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  • 7c34f05082 Merge remote-tracking branch 'origin/master' into intel David Roazen 2014-03-10 14:07:36 -0400
  • 5a6aa54673 Revert "Update HaplotypeCaller and VariantAnnotator test MD5s" David Roazen 2014-03-10 14:06:51 -0400
  • e7d6db033b Revert "Revert "Change default HaplotypeCaller PairHMM implementation back to LOGLESS_CACHING"" David Roazen 2014-03-10 14:05:51 -0400
  • 90ed6bd4ab Merge pull request #551 from broadinstitute/ami-splitVCF amilev 2014-03-10 11:02:38 -0400
  • 2a6f05a8a1 add an option to randomly (uniformly) split a vcf file/s to more than 2 files. The old code that allow split to two files (given in the input) is kept to allow uneven splitting between files. Ami Levy-Moonshine 2014-03-06 10:47:16 -0500
  • f070583f29 Update HaplotypeCaller and VariantAnnotator test MD5s David Roazen 2014-03-07 10:54:27 -0500
  • 6e98e9e589 Removed g_haplotype* global variables in native code so that it works with multi-threading in Java. Modified VectorLoglessPairHMM.java so that jniInitializeRegion and jniFinalizeRegion are empty Karthik Gururaj 2014-03-06 22:08:35 -0800
  • 3999677c93 Changed to delete[] where applicable Karthik Gururaj 2014-03-06 12:23:08 -0800
  • f706bcb1c0 Merge pull request #550 from broadinstitute/ami-updateHC_scipt amilev 2014-03-06 14:48:22 -0500
  • 4de989ebf1 update HC scala script to allow the RNA-seq mode parameters of HC Ami Levy-Moonshine 2014-03-06 14:45:51 -0500
  • a29777765d Binary library Karthik Gururaj 2014-03-06 11:14:46 -0800
  • 7844d956ac Modified delete to delete[] Karthik Gururaj 2014-03-06 11:13:34 -0800
  • 27e640d640 Modified SSE4.1 and 4.2 checks with _may_i_use_cpu_feature() Karthik Gururaj 2014-03-06 08:49:52 -0800
  • 6166d08183 Merge branch 'intel_pairhmm' of /data/broad/gsa-unstable into intel_pairhmm Karthik Gururaj 2014-03-06 08:38:12 -0800
  • 37f107cb3a Using Mustafa's function _may_i_use_cpu_feature() for AVX check Karthik Gururaj 2014-03-06 08:37:48 -0800
  • c0093be06a Merge pull request #549 from broadinstitute/eb_remove_DownsampleReadsQC Eric Banks 2014-03-06 11:03:20 -0500
  • 084750b807 Remove this bad, bad walker. It doesn't even belong in private. Eric Banks 2014-03-06 11:01:41 -0500
  • 3f3df90412 Revert "Change default HaplotypeCaller PairHMM implementation back to LOGLESS_CACHING" David Roazen 2014-03-06 10:15:35 -0500
  • 7f1973193c Fix linking bug in copy_release.sh script David Roazen 2014-03-06 07:26:17 -0500
  • 9df59bd8cc Update pom versions to mark the start of GATK 3.1 development David Roazen 2014-03-06 00:05:58 -0500
  • 8fedaf541c Merge remote-tracking branch 'unstable/master' David Roazen 2014-03-05 23:41:48 -0500
  • 34edcb8ddf Update pom versions for the 3.0 release David Roazen 2014-03-05 23:37:21 -0500
  • a9ddfdb7c0 Remove external-example module from public pom.xml David Roazen 2014-03-05 20:25:38 -0500
  • 53895e15cd Change default HaplotypeCaller PairHMM implementation back to LOGLESS_CACHING David Roazen 2014-03-05 19:26:37 -0500
  • 2defeba445 Merge pull request #548 from broadinstitute/ami-update-FullProcessingPipeline amilev 2014-03-05 15:49:34 -0500
  • d3de6413c9 Move warnings to debug logging status because they will definitely scare users Eric Banks 2014-03-05 15:05:21 -0500
  • 5b55380bdf Revert changes to archived build.xml David Roazen 2014-03-05 14:40:57 -0500
  • 60ebfbe543 upadte the script (for RNA pipeline and comment out RR from it) Ami Levy-Moonshine 2014-03-05 14:17:24 -0500
  • 51b8ea5d59 Reset version Karthik Gururaj 2014-03-05 11:19:08 -0800
