly VCF with select variants if the file doesn't exist Mark DePristo 2011-09-30 08:42:09 -0400
• d901fed617 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-09-30 08:41:44 -0400
• cabacf028d Intermediate commit to fix interval skipping Mauricio Carneiro 2011-09-29 18:45:12 -0400
• b71b51751e Bug fix for UnitTest Mark DePristo 2011-09-29 17:30:01 -0400
• 1765fbeb6b Merge branch 'master' into ped Mark DePristo 2011-09-29 17:18:51 -0400
• 98ecaf8aa0 Support for ReducedReads with reduced counts and average quals Mark DePristo 2011-09-29 17:18:39 -0400
• 9508220157 fixed hard clipping both ends inside deletion Mauricio Carneiro 2011-09-29 15:36:49 -0400
• 9458f01409 Test cleanup of Sample object Mark DePristo 2011-09-29 15:13:05 -0400
• 625ffb6a07 LocusIteratorByState and ReadBackedPileups no long use Sample Mark DePristo 2011-09-29 14:52:11 -0400
• b3a2371925 Merge branch 'master' into ped Mark DePristo 2011-09-29 14:32:17 -0400
• 68761a6e28 Removed sample from header Mark DePristo 2011-09-29 14:13:05 -0400
• a5e75cd14c Outputting both consensus base qualities and counts Mauricio Carneiro 2011-09-29 12:54:18 -0400
• d62f2f33bc Added indel specific context size parameter Mauricio Carneiro 2011-09-29 11:23:12 -0400
• 505416b6c0 Merge branch 'master' into ped Mark DePristo 2011-09-29 12:22:39 -0400
• 21c4abdd36 Disabling all SlidingReadUnitTests Mauricio Carneiro 2011-09-29 12:19:03 -0400
• 4086fa768f Disabling all ReadClipperUnitTests Mauricio Carneiro 2011-09-29 12:18:18 -0400
• 9536845e35 Cleaning up unused code in MV Mark DePristo 2011-09-29 12:20:07 -0400
• 5043d76c3d Removing more bad uses of SampleDataSource creation Mark DePristo 2011-09-29 12:16:34 -0400
• 5c9227cf5e Further cleanup of Sample database Mark DePristo 2011-09-29 11:50:05 -0400
• 6dec932ca9 Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Khalid Shakir 2011-09-29 11:47:13 -0400
• c08468eb9d A couple of updates while trying to get desired R 2.13 compactPDF support. Khalid Shakir 2011-09-29 11:21:50 -0400