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  • d74c46bbcb Convenient python script to update md5s in one go across all files Mark DePristo 2012-06-06 14:02:25 -0400
  • 982192e2e4 MD5DB for integrationtest management now writes out a md5mismatches files for clean analysis Mark DePristo 2012-06-06 14:02:01 -0400
  • aef4c5eec1 BCFvsVCF now tests subsetting of XCF to sites Mark DePristo 2012-06-05 14:36:49 -0400
  • 249d5e5533 Better tests for Genotype parsing Mark DePristo 2012-06-05 14:36:10 -0400
  • 4a4d3cde3d UnitTests for decodeIntArray method Mark DePristo 2012-06-05 12:44:55 -0400
  • 5b8bd81991 An option to not actually write out the results of select variants Mark DePristo 2012-06-04 19:03:43 -0400
  • 6f7a01e00d Bugfix for BCF2 reader / writer for > 0x0FFF samples :-) Mark DePristo 2012-06-04 19:02:59 -0400
  • 1d4eb46606 Efficient reading of genotype fields v1 Mark DePristo 2012-06-04 12:17:15 -0400
  • 3a70f8216b Updated BCF vs VCF performance logs Mark DePristo 2012-06-04 07:10:30 -0400
  • 96dbd8df63 Fix a nasty script bug in Queue Mark DePristo 2012-06-04 07:10:13 -0400
  • 37b8d70321 Hidden option to SelectVariants to force the genotypes information to be decoded by computing AC Mark DePristo 2012-06-04 07:04:14 -0400
  • 17fbd103d0 Smarter infrastructure to decode genotypes in BCF Mark DePristo 2012-06-03 12:20:08 -0400
  • 889e3c4583 Code cleanup before major refactor Mark DePristo 2012-06-02 20:21:27 -0400
  • cebd37609c Finalizing new Genotype object and associated routines Mark DePristo 2012-06-02 20:10:17 -0400
  • 8b0a629a31 Terrible bugfix Mark DePristo 2012-06-01 20:18:16 -0400
  • d37a8a0bc8 Efficient Genotype object Intermediate commit Mark DePristo 2012-06-01 19:25:11 -0400
  • a648b5e65e First step towards an efficient Genotype object Mark DePristo 2012-05-31 17:53:12 -0400
  • ff9ac4b5f8 BCF2 genotype decoding is now lazy Mark DePristo 2012-05-31 13:47:31 -0400
  • 9eb83a0771 Enable adding contigs to VariantContextWriters on output Mark DePristo 2012-05-31 11:21:08 -0400
  • 8fc1a26ac7 Fixed comparison of VCFHeader as the set.equals() isn't working as expected Mark DePristo 2012-05-31 11:20:41 -0400
  • b0ea14ef0f VCFHeader getMetaData returns 4.1 version not 4.0 Mark DePristo 2012-05-31 11:19:53 -0400
  • 5fda16bea9 Enable shadow BCF2 Mark DePristo 2012-05-29 10:59:31 -0400
  • 7d12429917 First step towards indel qualities in RR Mauricio Carneiro 2012-06-14 15:24:35 -0400
  • e68038c5d8 Refactor post-processing downsampling using David's generic downsampler interface Mauricio Carneiro 2012-06-14 15:24:15 -0400
  • 0398ae9695 I hate these disabled unit tests, #2 Eric Banks 2012-06-14 15:19:27 -0400
  • 676a57de7b I hate these disabled unit tests Eric Banks 2012-06-14 14:03:58 -0400
  • 065fe9a7b9 Updating md5 for bug fixes Eric Banks 2012-06-14 13:03:51 -0400
  • de5508fcea Bug fixes for cycle and context covariates Eric Banks 2012-06-14 13:01:14 -0400
  • 5c3c6cbc40 Long -> long conversions in BQSR Eric Banks 2012-06-14 09:07:02 -0400
  • 29a74908bb The next round of BQSR optimizations: no more Long[] array creation Eric Banks 2012-06-14 00:05:42 -0400
  • cd2074b1dc Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-06-13 20:59:30 -0400
  • 92669a0468 Second intermediate commit for indel pool caller - now works (more or less) in reference sample-free mode. Still needs a lot of cleanups/add more tests and not done w/refactoring quite yet Guillermo del Angel 2012-06-13 20:59:17 -0400
  • 0550b27799 Make downsampler classes themselves generic (instead of just the Downsampler interface) David Roazen 2012-06-13 14:42:10 -0400
  • fc36177004 Accidentally removed the scattering from this test Joel Thibault 2012-06-13 14:17:31 -0400
  • 67c0569f9c Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-06-13 11:50:00 -0400
  • 9a4c39357a Fixed bugs in previous commit Guillermo del Angel 2012-06-13 11:49:20 -0400
  • 81993b08e2 Don't put null entries into the key array Eric Banks 2012-06-13 11:43:44 -0400
  • bdf5945dcc Fixed bugs in DiagnoseTargets Roger Zurawicki 2012-06-12 16:49:52 -0400
  • 538cdf9210 Created the FindCoveredIntervals Roger Zurawicki 2012-06-11 16:19:57 -0400