  • cf87bdfbb7 Merge branch 'intel_pairhmm' of /data/broad/gsa-unstable into intel_pairhmm Karthik Gururaj 2014-03-05 10:12:20 -0800
  • 0bf8bef490 Meh Karthik Gururaj 2014-03-05 10:12:17 -0800
  • 0e4f2ac9e1 Added vectorized PairHMM implementation by Mohammad and Mustafa into the Maven build of GATK. Intel Repocontact 2014-03-05 09:30:29 -0800
  • c6ddb389a7 Added vectorized PairHMM implementation by Mohammad and Mustafa into the Maven build of GATK. Intel Repocontact 2014-03-05 09:30:29 -0800
  • b9afe800ae Merge correction Karthik Gururaj 2014-03-05 10:06:45 -0800
  • ec54528605 Fixed error in Sandbox.java Karthik Gururaj 2014-03-05 09:36:55 -0800
  • 8fcbf9272c Merge branch 'intel_pairhmm' of /data/broad/gsa-unstable into intel_pairhmm Karthik Gururaj 2014-03-05 09:35:50 -0800
  • 7ca4daf7a2 Merge pull request #546 from broadinstitute/ldg_CGPtests Eric Banks 2014-03-05 12:30:42 -0500
  • d81116eb1d Added vectorized PairHMM implementation by Mohammad and Mustafa into the Maven build of GATK. Intel Repocontact 2014-03-05 09:30:29 -0800
  • 43fdd38342 Add error handling to CalculateGenotypePosteriors to catch multiallelic variants with wrong number of ACs -- throws UserException; added tests in PosteriorLikelihoodsUtilsUnitTests Add error handling to CalculateGenotypePosteriors for cases where MLEAC>AN; add tests in PosteriorLikelihoodsUtilsUnitTests Add unit tests to confirm that CalculateGenotypePosteriors has the ability to switch genotypes for four cases Laura Gauthier 2014-02-18 11:44:19 -0500
  • 7f9f58dbd1 Added hidden flag to GenotypeConcordance to output sites of discordant genotypes (to System.out) Revised ConcondanceMetrics tests to adapt to change Added comments to PosteriorLikelihoodsUtils Laura Gauthier 2014-02-27 15:48:40 -0500
  • 1a1fb8cf6f Merge pull request #545 from broadinstitute/jt_logging droazen 2014-03-05 11:40:35 -0500
  • 2648b41398 Added vectorized PairHMM implementation by Mohammad and Mustafa into the Maven build of GATK. Karthik Gururaj 2014-02-25 21:44:20 -0800
  • 6aa67a2585 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Intel Repocontact 2014-03-05 08:14:32 -0800
  • c5751870ca Script to manually create private/testdata symlinks David Roazen 2014-03-05 10:41:14 -0500
  • 57747ad35e Logger output should go to STDERR instead of STDOUT Joel Thibault 2014-03-04 19:40:08 -0500
  • b4dde6a78c Add WARN to the valid log types error message - order if statements and error message in increasing severity Joel Thibault 2014-02-27 10:07:38 -0500
  • 243d1bc07a Merge pull request #542 from broadinstitute/vrr_efficient_find_best_haplotypes Valentin Ruano Rubio 2014-03-05 09:44:50 -0500
  • 58905e8fe0 Disable the intermittently-failing and flawed ProgressMeterDaemonUnitTest David Roazen 2014-03-05 09:15:26 -0500
  • 660a70fb61 Update gatkdocs publishing script for maven David Roazen 2014-03-05 08:23:50 -0500
  • 1de2d2546e Merge branch 'master' of github.com:broadinstitute/gsa-unstable Intel Repocontact 2014-03-05 00:04:21 -0800
  • 69bf2b3247 Added a more efficient implementation of the KBest haplotype finder code (CONT.) Valentin Ruano-Rubio 2014-03-03 16:33:05 -0500
  • 7acf2eb0e7 Added a more efficient implementation of the KBest haplotype finder code. Valentin Ruano-Rubio 2014-02-27 03:04:41 -0500
  • 09d2415bea Merge pull request #541 from broadinstitute/eb_HC_sensitivity Eric Banks 2014-03-03 23:56:06 -0500
  • b99bf85ec8 Fixed bug where dangling tail merging occasionally created a cycle in the graph. Eric Banks 2014-03-03 22:42:56 -0500
  • 4d69af189e Minor change: make the --dontUseSoftClippedBases @Advanced instead of @Hidden Eric Banks 2014-02-27 13:29:10 -0500
