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  • 74b51c5c7a Improve test suite tmp file cleanup David Roazen 2014-05-27 13:41:44 -0400
  • b24cff780b Removing HWP from GenotypeSummaries because of integer overflow issues with 91K samples. Removing CCC because it is redundant. Ryan Poplin 2014-05-27 09:59:52 -0400
  • 3696c2d817 Merge pull request #639 from broadinstitute/rp_dont_merge_tails_in_exomes Eric Banks 2014-05-27 09:37:49 -0400
  • ec7c4ea2ba Unfortunately dangling tail recovery is dangerous in exome data. Turning it off by default for now. Ryan Poplin 2014-05-22 10:20:01 -0400
  • cfde6e72bf Merge pull request #633 from broadinstitute/vrr_sw_pairwise_alignment Valentin Ruano Rubio 2014-05-23 09:27:55 -0400
  • 979ab0453e Moved GlobalEdgeGreedySWPairwiseAlignment to the archive Valentin Ruano-Rubio 2014-05-21 10:17:55 -0400
  • 7c8a1ae892 Fix for SW to make double comparisons with a tolerance Valentin Ruano-Rubio 2014-05-20 18:32:03 -0400
  • d4340de179 Merge pull request #637 from broadinstitute/ks_package_rename_patches kshakir 2014-05-22 21:06:25 -0400
  • b7e98bdae9 Fixed GATK docs artifact, moved protected ExampleUG tests. Khalid Shakir 2014-05-20 13:17:30 -0400
  • 248f7394ca Update manual private testdata linking script for maven changes David Roazen 2014-05-20 14:16:33 -0400
  • 56445f6eef Update nightly build and internal build release scripts for maven changes David Roazen 2014-05-20 13:20:29 -0400
  • f24fb4e518 Merge pull request #635 from broadinstitute/rp_HC_gvcf_banding_docs Ryan Poplin 2014-05-20 11:01:41 -0400
  • 581843d994 Minor updates to HC docs. Ryan Poplin 2014-05-20 10:01:11 -0400
  • 40f289c622 Merge pull request #632 from broadinstitute/ks_package_rename kshakir 2014-05-19 18:05:07 -0400
  • 88d7e23c44 After talking with Mauricio and Karthik, updated MD5s and added a note about PairHMM causing test variability. Khalid Shakir 2014-05-13 23:43:53 +0800
  • 972a82d386 Changed 'sting' to 'gatk' in the VectorLoglessPairHMM classes and the C++ code Karthik Gururaj 2014-05-09 10:43:01 -0700
  • 3939971d78 After renaming the packages, instead of updating the JNI library used for testing bwa, moving the classes to the archive. NOTE: The migrated READEME.md has been added that will allow others to possibly ressurect this code as needed. Khalid Shakir 2014-04-02 03:55:21 +0800
  • 2c854e554a Refactored maven directories and java packages replacing "sting" with "gatk". To reduce merge conflicts, this commit modifies contents of files, while file renamings are in previous commit. See previous commit message for list of changes. Khalid Shakir 2014-03-04 23:10:36 +0700
  • 4e6d43d003 Refactored maven directories and java packages replacing "sting" with "gatk". To reduce merge conflicts, this commit only renames files, while file modifications are in next commit. Some updates/fixes here are actually included in the next commit. = Maven updates Moved artifacts to new package names: * private/queue-private -> private/gatk-queue-private * private/gatk-private -> private/gatk-tools-private * public/gatk-package -> protected/gatk-package-distribution * public/queue-package -> protected/gatk-queue-package-distribution * protected/gatk-protected -> protected/gatk-tools-protected * public/queue-framework -> public/gatk-queue * public/gatk-framework -> public/gatk-tools-public New poms for new artifacts and packages: * private/gatk-package-internal * private/gatk-queue-package-internal * private/gatk-queue-extensions-internal * protected/gatk-queue-extensions-distribution * public/gatk-engine Updated references to StingText.properties to GATKText.properties. Updated ant-bridge.sh to use gatk.