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  • 1f1233b669 Fix for a rare but insidious bug in position tracking during async BAM file reading. Matt Hanna 2012-01-08 22:03:35 -0500
  • f741ec6c6a Replaced dotFile with shortDescription, as per Khalid's latest update Menachem Fromer 2012-01-08 12:51:50 -0500
  • 87a690e6df Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2012-01-08 12:23:21 -0500
  • 1ddac59a49 Added alpha version of Exome CNV calling pipeline script. To run it, you would need to checkout and compile our C++ code by 'git clone /psych/genetics_data/projects/seq/exome/CNV/git_master/xhmm', though this is not yet recommended since this process is all still preliminary Menachem Fromer 2012-01-08 12:22:18 -0500
  • 5793625592 No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice. QScript accessor to QSettings to specify a default runName and other default function settings. Because log files are no longer pseudo-random their presense can be used to tell if a job without other file outputs is "done". For now still using the log's .done file in addition to original outputs. Gathered log files concatenate all log files together into the stdout. InProcessFunctions now have PrintStreams for stdout and stderr. Updated ivy to use commons-io 2.1 for copying logs to the stdout PrintStream. Removed snakeyaml. During graph tracking of outputs the Index files, and now BAM MD5s, are tracked with the gathering of the original file. In Queue generated wrappers for the GATK the Index and MD5s used for tracking are switched to private scope. Added more detailed output when running with -l DEBUG. Simplified graphviz visualization for additional debugging. Switched usage of the scala class 'List' to the trait 'Seq' (think java.util.ArrayList vs. using the interface java.util.List) Minor cleanup to build including sending ant gsalib to R's default libloc. Khalid Shakir 2012-01-08 12:11:55 -0500
  • 90cc17ee2a Merged bug fix from Stable into Unstable Mark DePristo 2012-01-06 18:14:51 -0500
  • 63b7a70c44 Removing very costly analyses of all GATK versions. Will be replaced by Tableau website Mark DePristo 2012-01-06 18:13:19 -0500
  • 1f88a1bfe2 Small fix to RRead script Mauricio Carneiro 2012-01-06 17:25:04 -0500
  • f6a18aea63 Updated MDCP with INDEL best practices Mauricio Carneiro 2012-01-04 12:05:08 -0500
  • 65c614fb4b Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2012-01-06 16:38:26 -0500
  • d9da37f9b4 Added SQL table creation and log loading to analyzeRunReports Mark DePristo 2012-01-06 16:35:53 -0500
  • d4e7655d14 Added ability to call multiallelic indels, if -multiallelic is included in UG arguments. Simple idea: we genotype all alleles with count >= minIndelCnt. To support this, refactored code that computes consensus alleles. To ease merging of mulitple alt alleles, we create a single vc for each alt alleles and then use VariantContextUtils.simpleMerge to carry out merging, which takes care of handling all corner conditions already. In order to use this, interface to GenotypeLikelihoodsCalculationModel changed to pass in a GenomeLocParser object (why are these objects to hard to handle??). More testing is required and feature turned off my default. Guillermo del Angel 2012-01-06 11:24:38 -0500
  • 616ff8ea01 fixed typo in help text Ryan Poplin 2012-01-06 10:36:11 -0500
  • 43224ef364 Turning the Adaptive Downsampler on with 100 by default Mauricio Carneiro 2012-01-05 23:46:31 -0500
  • dd80ffbbbe Merged bug fix from Stable into Unstable Mark DePristo 2012-01-05 21:51:48 -0500
  • c96fee477c Bug fix for VariantSummary Mark DePristo 2012-01-05 21:49:02 -0500
  • f5e10e9879 Merged bug fix from Stable into Unstable Eric Banks 2012-01-05 15:35:09 -0500