  • fa65716fe9 Added code to retrieve dangling heads from the read threading graph (previously we were rescuing just the tails). Eric Banks 2014-02-02 04:16:31 -0500
  • cecdd2f2c5 Merge pull request #539 from broadinstitute/eb_hard_clip_exon_overhangs_for_ami amilev 2014-03-03 12:23:11 -0500
  • a893765ae2 Added license to Makefile Karthik Gururaj 2014-03-03 09:11:02 -0800
  • 7cd23543a1 Added public license text to all C++ files Karthik Gururaj 2014-03-03 09:04:00 -0800
  • f7d10b9781 Merge pull request #544 from broadinstitute/eb_archive_reduce_reads MauricioCarneiro 2014-03-03 11:29:12 +0900
  • 6c872308d8 Add the capability to the N-cigar splitter to also hard-clip off overhangs based on observed split positions. Eric Banks 2014-02-13 10:50:53 -0500
  • 22ad18b919 Moving Reduce Reads to the archive. Eric Banks 2014-02-28 02:05:02 -0500
  • 293234a8dc Merge pull request #540 from broadinstitute/eb_add_ability_to_ignore_individual_filters Eric Banks 2014-03-01 22:27:10 -0500
  • db85dc6fc0 Add an option to AssessNA12878 to be able to ignore one or more specific filters (instead of either all or none). Eric Banks 2014-02-26 15:50:35 -0500
  • e16996d881 Merge pull request #543 from broadinstitute/ks_mvn_gc_config kshakir 2014-03-01 23:09:21 +0700
  • 387188e5bb Attempting to limit gc during Maven tests, using defaults found in JavaCommandLineFunction Khalid Shakir 2014-03-01 15:13:58 +0800
  • 1b395a871a 1. Changed logger.info to logger.warn in PairHMMLikelihoodCalculationEngine.java 2. Committing the right set of files after rebase Karthik Gururaj 2014-02-28 16:08:28 -0800
  • 37526dfad5 1. Added the catch UnsatisfiedLinkError exception in PairHMMLikelihoodCalculationEngine.java to fall back to LOGLESS_CACHING in case the native library could not be loaded. Made VECTOR_LOGLESS_CACHING as the default implementation. 2. Updated the README with Mauricio's comments 3. baseline.cc is used within the library - if the machine supports neither AVX nor SSE4.1, the native library falls back to un-vectorized C++ in baseline.cc. 4. pairhmm-1-base.cc: This is not part of the library, but is being heavily used for debugging/profiling. Can I request that we keep it there for now? In the next release, we can delete it from the repository. 5. I agree with Mauricio about the ifdefs. I am sure you already know, but just to reassure you the debug code is not compiled into the library (because of the ifdefs) and will not affect performance. Karthik Gururaj 2014-02-28 08:59:55 -0800
  • 523eeecc15 Merge pull request #537 from broadinstitute/cw_duplicatevcfcheck_66084436 cwhelan 2014-02-27 13:39:09 -0500
  • e61ba8b340 Added command line checks for duplicate files in ROD lists Chris Whelan 2014-02-26 11:40:01 -0500
  • 2d0ce45bb0 Moved JNI_README Karthik Gururaj 2014-02-27 10:12:23 -0800
  • 4395d25726 Merge pull request #538 from broadinstitute/ks_integration_test_fix Eric Banks 2014-02-26 21:04:06 -0500
  • c645725fc3 1. Renamed directory structure from public/c++/VectorPairHMM to public/VectorPairHMM/src/main/c++ as per Khalid's suggestion 2. Use java.home in public/VectorPairHMM/pom.xml to pass environment variable JRE_HOME to the make process. This is needed because the Makefile needs to compile JNI code with the flag -I<JRE_HOME>/../include (among others). Assuming that the Maven build process uses a JDK (and not just a JRE), the variable java.home points to the JRE inside maven. 3. Dropped all pretense at cross-platform compatibility. Removed Mac profile from pom.xml for VectorPairHMM Karthik Gururaj 2014-02-26 15:17:15 -0800