* properties instead of sting.*. = Engine updates Renaming files containing engine parts from o.b.gatk.tools to o.b.gatk.engine. Changed package references from tools to engine for CommandLineGATK, GenomeAnalysisEngine, ReadMetrics, ReadProperties, and WalkerManager. Changed package reference tools.phonehome to engine.phonehome. Renamed classes *Sting* to *GATK*, such as ReviewedGATKException. = Test updates Moved gatk example resources. Moved test engine files from tools to engine packages. Moved resources for phonehome to proper package. Moved test classes under o.b.gatk into packages: * o.b.g.utils.{BaseTest,ExampleToCopyUnitTest,GATKTextReporter,MD5DB,MD5Mismatch,TestNGTestTransformer} * o.b.g.engine.walkers.WalkerTest Updated package names in DependencyAnalyzerOutputLoaderUnitTest's data. = Queue updates Moving queue scripts to location where generated extensions can be used. Renamed *.q to *.scala, updating licenses previously missed by git hooks. Moved queue extensions to new artifact gatk-queue-extensions. Fixed import statments frequently merge-conflicting on FullProcessingPipeline.scala. = BWA Added README on how to obtain and include bwa as a library. Updated libbwa build. Fixed packaged names under bwa/java implementation. Updated contents of BWCAligner native implementation. = Other fixes Don't duplicate the resource bundle entries by both unpacking *and* appending. (partial fix) Staged engine and utils poms to build GATKText.properties, once Utils random generator dependency on GATK engine is fixed. Re-enabled custom testng listeners/reporters and moved testng dependencies to the gatk-root. Updated comments referencing Sting with GATK. Moved a couple untangled classes from gatk-tools-public to gatk-utils and gatk-engine. Khalid Shakir 2014-03-04 22:08:01 +0700
  • 6dff219bb1 Merge pull request #634 from broadinstitute/ldg_newSingleSampleScript Eric Banks 2014-05-19 15:14:16 -0400
  • 3dea8fed63 Updated single sample exome calling script to use HaplotypeCaller and GenotypeGVCFs Laura Gauthier 2014-05-19 15:07:45 -0400
  • d15dbadeca Merge pull request #631 from broadinstitute/pd_queue_final_status_line jmthibault79 2014-05-16 12:03:28 -0400
  • a5abc079dc Revised final Queue status line to display number of jobs in each state when the script fails * Addresses PT 61552466 * Included a simple scala script in private/testdata that will always fail Phillip Dexheimer 2014-05-14 22:31:46 -0400
  • 1b2d6ae5e4 Merge pull request #629 from broadinstitute/jg_add_gather_bqsr Eric Banks 2014-05-14 12:09:15 -0400
  • 78560212d0 Merge pull request #630 from broadinstitute/pd_blank_lines_in_listfile jmthibault79 2014-05-14 11:32:44 -0400
  • 8297cd1a1a Merge pull request #619 from broadinstitute/pd_intervalmerge_doc droazen 2014-05-14 11:22:18 -0400
  • 77449961ab Allow blank lines in a (non-BAM) list file * Addresses PT Bug 67841052 * Added Unit Test Phillip Dexheimer 2014-05-13 22:11:17 -0400
  • 88ae203075 Add a (picard) command line wrapper around BQSRGatherer geoffjentry 2014-05-13 11:39:38 -0400
