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  • d8a4d78854 Bugfix for exceptions with unknown source whose error was not being shown in tableau Mark DePristo 2012-01-31 10:49:06 -0500
  • faba3dd530 Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2012-01-31 10:25:29 -0500
  • 17dbe9a95d A few cleanups in the LocusIteratorByState Mauricio Carneiro 2012-01-30 21:37:02 -0500
  • e7ace8efc4 Fix NullPointerException caused in cases with too many ALT alleles Menachem Fromer 2012-01-30 21:00:16 -0500
  • f9162ea705 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-01-30 19:45:19 -0500
  • abb91cf26b Increasing the size of the active regions that are produced by the active probability integrator, more context is needed to call more complex events Ryan Poplin 2012-01-30 15:36:12 -0500
  • d5d4fa8a88 Fixed discordance bug reported by Brad Chapman Mauricio Carneiro 2012-01-30 09:50:14 -0500
  • f1e07f169e Only apply filters if there are filters to apply Menachem Fromer 2012-01-30 02:22:13 -0500
  • d1aa5204d7 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2012-01-29 23:39:34 -0500
  • 3186f0f1b0 Try more memory and fewer ALT alleles so that we don't run out of memory Menachem Fromer 2012-01-29 23:38:32 -0500
  • 3164c8dee5 S3 upload now directly creates the XML report in memory and puts that in S3 Mark DePristo 2012-01-29 15:14:58 -0500
  • 0e17cbbce9 Merged bug fix from Stable into Unstable Menachem Fromer 2012-01-27 16:03:16 -0500
  • a9671b73ca Fix to permit proper handling of mapping qualities between 128 to 255 (which get converted to byte values of -128 to -1) Menachem Fromer 2012-01-27 16:01:30 -0500
  • f7ac1f4a69 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-01-27 15:12:55 -0500
  • fc08235ff3 Bug fix in active region traversal, locusView.getNext() skips over pileups with zero coverage but still need to count them in the active probability integrator Ryan Poplin 2012-01-27 15:12:37 -0500
  • 052a4bdb9c Turning off PHONE HOME option in the MDCP Mauricio Carneiro 2012-01-27 11:13:30 -0500
  • f8f2152f9c fixing ReduceReads MD5s Mauricio Carneiro 2012-01-27 10:53:24 -0500
  • 0f2e8400b5 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2012-01-27 10:12:50 -0500
  • ec9920b04f Updating the SAM TAG for Original Alignment Start to "OP" Mauricio Carneiro 2012-01-27 08:51:39 -0500
  • 13d1626f51 Minor improvements in ref QC walker. Unfortunately this doesn't actually catch Chris's error Mark DePristo 2012-01-27 08:24:17 -0500
  • cb04c0bf11 Removing javaassist 3.7, lucene library dependancies Mark DePristo 2012-01-27 08:20:45 -0500
  • 2a565ebf90 embarrassing fix-up, thanks Khalid. Mauricio Carneiro 2012-01-26 19:58:42 -0500
  • 0de6aca29b Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2012-01-26 18:26:41 -0500
  • d54e237671 Take advantage of Eric's fix for multiAllelic AC calculation, and also add fix to have the original allele's INFO field be passed through for batch merging Menachem Fromer 2012-01-26 18:25:30 -0500
  • 246e085ec9 Unit tests for GATKSAMRecord class Mauricio Carneiro 2012-01-26 16:59:08 -0500
  • 0d4027104f Reduced reads are now aware of their original alignments Mauricio Carneiro 2012-01-26 16:07:29 -0500
  • 07f72516ae Unsupported platform should be a user error Eric Banks 2012-01-26 16:14:25 -0500
  • cdff23269d HaplotypeCaller now uses insertions and softclipped bases as possible triggers. LocusIteratorByState tags pileup elements with the required info to make this calculation efficient. The days of the extended event pileup are coming to a close. Ryan Poplin 2012-01-26 15:56:33 -0500