  • bd71ba35e5 Moved pom.xml to VectorPairHMM and updated artifactId Karthik Gururaj 2014-02-26 14:01:46 -0800
  • da587d48ed Using absolute paths in generated diff commands, to ease running them from any directory. Khalid Shakir 2014-02-27 04:43:29 +0800
  • c163e6d0d2 Separate failsafe directories for each of the integration test types [#66515572] Khalid Shakir 2014-02-27 01:56:00 +0800
  • da23f2020a Merge branch 'intel_pairhmm' of /data/broad/gsa-unstable into intel_pairhmm Karthik Gururaj 2014-02-26 11:48:27 -0800
  • b81e2c2948 Native library part of git repo Karthik Gururaj 2014-02-26 11:44:28 -0800
  • 0fe843bfd9 Followed Khalid's suggestion for packing libVectorLoglessCaching into the jar file with Maven Karthik Gururaj 2014-02-26 10:53:51 -0800
  • 15fe244e4b Now has PAPI values Karthik Gururaj 2014-02-25 21:44:20 -0800
  • e32e9e6af6 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Intel Repocontact 2014-02-26 11:47:01 -0800
  • 53d5bc93b2 Native library part of git repo Karthik Gururaj 2014-02-26 11:44:28 -0800
  • 0d5627c2f1 Followed Khalid's suggestion for packing libVectorLoglessCaching into the jar file with Maven Karthik Gururaj 2014-02-26 10:53:51 -0800
  • 84d8b0e9a1 Merge pull request #535 from broadinstitute/ks_pd_queuelogdir_gatherbam_patches Eric Banks 2014-02-26 08:55:10 -0500
  • ac1cefce29 Merge branch 'intel_pairhmm' of /data/broad/gsa-unstable into intel_pairhmm After rebase into local repo Karthik Gururaj 2014-02-25 21:51:57 -0800
  • a058e96c34 Now has PAPI values Karthik Gururaj 2014-02-25 21:44:20 -0800
  • ff2a972ab5 Merge branch 'master' of github.com:broadinstitute/gsa-unstable Intel Repocontact 2014-02-25 20:56:28 -0800
  • f02ce6eca7 Added tests for cleaning up scattered .bai files, and using the log directory. Re-added import java.io.File for BamGatherFunction. Other cleanup to resolve scala syntax warnings from intellij. Moved Example UG script to from protected to public. Khalid Shakir 2014-02-24 19:33:22 +0800
  • 0405afeab2 Inherit BamGatherFunction from MergeSamFiles rather than PicardBamFunction pdexheimer 2013-11-27 10:47:04 -0500
  • 504c125c26 Ensure .out files are saved into logDirectory pdexheimer 2013-11-25 11:03:01 -0500
  • 51dcd364a5 Added logDirectory argument pdexheimer 2013-11-25 11:00:55 -0500
  • e340b6237a Merge pull request #534 from broadinstitute/ks_queue_private_link_qscripts kshakir 2014-02-25 06:16:50 -0500
  • a90745bbe5 Added missing private qscripts symbolic links to queue-private module. Khalid Shakir 2014-02-25 17:46:47 +0800
  • b1885d449b Merge pull request #533 from broadinstitute/eb_normalize_FS_contingency_table Eric Banks 2014-02-25 02:18:01 -0500
  • 0f30df0356 Stopgap procedure to rescue Fisher Strand for cases where there's lots of data. Eric Banks 2014-02-14 15:02:00 -0500
  • e8ea9f58d3 Merge pull request #531 from broadinstitute/ks_build_patches droazen 2014-02-24 15:13:16 -0500
  • 1c7eac50fc Merge pull request #532 from broadinstitute/vrr_graphbased_there_is_no_such_edge_fix Valentin Ruano Rubio 2014-02-24 12:08:47 -0500
  • 0b3a70b8c1 Fix for a bug a bug in (Assembly Graph) Routes. Valentin Ruano-Rubio 2014-01-28 11:03:31 -0500
  • 7e516b294f Replaced local drmaa and Jama artifacts with versions from maven central. Removed unused caliper binary from local repo. Khalid Shakir 2014-02-18 04:03:54 +0800
  • 9b7fc37b14 Moved private/scala/test to private/queue-private/src/test/scala Added junction/symbolic links so that queue-private tests will run. Khalid Shakir 2014-02-18 03:56:17 +0800