  • aee66ab157 Big UG refactoring and intermediate commit to support indels in pool caller (not done yet). Lots of code pulled out of long spaghetti-like functions and modularized to be easily shareable. Add functionality in ErrorModel to count indel matches/mismatches (but left part disabled as not to change integration tests in this commit), add computation of pool genotype likelihoods for indels (not fully working yet in more realistic cases, only working in artificial nice pools). Lot's of TBD's still but existing UG and pool SNP functionality should be intact Guillermo del Angel 2012-06-13 11:14:44 -0400
  • bb77aa88c3 Drat, forgot the unit tests again Eric Banks 2012-06-12 19:00:47 -0400
  • bacd25d1a4 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-06-12 16:15:36 -0400
  • 37f56ce8fd A couple of minor updates to BQSR Eric Banks 2012-06-12 16:12:13 -0400
  • 277493dd83 Yet more instances of Lists changed over to native arrays Eric Banks 2012-06-12 15:56:09 -0400
  • 613badc835 Very minor optimizations for the context covariate Eric Banks 2012-06-12 15:47:32 -0400
  • c8cda209b5 Make intersection easy to change Joel Thibault 2012-06-11 13:39:14 -0400
  • 0f79adb2aa Changing more Java Lists to native arrays in BQSR for performance optimization. Eric Banks 2012-06-12 15:41:01 -0400
  • 1da3e43679 Wow, apparently it's way, way less efficient to iterate over Java Lists than native arrays. With this change and the bit fiddling, Ryan's 10-day test case now runs in 1 day. More to come. Eric Banks 2012-06-12 13:32:56 -0400
  • a96c5da884 Oops, forgot to push the unit tests Eric Banks 2012-06-12 11:38:30 -0400
  • a057cf31b3 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-06-12 11:02:50 -0400
  • fec0bd5e11 Fixing UG argument docs Eric Banks 2012-06-12 09:46:16 -0400
  • a4defdfb29 Adding a GT header line to SomaticIndelDetector output Eric Banks 2012-06-12 09:39:17 -0400
  • 891ce51908 Refactoring of BQSRv2 to use longs (and standard bit fiddling techniques) instead of Java BitSets for performance improvements. Eric Banks 2012-06-12 09:19:36 -0400
  • 0c98c34f5f Fixing bugs caught by Eric Mauricio Carneiro 2012-06-11 17:32:22 -0400
  • e0fbffac3a Fixing bugs caught by Eric Mauricio Carneiro 2012-06-11 16:05:15 -0400
  • ff5749599d Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-06-11 15:46:17 -0400
  • fea625632f Don't use asList because it maintains an iterator to the original list and then the result can't be used to create a new one Eric Banks 2012-06-11 15:45:58 -0400
  • 41ef22fe7c Re-enabling BQSR integration tests Eric Banks 2012-06-11 15:44:55 -0400
  • e4d371dc80 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-06-11 10:38:50 -0400
  • 683d4b508e Bug fix in fragment utils: the read name wasn't being set in the merged read. Misc minor updates to the HaplotypeCaller. Ryan Poplin 2012-06-11 10:38:35 -0400
  • 4aad7e23ef New ReduceReads v2 with unclipped variant regions and soft-clipped bases Mauricio Carneiro 2012-05-14 13:39:42 -0400
  • edf08ca928 Updates to ReduceReads Mauricio Carneiro 2012-05-03 12:23:49 -0400
  • afa9b2718a Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-06-08 13:54:48 -0400
  • 92280b4068 BQSR optimization: cache the BitSetUtils.bitSetFrom() calls since they are called over and over again with the same values. Another 10% reduction in runtime. Eric Banks 2012-06-08 13:54:37 -0400
  • 898a0e6161 Minor optimizations Eric Banks 2012-06-08 12:07:58 -0400
  • 0a37e19998 Bug fix in VQSR so that the VCF index will be created for the recalFile. Ryan Poplin 2012-06-08 11:51:28 -0400
  • d463ab2cbf BQSR optimization: String manipulation is extremely expensive in Java (accounts for 8% of BQSR runtime). Instead use byte[] and StringBuilder when possible. Eric Banks 2012-06-08 10:42:42 -0400
  • 2bd48a7351 Bad comments made it into the previous commit Eric Banks 2012-06-07 23:12:56 -0400
  • 31c3a6be48 BQSR optimization: getRequiredCovariates() and getOptionalCovariates() were creating a new List every time they were being called, and unfortunately getRequiredCovariates().size() is used as the stop condition in for-loops throughout the code. Just maintaining the original list of covariates results in a 15% reduction in runtime for BQSR. Eric Banks 2012-06-07 20:04:10 -0400
  • 0fb9179f76 BQSR optimization: don't clone the original quals for each read, we can just overwrite the original array Eric Banks 2012-06-07 19:41:03 -0400