  • 44c3a41f67 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-01-26 13:25:33 -0500
  • dbe9eb70fe Updating HC integration tests after merge Ryan Poplin 2012-01-26 13:25:22 -0500
  • 673ceadd11 While this fix worked for the evaluator module, it could potentially have bad effects in the phasing walkers. Special-case nocalls in the PhasingEvaluator and return AllelePair to previous state. Christopher Hartl 2012-01-26 13:06:36 -0500
  • 9c6fda7e15 Yup. I was right. Christopher Hartl 2012-01-26 12:54:11 -0500
  • bd27f3bc9b Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-01-26 12:52:16 -0500
  • 67c89cadad Fixes for pool caller to match UG outputs at certain sites: implement min base qual/min mapping qual read filter so those reads are filtered from pileups, and implemented filter for sites that have a too large a fraction of deletions Guillermo del Angel 2012-01-26 12:52:00 -0500
  • 7d059540a4 Allow segments of genome to be excluded in generating a reference panel. Occasionally targets would contain no variation (typically, in the middle of the centromere), which beagle doesn't particularly like, and errors out rather than producing empty output files. The best way to deal with these is to just exclude the regions on a second-pass, and the remaining bits will be gathered with no additional work. Christopher Hartl 2012-01-26 12:43:52 -0500
  • 9d4b84f6bd Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2012-01-26 12:38:24 -0500
  • 25532bdc37 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-01-26 11:43:32 -0500
  • 390d493049 Updating ActiveRegionWalker interface to output a probability of active status instead of a boolean. Integrator runs a band-pass filter over this probability to produce actual active regions. First version of HaplotypeCaller which decides for itself where to trigger and assembles those regions. Ryan Poplin 2012-01-26 11:37:08 -0500
  • 9a63a9ae3c Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-01-26 00:38:25 -0500
  • 859dd882c9 Don't make it standard for now Eric Banks 2012-01-26 00:38:16 -0500
  • c5e81be978 Adding pairwise AF table. Not polished at all, but usable none-the-less. Eric Banks 2012-01-26 00:37:06 -0500
  • 774e540042 Fixing broken test Eric Banks 2012-01-26 00:31:41 -0500
  • 5b9c8ab01b Another quick update missed in the merge Eric Banks 2012-01-25 21:53:20 -0500
  • 702a2d768f Initial version of multi-allelic summary module in VariantEval Eric Banks 2012-01-25 19:42:55 -0500
  • 9a60887567 Lost an import in the merge Eric Banks 2012-01-25 19:41:41 -0500
  • cba5f1a8b1 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-01-25 19:19:03 -0500
  • ddaf51a50f Updated one integration test for indels Eric Banks 2012-01-25 19:18:51 -0500
  • add6918f32 Cleaner, more efficient way of determining the last dependent set in the queue. Eric Banks 2012-01-25 16:21:10 -0500
  • db645a94ca Added options to make the batch-merger more all-inclusive: keep all indels, SNPs (even filtered ones) but maintain their annotations. Also, VariantContextUtils.simpleMerge can now merge variants of all types using the Hidden non-default enum MultipleAllelesMergeType=MIX_TYPES Menachem Fromer 2012-01-25 16:10:59 -0500
  • d405ec2a0d Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-01-25 15:53:32 -0500
  • 4337dcd7e4 More pool caller bug fixes: the QUAL field was actually multiplied by 10 (accounting for a lot of singletons that shouldn't have been there), and correct AD output Guillermo del Angel 2012-01-25 15:53:03 -0500