  • cca3d167db Merge pull request #627 from broadinstitute/ks_picard_htsjdk_package_rename kshakir 2014-05-08 13:12:22 -0400
  • 67e44985b1 Java/Scala imports updated for new package names. Fourth of four commits for picard/htsjdk package rename. Khalid Shakir 2014-05-07 06:58:19 +0800
  • cc3f1f2b96 Revved picard libraries. Third of four commits for picard/htsjdk package rename. Khalid Shakir 2014-05-07 13:49:30 +0800
  • a894a2dddb Updates to GATK classes and POMs that need updating, plus RodSystemValidation md5 updates. GATK classes accessing package protected htsjdk classes changed to new package names. POMs updated to support merging of sam/tribble/variant -> htsjdk and changes to picard artifact. RodSystemValidation outputs changed due to variant codec packages changes, requiring test md5 updates. Second of four commits for picard/htsjdk package rename. Khalid Shakir 2014-05-07 06:54:00 +0800
  • 3ce3e27aa1 Moved GATK classes and POMs that will need updating. GATK classes accessing package protected htsjdk classes will need new package names. POMs will merge sam/tribble/variant into htsjdk. Move only, contents updated in next commit. First of four commits for picard/htsjdk package rename. Khalid Shakir 2014-05-07 12:50:28 +0800
  • 53b2364cf8 Merge pull request #623 from broadinstitute/ldg_concordanceSites ldgauthier 2014-05-07 10:19:09 -0400
  • bf7b97393e Add ability to output to a file discordant loci and their respective genotypes for each sample Laura Gauthier 2014-05-02 14:50:17 -0400
  • f03a12263a Merge pull request #625 from broadinstitute/intel_updateCell_inlined MauricioCarneiro 2014-05-07 10:11:09 -0400
  • bd33c3334e Merge pull request #626 from broadinstitute/intel_pairhmm MauricioCarneiro 2014-05-06 19:23:35 -0400
  • d9c489f928 Removed scary warning messages for VectorPairHMM Karthik Gururaj 2014-05-06 10:59:24 -0700
  • fb8578ec8e Inlined the code from updateCell - helps Java JIT to detect hotspots and produce good native code Karthik Gururaj 2014-05-06 10:32:07 -0700
  • 587e81fbd9 Merge pull request #573 from broadinstitute/intel_pairhmm MauricioCarneiro 2014-05-05 16:27:04 -0400
  • f6ea25b4d1 Parallel version of the JNI for the PairHMM Karthik Gururaj 2014-03-17 11:42:19 -0700
  • 38b7cfbda9 Merge pull request #621 from broadinstitute/vrr_combine_gvcf_bugfix Ryan Poplin 2014-05-02 11:52:32 -0400
  • 4957359963 Merge pull request #620 from broadinstitute/ldg_fixCGL Ryan Poplin 2014-05-02 11:38:06 -0400
  • d563072282 Fix for CombineGVCFs and GenotypeGVCFs recurrent exception about missing PLs Valentin Ruano-Rubio 2014-04-29 23:07:30 -0400
  • e64479d4f5 Fixed GP annotation reading bug and updated integration test Laura Gauthier 2014-05-02 08:29:00 -0400
  • cb97afd7d8 Merge pull request #618 from broadinstitute/mm_java_8 jmthibault79 2014-05-01 10:33:31 -0400
  • 7a2b70a10f Made IntervalSharder respect the IntervalMergingRule specified on the command line * This addresses PT Bug 69741902 * Added a required IMR argument to FilePointer, BAMScheduler, IntervalSharder, and SAMDataSource * This rule is used by FilePointer.combine and FilePointer.union * Added unit and integration tests Phillip Dexheimer 2014-04-24 22:49:52 -0400
  • fe3c68cb2d Java 8 compatability fix: `Reflections` NPE bugfix. Michael McCowan 2014-04-29 13:06:05 -0400