  • 18ed954741 Compute Ti/Tv only if bi-allelic Eric Banks 2012-01-05 15:33:26 -0500
  • a6886a4cc0 Initial commit of the Active Region Traversal. Not ready to be used by anyone yet. Ryan Poplin 2012-01-04 17:03:21 -0500
  • 58d4539304 Enabled banded indel computation by default. Reversed logic in input UG argument so that we can still disable it if required. Minor changes to integration tests due to minor differences in GL's and in annotations Guillermo del Angel 2012-01-04 15:28:26 -0500
  • 5cdde168af Switch from using BWA to direct edit distance inspection. Seems to work quite well. Christopher Hartl 2012-01-04 14:25:43 -0500
  • 310c05bd09 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Christopher Hartl 2012-01-04 01:12:23 -0500
  • 31ecc38db8 Initial implementation of a walker for redesigning low or high GC baits using a fairly textbook genetic algorithm. Christopher Hartl 2012-01-04 01:10:28 -0500
  • fe67276e1e Merged bug fix from Stable into Unstable David Roazen 2012-01-04 00:54:02 -0500
  • 253a07fdb1 Implicits conversion issue/bug: QScript String<==>File shortcuts at compile time do not make String.equals(File) at runtime. Khalid Shakir 2012-01-03 18:43:45 -0500
  • 9ff8a01da2 Merged bug fix from Stable into Unstable Mauricio Carneiro 2012-01-03 18:10:39 -0500
  • 9b55505c03 Fixing PairHMMIndelErrorModel array out of bounds Mauricio Carneiro 2012-01-03 18:08:46 -0500
  • 2c3a9ce02f Merge branch 'master' of ssh://tin.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable Christopher Hartl 2012-01-03 17:25:56 -0500
  • 621ee2b613 Merged bug fix from Stable into Unstable David Roazen 2012-01-03 16:56:49 -0500
  • 9093de1132 Cleanup: remove code to calculate the MLE AC in the UGE. Christopher Hartl 2012-01-03 15:58:51 -0500
  • 2d093828a4 Final changes to Junky (been frozen for a while, but uncommitted) and the qscript for it. A first cursory implementation of the trellis-based Exact AC-constrained genotyping algorithm in UGE. Nothing calls into it, so this should be entirely safe (and, no surprise, it passes UG integration tests). Christopher Hartl 2012-01-03 15:33:04 -0500
  • ea6e718cb8 SnpEff 2.0.5 support. Re-enabled SnpEff in the HybridSelectionPipeline. David Roazen 2012-01-02 21:57:03 -0500
  • 93e1417b6e Update to the VSS GATK documentation. Christopher Hartl 2012-01-03 13:39:31 -0500
  • 4984ca5e31 Merged bug fix from Stable into Unstable David Roazen 2012-01-03 11:03:30 -0500
  • f3f01da1af Enforce serial dependencies in RecalibrationWalkersIntegrationTest David Roazen 2012-01-03 10:42:41 -0500
  • 055364d786 Always use full, three-part version numbers. David Roazen 2012-01-03 10:18:45 -0500
  • ab8d47d9a5 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-01-03 09:38:49 -0500
  • ca669ae744 Optimizations to the CoverageByRG walker Mauricio Carneiro 2012-01-02 16:19:31 -0500
  • 3d4bf273de Added getPileupForReadGroups to ReadBackPileup Mauricio Carneiro 2012-01-02 16:17:57 -0500
  • caa5da2fd2 Added parameter to combine RGs in CoverageByRG Roger Zurawicki 2011-12-31 02:14:29 -0500
  • 18f06ad913 Script to calculate gc content of intervals independently Mauricio Carneiro 2012-01-02 02:45:08 -0500
  • 0bdeda6f3f Added single sample option for the ReduceReads calling script Mauricio Carneiro 2012-01-02 23:35:46 -0500
  • 4a208c7c06 Refactor of the downsampling machinery to accept different strategies Mauricio Carneiro 2012-01-02 18:26:31 -0500
  • cce8511d29 Some WGS performance upgrades for ReduceReads Mauricio Carneiro 2012-01-01 21:55:04 -0500
  • 21ae3ef5f9 Added downsampling support to ReduceReads Mauricio Carneiro 2011-12-31 13:56:41 -0500
  • cd68cc239b Added knuth-shuffle (KS) and randomSubset using KS to MathUtils Mauricio Carneiro 2011-12-29 00:41:59 -0500