  • 66772d0ebf Next iteration in the pool caller: more bug fixes, start of big refactoring to clean up interfaces, moved up a lot of attributes that really belonged to a site up from the Pool class, added by default option to filter out a call if there's no reference depth (instead of just skipping the call which makes it hard to figure out what happened afterwards). Guillermo del Angel 2012-01-25 15:41:08 -0500
  • ef335a5812 Better implementation of the fix; PL index is now traversed in order. Eric Banks 2012-01-25 15:15:42 -0500
  • 8e2d372ab0 Use remove instead of setting the value to null Eric Banks 2012-01-25 14:41:34 -0500
  • 05816955aa It was possible that we'd clean up a matrix column too early when a dependent column aborted early (with not enough probability mass) because we weren't being smart about the order in which we created dependencies. Fixed. Eric Banks 2012-01-25 14:28:21 -0500
  • 2799a1b686 Catch exception for bad type and throw as a TribbleException Eric Banks 2012-01-25 12:15:51 -0500
  • 96b62daff3 Minor tweak to the warning message. Eric Banks 2012-01-25 11:55:33 -0500
  • fb863dc6a7 Warn user when trying to run with EMIT_ALL_SITES with indels; better docs for that option. Eric Banks 2012-01-25 11:50:12 -0500
  • e349b4b14b Allow appending with the dbSNP ID even if a (different) ID is already present for the variant rod. Eric Banks 2012-01-25 11:35:54 -0500
  • ea3d4d60f2 This annotation requires rods and should be annotated as such Eric Banks 2012-01-25 11:35:13 -0500
  • 7a26fcb86f Setting the max alternate alleles for the exact model in the HaplotypeCaller's copy of the UG engine. Ryan Poplin 2012-01-25 09:51:13 -0500
  • bbefe4a272 Added option to be able to write out the active regions to an interval list file Ryan Poplin 2012-01-25 09:47:06 -0500
  • 9818c69df6 Can now specify active regions to process at the command line, mainly for debugging purposes Ryan Poplin 2012-01-25 09:32:52 -0500
  • 8f7d9bff0a Fix MultiplyLikelihood logic, minor alterations to scala scripts. Christopher Hartl 2012-01-25 00:12:19 -0500
  • 22f0caccac Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-01-24 16:22:39 -0500
  • 97499529c7 another small bug with the file extension. Mauricio Carneiro 2012-01-24 16:13:53 -0500
  • ffd61f4c1c Refactor the Pileup Element with regards to indels Mauricio Carneiro 2012-01-17 18:56:50 -0500
  • 4aacaf8916 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2012-01-24 15:32:26 -0500
  • c312bd5960 Weirdly, PicardException inherits from SAMException, which means that our specialty code for reporting malformed BAMs was actually misreporting any error that happened in the Picard layer as a BAM ERROR. Matt Hanna 2012-01-24 15:30:04 -0500
  • 47f4440aea Merged bug fix from Stable into Unstable David Roazen 2012-01-24 15:19:29 -0500
  • b07fdb1089 Rename alltests* targets in build.xml David Roazen 2012-01-24 14:53:31 -0500
  • 8aaca83e91 Next intermediate iteration on pool caller: start using UnifiedArgumentCollection in order to have similar syntax to UG, several numerical bug fixes, add more logging to vcf (not done yet) Guillermo del Angel 2012-01-24 11:45:19 -0500
  • 7c7ca0d799 fixing bug with fastq extension Mauricio Carneiro 2012-01-24 10:59:25 -0500
  • 0a3172a9f1 Fix for ref 0 bases for Chris Mark DePristo 2012-01-24 10:53:37 -0500
  • 945cf03889 IntelliJ ate my import! Mauricio Carneiro 2012-01-23 21:46:45 -0500
  • 2bb9525e7f Don't set base qualities if fastQ is provided Mauricio Carneiro 2012-01-23 17:56:27 -0500
  • b6c816fe12 Turn off unnecessary printing in analyzeRunReports Mark DePristo 2012-01-23 17:04:12 -0500
  • 1172517abb Bugfix for version parsing. Mark DePristo 2012-01-23 16:02:53 -0500