  • 4ce09d8693 Merge pull request #617 from broadinstitute/rp_GenotypeGVCF_trimAD Valentin Ruano Rubio 2014-04-28 19:53:41 -0400
  • 41d3069213 When we subset PLs because Alleles are removed during genotyping we also need to subset AD. Ryan Poplin 2014-04-28 14:39:18 -0400
  • 10ee35eafa Merge pull request #616 from broadinstitute/ks_cjav_pbsengine_no_default_queue kshakir 2014-04-28 14:24:51 -0400
  • 06dbe74a23 Merge pull request #609 from kcibul/kc_cancersimreads Ryan Poplin 2014-04-28 13:31:56 -0400
  • 8d5a7d412b Merge pull request #615 from broadinstitute/ami-createCigarDNFilter Ryan Poplin 2014-04-28 13:31:04 -0400
  • b7a59e01aa Removed setting of a default queue in PbsEngineJobRunner. Discussed here: http://gatkforums.broadinstitute.org/discussion/3959/would-it-be-possible-for-pbsengine-jobrunner-not-to-set-a-default-queue Carlos Borroto 2014-04-26 12:41:47 -0400
  • 13dd755468 create a new read transformer that refactor NDN cigar elements to one N element. Ami Levy-Moonshine 2014-04-25 15:52:49 -0400
  • 385fe5fb56 Merge pull request #614 from broadinstitute/rp_fix_GenotypeGVCF_VCF_headers Eric Banks 2014-04-25 15:36:35 -0400
  • 221b999cb0 GenotypeGVCF was pulling the headers from all input rods including DBsnp. Now it pulls from just the input variant rods. Ryan Poplin 2014-04-25 11:12:11 -0400
  • 147ae21253 Merge pull request #606 from broadinstitute/ldg_CalibrateLikelihoodsForCGP ldgauthier 2014-04-24 10:58:40 -0400
  • 9f3cbb2ef1 Improvements to CalculateGenotypePosteriors and CalibrateGenotypeLikelihoods Laura Gauthier 2014-03-17 08:51:02 -0400
  • 92a3aa35d5 Merge pull request #613 from broadinstitute/ami-RNAEdttingTool amilev 2014-04-23 17:17:02 -0400
  • 9e5333f1d1 create a new tool CountMutationTypes Ami Levy-Moonshine 2014-03-19 15:23:00 -0400
  • 58c8b2dd84 Merge pull request #611 from broadinstitute/mm_otf_sample_rename_support_whitespacing_sample_names droazen 2014-04-22 13:01:15 -0400
  • 8290d3c8ac Allow for non-tab whitespace in sample names when performing on-the-fly sample-renaming. Michael McCowan 2014-04-18 13:55:41 -0400
  • d38835822e Merge pull request #612 from broadinstitute/vrr_integration_test_error_quickfix Valentin Ruano Rubio 2014-04-20 18:40:22 -0400
  • e610373169 Fixed integration test problems from previous premature merge Valentin Ruano-Rubio 2014-04-20 17:11:51 -0400
  • f03e5ffeb1 Merge pull request #604 from broadinstitute/vrr_hc_omniploidy_general_api MauricioCarneiro 2014-04-20 07:43:23 -0400
  • 4e5850966a Reengineer engine constructors Valentin Ruano-Rubio 2014-04-19 17:58:14 -0400
  • 7455ac9796 Addressed revisions Valentin Ruano-Rubio 2014-04-18 15:43:54 -0400
  • a9a48f2459 Merge pull request #607 from broadinstitute/mm_bugfix_raise_mathutils_n_ceiling Ryan Poplin 2014-04-17 13:32:34 -0400
  • b840cf6b3f Merge pull request #610 from broadinstitute/jt_block_compressed_vcfs jmthibault79 2014-04-17 12:32:49 -0400
  • 1ab50f4ba8 CatVariants now handles BCF and Block-Compressed VCF Joel Thibault 2014-04-09 16:38:11 -0400
  • 6b9e38c8bb incorporated comments from review, made variables final, made AF paramater hidden, and added bounds checking to AF value Kristian Cibulskis 2014-04-16 19:29:25 -0400
  • 7115cadbd8 extended SimulateReadsForVariants to optionally use the AF field to indicate allele fraction of the simulated event, useful in cancer and other variable ploidy use cases Kristian Cibulskis 2014-04-16 15:45:36 -0400