  • a13d125ba1 Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters) Menachem Fromer 2012-06-07 16:56:32 -0400
  • 32e4fe5c87 Enable zero-sample testing Joel Thibault 2012-06-06 17:41:29 -0400
  • fe9dc0cc3f Explicitly set intervals in new test Joel Thibault 2012-06-06 17:36:43 -0400
  • 0ac4ba9ad3 unintended change crept in Ryan Poplin 2012-06-07 10:59:04 -0400
  • d449f169d3 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-06-07 10:56:55 -0400
  • 0b4281fdd0 misc minor update to HC debug output for when there are a lot of samples Ryan Poplin 2012-06-07 10:56:41 -0400
  • bad50a1b05 Fix docs Eric Banks 2012-06-06 22:45:38 -0400
  • b093ba9dcc Stabilized NGSPlatform code: don't assume all reads have read groups (e.g. artificial SAM records) Eric Banks 2012-06-06 15:17:30 -0400
  • 54f682a99c Unify to NGSPlatform framework. TechnologyComposition annotation now generalizes to Illumina and not just SLX. Eric Banks 2012-06-06 11:44:37 -0400
  • dd46d843fb IR should skip Ion reads just like it does with 454 reads; Tim has confirmed that official platform name for Ion. Eric Banks 2012-06-06 11:04:55 -0400
  • b6a7c3f780 Merged bug fix from Stable into Unstable David Roazen 2012-06-05 17:44:44 -0400
  • 3b2fab9a37 Update stable for shptmp -> hptmp migration David Roazen 2012-06-05 17:38:06 -0400
  • 2cbd6e5f90 Merged bug fix from Stable into Unstable Guillermo del Angel 2012-06-05 15:58:23 -0400
  • ce4dc2128d Adding minor clarification to -mbq argument documentation Guillermo del Angel 2012-06-05 15:17:56 -0400
  • e02ec8c8b6 Don't update the record ID unless we are actually going to emit the record Eric Banks 2012-06-04 14:58:50 -0400
  • 8405156ae1 Refactored VariantsToTable so that 1) genotype-level fields can be specified (stabilized and supported code) and 2) the --moltenize argument could be supported to produce molten output of the data. Added tests that cover these capabilities. Eric Banks 2012-06-04 14:28:32 -0400
  • f11e7ebc3a Fixing the previous fix related to clipping. Adding extra reference padding in the HaplotypeCaller to get those larger alleles during GGA. Ryan Poplin 2012-06-04 12:49:36 -0400
  • 320956ee4b Bug fix in clipping function in ReadUtils for when the read ends at exactly the clipping boundary. Bug fixes in HaplotypeCaller GGA mode for when Smith-Waterman produces a different allele than what was given in the input alleles VCF. GGA mode now works with multiallelic records. Adding min pruning factor argument which is combined with the pruning factor that is determined dynamically by the coverage. Ryan Poplin 2012-06-04 10:55:36 -0400
  • 7a54baf08c Merged bug fix from Stable into Unstable Guillermo del Angel 2012-06-03 08:42:08 -0400
  • 47df7bbc14 Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Guillermo del Angel 2012-06-03 08:38:54 -0400
  • 2ddbdee3bc Fixed broken VariantEval stratifications VariantType and IndelSize - integration tests to follow Guillermo del Angel 2012-06-03 08:38:38 -0400
  • 12a8c54f9a Fixing VCF header for filter elements (thanks Eric) Mauricio Carneiro 2012-06-01 15:45:15 -0400
  • 3b20b4615d ant fasttest: for when you just can't wait David Roazen 2012-06-01 15:03:43 -0400
  • 2e3af1a739 Enable contracts for the release jar tests (whoops...) David Roazen 2012-06-01 13:08:46 -0400
  • fdf607c3a9 One-off walker but techdev may find it useful and expand on it: given a BAM, output series of intervals to file (as interval_list [default] or BED [if -bed used]) where there is coverage. Additionally, print out to stdout at the end total covered bases and total covered bases including soft-clips Guillermo del Angel 2012-05-31 20:47:37 -0400
  • 3a15ba2102 Malformed VCF headers should be User Errors Eric Banks 2012-05-31 16:05:53 -0400
  • d1822c926c Temporary fake release directories for Bamboo testing purposes David Roazen 2012-05-31 16:02:57 -0400
  • 1aa9742e55 Decrease block size from 1Mb to 100Kb Joel Thibault 2012-05-30 15:32:32 -0400
  • c4f7df4dce When an underlying exception occurs because of the user error, if the exception instance does not include a message instead of telling the user "because null", tell them "because <exception class name>". Khalid Shakir 2012-05-30 16:39:06 -0400
  • 421d0d1435 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-05-30 15:21:35 -0400