  • ceca7e0b37 Bugfix to now separate completed, sting and user exceptions. Added dry run mode Mark DePristo 2012-01-23 12:12:38 -0500
  • 1f620c79e6 Add busers and bugroup information to queueStatus Mark DePristo 2012-01-23 12:12:00 -0500
  • 10bc26079d bugfix to actually run correct python script Mark DePristo 2012-01-23 12:11:38 -0500
  • 4b17fc3cc1 Parallel implementation of random forest training. Very cool (and easy) example of parallel processing in R Mark DePristo 2012-01-23 12:06:46 -0500
  • bb203ccf0a combined analyses of snps and indels. Mark DePristo 2012-01-23 10:51:07 -0500
  • 0ec6f86c21 Tests for event length, combined snps and indels. Partial infrastructure to train and eval trees. Mark DePristo 2012-01-21 14:08:25 -0500
  • c18beadbdb Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc. Attempted workaround for xdr_resourceInfoReq unsatisfied link during loading of libbat.so. Khalid Shakir 2012-01-23 16:17:04 -0500
  • cc4ba7372f Why is reference_bases even an option anymore? Christopher Hartl 2012-01-23 15:18:59 -0500
  • 3392d67c1a Maybe a switch to reference bases will fix this Christopher Hartl 2012-01-23 15:10:03 -0500
  • 15c0c294c1 Adding in this walker to try to debug the 0-byte ref bases Christopher Hartl 2012-01-23 14:51:24 -0500
  • 02450e4b12 Merged bug fix from Stable into Unstable Mark DePristo 2012-01-23 12:08:39 -0500
  • 798596257b Enable the Genotype Phasing Evaluator. Because it didn't have the same argument structure as the base class, update2 of VariantEvaluator was being called, rather than update2 of the actual module. Christopher Hartl 2012-01-23 10:50:16 -0500
  • 80a4ce0edf Bugfix for incorrect error messages for missing BAMs and VCFs Mark DePristo 2012-01-23 09:52:07 -0500
  • 31d2f04368 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-01-23 09:23:03 -0500
  • 966387ca0b Next intermediate commit in the pool caller. Lots of bug fixes and now we can emit true vcf's with calls in discovery mode (still of unknown quality) - old validation mode is temporarily broken,will be fixed in next refactoring. Guillermo del Angel 2012-01-23 09:22:31 -0500
  • 4a08e8ca6e Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .) Christopher Hartl 2012-01-23 08:25:34 -0500
  • 4d6312d4ea HaplotypeCaller is now an ActiveRegionWalker. Ryan Poplin 2012-01-22 14:31:01 -0500
  • 3b1aad4f17 After a minor and abject freakout, alter the T2D script to seek out truth sensitivities between 80 and 100, rather than between 0.8 and 1. Also, don't consider a genotype "changed by beagle" if the initial genotype is a no-call. Christopher Hartl 2012-01-20 23:43:51 -0500
  • 9b4f6afa21 Alterations to scripts for better performance. Grid search now expands the sens/spec tradeoff (90 was far too aggressive against hapmap chr20), and 20 max gaussians was too many, and caused errors. For consensus genotypes: remember to gunzip the beagle outputs before converting to VCF. Also, beagle can in fact create 'null' alleles in certain circumstances. I'm not sure what exactly those circumstances are, but those sites should be ignored. When it does, all alleles apear to be set to null, so this should not affect the actual phasing in the output VCF. Christopher Hartl 2012-01-20 23:07:59 -0500
  • f3564bbf43 Ugh. Darn intelliJ not telling me I was missing an import statement. Christopher Hartl 2012-01-20 13:25:11 -0500
  • b902d778ca . Christopher Hartl 2012-01-20 13:22:46 -0500
  • 7c6a9471e8 After ensuring MultiplyLikelihoods does what I want it to do, add a quick and simple integration test to ensure I don't break it. Christopher Hartl 2012-01-20 13:20:13 -0500