  • 4c74319578 Update for Picard refactoring which improves block-compressed VCF reading Joel Thibault 2014-04-16 13:11:06 -0400
  • fd09cb7143 Rev Picard 1.111.1920 Joel Thibault 2014-04-11 16:34:12 -0400
  • f98df5c071 Integration test for the file extensions CatVariants should handle Joel Thibault 2014-04-04 16:10:04 -0400
  • bdd7024d00 Integration test for block-compressed VCF reading Joel Thibault 2014-04-11 16:20:35 -0400
  • ce770b032a Move execAndCheck() to ProcessController Joel Thibault 2014-04-09 14:29:26 -0400
  • b197618d13 This comment is no longer true Joel Thibault 2014-04-11 15:57:28 -0400
  • 34ece31f4a Merge pull request #605 from broadinstitute/ks_escape_dir_names MauricioCarneiro 2014-04-15 05:56:35 -0400
  • 218fe3875a Quoting -out parameter during resource bundle (StingText.properties) creation. Fixes case where directory has parenthesis in it, like "Dropbox (Broad Dropbox1)". Khalid Shakir 2014-04-15 17:06:49 +0800
  • f0732d386c Support more samples in math utilities. Mike 2014-04-14 12:05:38 -0400
  • 08203b516e Disentangle UG and HC Genotyper engines. Valentin Ruano-Rubio 2014-03-21 10:16:26 -0400
  • 4b140c9e48 Merge pull request #600 from broadinstitute/rp_random_forest_no_QUAL Ryan Poplin 2014-04-11 13:41:05 -0400
  • 04ddbac585 Improvements to the Random Forest pipeline based on Marathon results. Ryan Poplin 2014-04-08 10:39:18 -0400
  • 6d58e61f23 Merge pull request #603 from broadinstitute/ks_specify_columns_analyzerunreports kshakir 2014-04-11 04:30:31 +0800
  • c84235c17c Mapping fields to explicit column names in analyzeRunReports.py. Removed SQLSetupTable support. Khalid Shakir 2014-04-11 03:54:24 +0800
  • e38a295ebd Merge pull request #601 from broadinstitute/ami-updateScalaScript Eric Banks 2014-04-10 16:01:02 -0400
  • 1590f06322 Merge pull request #602 from broadinstitute/use_version_controlled_scripts_for_s3_dl droazen 2014-04-10 15:40:37 -0400
  • 147bd88d26 Use version-controlled copies of scripts in GATKReports downloader David Roazen 2014-04-10 15:39:06 -0400
  • 40360ddb56 update scala scrits to include more of the pipeline stpes Add a new script for evaluating the RNA-seq downsample results Ami Levy-Moonshine 2014-03-19 15:23:00 -0400
  • c275d76a3e Merge pull request #599 from broadinstitute/jt_logging_test jmthibault79 2014-04-09 15:31:51 -0400
  • c84126205b Test that stdout redirects and log files do not affect output Joel Thibault 2014-02-26 14:46:53 -0500
  • 1103fd231a Better exception message Joel Thibault 2014-04-08 14:30:11 -0400
  • 1001a75d0e Merge pull request #598 from broadinstitute/rp_random_forest_fix_tranches Ryan Poplin 2014-04-09 09:28:23 -0400
  • 5b32b7b191 Merge pull request #595 from broadinstitute/ks_picard_matecigar_update kshakir 2014-04-09 10:30:22 +0800
  • edd15add7c Bug fix for correctly parsing the tranche tag in the RandomForestWalker. Ryan Poplin 2014-04-08 15:20:36 -0400
  • a6b0754990 After comments from @nh13, updated latest picard and setMateInfo call. Khalid Shakir 2014-04-08 09:52:04 +0800
  • cc580ac75f Merge pull request #593 from broadinstitute/ks_bqsrgatherer_missing_readgroups_68720468 kshakir 2014-04-09 03:17:53 +0800
  • 3047d6ff32 BQSRGatherer handles missing read groups from some input files. [#68720468] Khalid Shakir 2014-04-08 02:59:51 +0800