  • 94791a2a75 Add support for reads starting with insertion Mauricio Carneiro 2011-12-28 12:15:53 -0500
  • 3ecb9a0bf7 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2012-01-02 13:56:55 -0500
  • b3e613647a GATKPerformanceOverTime bug fixes Mark DePristo 2012-01-02 13:56:44 -0500
  • 188bd48139 runGATKReport only archives and shows errors for last days runs Mark DePristo 2012-01-02 10:39:05 -0500
  • d05f0c2318 GATKPerformanceOverTime script update Mark DePristo 2012-01-02 09:58:46 -0500
  • a837970ea2 Merged bug fix from Stable into Unstable Mauricio Carneiro 2012-01-01 22:20:53 -0500
  • 1b6d52817e fixing adaptor clipping effect on recalibration integration test Mauricio Carneiro 2012-01-01 22:20:06 -0500
  • e45ca8bfa2 Protect against too many alternate alleles in the haplotype caller. Ryan Poplin 2012-01-01 19:12:48 -0500
  • 393993e0c7 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-12-31 20:42:46 -0500
  • b0d68eb0e3 Merge remote-tracking branch 'unstable/master' Eric Banks 2011-12-31 20:26:44 -0500
  • 55cfa76cf3 Updated integration tests for the new adaptor clipping fix. Mauricio Carneiro 2011-12-30 12:50:40 -0500
  • c7d0a9ebee Forgot to test for inter-chromosomal mates in the adaptor clipping Mauricio Carneiro 2011-12-30 00:19:24 -0500
  • a259bfefd4 First commit addressing problems running RTC in parallel. Matt Hanna 2011-12-29 16:22:14 -0500
  • e6e80e8d3f Update Picard to fix a bug Mauricio found in Picard where Picard unnecessarily depends on Snappy during some usages of SortingCollection. Matt Hanna 2011-12-29 14:35:02 -0500
  • 1a45ea5a05 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-12-29 11:37:15 -0500
  • efe33a0a1b BUG FIX: Output is correct Roger Zurawicki 2011-12-28 22:35:47 -0500
  • 5672688a73 Optimized CoverageByRG and Added GCContent Roger Zurawicki 2011-12-28 11:29:18 -0500
  • 0c05998c4c Added CoverageByRG LocusWalker Roger Zurawicki 2011-12-27 14:05:33 -0500
  • f692911903 GATKSAMRecord emptyRead static constructor Mauricio Carneiro 2011-12-27 17:00:47 -0500
  • 8259c748f2 No more Filtered Reads tag. Mauricio Carneiro 2011-12-27 14:54:35 -0500
  • d20a25d681 A much better way of choosing the alternate allele(s) to genotype in the SNP model of UG: instead of looking at the sum of base qualities (which can and did lead to us over-genotyping esp. when allowing multiple alternate alleles), we look at the likelihoods themselves (free since we are already calculating likelihoods for all 10 genotypes). Now, even if the base quals exceed some arbitrary threshold, we only bother genotyping an alternate allele when there's a sample for which it is more likely than ref/ref (I can generate weird edge cases where this falls apart, but none that model truly variable sites that we actually want to call). This leads to a huge efficiency improvement esp. for exomes (and esp. for many samples) where we almost always were trying to genotype all 3 alternate alleles. Integration tests change only because ref calls have slight QUAL differences (because the best alt allele is still chosen arbitrarily, but differently). Eric Banks 2011-12-27 16:50:38 -0500
  • ef31b2f0a7 fixing merge conflicts. Ryan Poplin 2011-12-27 14:26:36 -0500
  • 4f09a95221 Updating HaplotypeCaller for the new contracts in the adapter clipping. Ryan Poplin 2011-12-27 14:25:03 -0500
  • adff40ff58 Minor optimizations to avoid extra processing (esp. for reduced reads) Eric Banks 2011-12-27 13:16:25 -0500
  • 17bfe48d5e Made all class methods private in the ReadClipper Mauricio Carneiro 2011-12-27 01:29:13 -0500
  • ce493bf257 Added adaptor clipping to ReduceReads Mauricio Carneiro 2011-12-27 01:19:06 -0500
  • f7a5752025 Let this one slip through my commits. Mauricio Carneiro 2011-12-26 21:55:02 -0500
  • c1eaf7cf81 ReduceReads will allows different context sizes for different events Mauricio Carneiro 2011-12-26 15:05:49 -0500
  • 4633637af6 Moved ReduceReads to static ReadClipper Mauricio Carneiro 2011-12-26 01:05:24 -0500
  • 9aa1c0c6e5 Better documentation and contracts for ReduceReads Mauricio Carneiro 2011-12-26 00:47:11 -0500
  • 3051cdf9c5 fixed reduced reads integration tests Mauricio Carneiro 2011-12-25 18:59:22 -0500
  • 256a7d8bd2 fixing the arguments for RRead script Mauricio Carneiro 2011-12-24 14:43:56 -0500
  • dd990061f6 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-12-26 14:45:35 -0500
  • 2130b39f33 Found the bug in the engine: RodLocusView was using the wrong seek method so that it would only move to the first locus of a shard (and with multi-locus shards, this meant that we never processed RODs from the other positions). In fact, because the seek(Shard) method is extremely misleading and now no longer used, I think it's safer to delete it and make everyone use the much more transparent seek(GenomeLoc). Note that I have not re-enabled my improvements to the intervals accumulation of ReferenceDataSource because that inefficiency is still present downstream in RodLocusView; need to discuss those changes with Matt. Eric Banks 2011-12-26 14:45:19 -0500
  • 02495a5fd5 renaming script, once more Mauricio Carneiro 2011-12-23 20:01:25 -0500
  • afc58b81b2 changing permissions on the scala script Mauricio Carneiro 2011-12-23 19:47:48 -0500
  • 5198f3a287 Making -e optional and renaming script Mauricio Carneiro 2011-12-23 19:35:38 -0500
  • 35c41409a1 Better contracts and docs for the ReadClipper Mauricio Carneiro 2011-12-23 19:35:00 -0500
  • 506c0e9c97 Disabling SnpEff support in the GATK and SnpEff annotation in the HybridSelectionPipeline David Roazen 2011-12-23 16:44:28 -0500
  • 24c84da60d 'Fixing' the changes in ReferenceDataSource so that a shard properly contains a list of GenomeLocs instead of a single merged one. However, that uncovered a probable bug in the engine, so instead of letting this code fester unfixed in the build (affecting everyone in the group) I've decided to revert the previous (slow, but working) version and fix the engine in my own branch. Eric Banks 2011-12-23 15:39:12 -0500
  • 8762313a0d Better TODO message Eric Banks 2011-12-22 20:54:35 -0500
  • a815e875a8 Removing debugging output Eric Banks 2011-12-22 15:49:11 -0500
  • deef542a38 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-12-22 15:44:58 -0500
  • 6d260ec6ae Start printing traversal stats after 30 seconds. I can't stand waiting 2 minutes. Eric Banks 2011-12-22 15:40:59 -0500
  • 510c71158c Merged bug fix from Stable into Unstable David Roazen 2011-12-22 10:49:52 -0500
  • 32cdef9682 Rename *PerformanceTest test classes to *LargeScaleTest David Roazen 2011-12-22 10:38:49 -0500
  • 473af102c1 Added 'expand intervals' option to reduce reads scala script Mauricio Carneiro 2011-12-21 15:15:45 -0500
  • 3358c132a8 Updating the MD5s Mauricio Carneiro 2011-12-21 15:14:05 -0500
  • a333144aaf more verbose output for updateSampleList.lua Mauricio Carneiro 2011-12-21 13:30:35 -0500
  • 2e232e26da New name for ReduceReads scala script Mauricio Carneiro 2011-12-21 13:13:07 -0500
  • 98f4cdecc8 Renaming ReduceReads script Mauricio Carneiro 2011-12-21 13:11:34 -0500
  • 4d65aefc7b Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Matt Hanna 2011-12-20 21:43:57 -0500
  • d50f9b98bb Make sure that the temporary ReadWalker performance improvement hack works well in the binary release, jic GATK 1.4 arrives before I get a Picard patch. Matt Hanna 2011-12-20 21:42:30 -0500
  • 731a463415 Updated IntegrationTests with new adaptor clipper Mauricio Carneiro 2011-12-20 17:44:21 -0500