Graph ofHTSeqGenie
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  • 84dba93 (HEAD -> master, origin/master, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:07:30 -0400;
  • b027af7 (origin/RELEASE_3_16, RELEASE_3_16) bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:07:30 -0400;
  • 3c6ad4f bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:12:25 +0000;
  • a3c4a34 (origin/RELEASE_3_15, RELEASE_3_15) bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:12:25 +0000;
  • c66a4ad Pass serialized S4 instances thru updateObject() by Hervé Pagès <hpages.on.github@gmail.com> 2021-11-21 00:18:55 -0500;
  • de7a7d4 bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:05:03 +0000;
  • eb291fb (origin/RELEASE_3_14, RELEASE_3_14) bump x.y.z version to even y prior to creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:05:03 +0000;
  • 8385ac5 bump x.y.z version to odd y following creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 15:54:22 +0000;
  • ddd1eb5 (origin/RELEASE_3_13, RELEASE_3_13) bump x.y.z version to even y prior to creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 15:54:22 +0000;
  • 14d3962 bump x.y.z version to odd y following creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 10:47:41 -0400;
  • 1967349 (origin/RELEASE_3_12, RELEASE_3_12) bump x.y.z version to even y prior to creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 10:47:41 -0400;
  • 89d8677 bump x.y.z version to odd y following creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:31:40 +0000;
  • e1dc89d (origin/RELEASE_3_11, RELEASE_3_11) bump x.y.z version to even y prior to creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:31:40 +0000;
  • dfbe4b0 fix bug in reportPipelineQA.R by Jens Reeder <reeder.jens@gene.com> 2020-04-21 21:03:56 -0700;
  • 4a4256f - make countGenomicFeatures work with subclasses of GRangesList by Jens Reeder <reeder.jens@gene.com> 2020-03-16 17:22:54 -0700;
  • da771dc bump x.y.z version to odd y after creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:36:24 -0400;
  • 481e232 (origin/RELEASE_3_10) bump x.y.z version to even y prior to creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:08:34 -0400;
  • ab32c61 bump x.y.z versions to odd y after creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 12:11:15 -0400;
  • 8a95eba (origin/RELEASE_3_9, RELEASE_3_9) bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 11:53:38 -0400;
  • 6ed756a bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:30 -0400;
  • 56fca6c (origin/RELEASE_3_8, RELEASE_3_8) bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:41:49 -0400;
  • 50eb3d9 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:39 -0400;
  • 39182b1 (origin/RELEASE_3_7, RELEASE_3_7) bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:35:27 -0400;
  • c94cc72 use is(x, "GRangesList") instead of class(x) == "GRangesList" by Hervé Pagès <hpages@fredhutch.org> 2018-02-04 22:27:59 -0800;
  • 80cc972 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:52:33 -0400;
  • 2acd6cd (origin/RELEASE_3_6, RELEASE_3_6) bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:39:52 -0400;
  • 1a49bae bump x.y.z versions to odd y after creation of 3_5 branch by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:50:57 +0000;
  • 0b2158b (origin/RELEASE_3_5, RELEASE_3_5) Creating branch for BioC 3.5 release by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:45:44 +0000;
  • bc083d7 bump x.y.z versions to even y prior to creation of 3_5 branch by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:25:24 +0000;
  • 627c603 fix variant calling tests after changes to bam_tally in gmapR by Jens Reeder <reeder.jens@gene.com> 2017-03-31 21:50:42 +0000;
  • 119ad0b bump x.y.z versions to odd 'y' after creation of 3_4 branch by Herve Pages <hpages@fhcrc.org> 2016-10-17 19:10:43 +0000;
  • ac9bc83 (origin/RELEASE_3_4, RELEASE_3_4) Creating branch for BioC 3.4 release by Herve Pages <hpages@fhcrc.org> 2016-10-17 19:00:47 +0000;
  • 0ff8661 bump x.y.z versions to even 'y' prior to creation of 3_4 branch by Herve Pages <hpages@fhcrc.org> 2016-10-17 18:45:06 +0000;
  • e072929 add doc sections for annotateVariants by Jens Reeder <reeder.jens@gene.com> 2016-10-07 04:18:54 +0000;
  • 4f49863 remove 1k genoes annotation fro vep defualt call and turn on --database by Jens Reeder <reeder.jens@gene.com> 2016-10-04 22:23:43 +0000;
  • 7ab2359 move --cache option from vep test as those might not be installed on test server. by Jens Reeder <reeder.jens@gene.com> 2016-10-04 22:05:54 +0000;
  • ad6a886 bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
  • 39b1246 (origin/RELEASE_3_3, RELEASE_3_3) Creating branch for BioC 3.3 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:26:31 +0000;
  • 3dc7950 Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
  • 1c6390f added missing comma by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-03-15 21:05:44 +0000;
  • 8ef0071 fix imports by Jens Reeder <reeder.jens@gene.com> 2016-03-14 16:45:35 +0000;
  • 1cd5caf - fix variant calling tests. VT changed filtering behaviour. - remove last remnants of mergeReads steps using pear. Not ready for primetime yet. by Jens Reeder <reeder.jens@gene.com> 2016-03-12 23:56:50 +0000;
  • 212aa59 fix erroneous imports by Michael Lawrence <lawremi@iastate.edu> 2016-03-12 19:11:52 +0000;
  • 0c55cf4 - re-roxygenize by Jens Reeder <reeder.jens@gene.com> 2016-03-11 23:55:45 +0000;
  • 81b6832 add many @import[Methods]From directives; roxygen not re-run by Michael Lawrence <lawremi@iastate.edu> 2016-03-11 23:44:12 +0000;
  • 56ca761 use accessors instead of direct slot access on Hits objects by Herve Pages <hpages@fhcrc.org> 2016-02-22 10:10:07 +0000;
  • 1e459de use setdiff/intersect instead of psetdiff/pintersect on GRangesList objects by Herve Pages <hpages@fhcrc.org> 2016-02-21 21:04:36 +0000;
  • 3794447 Version 4.1.15: - investigating a memory fault produced by tallyVariants() in the test.callVariantsVariantTools.genotype() unit test by Gregoire Pau <gregoire.pau@gmail.com> 2016-01-29 10:41:57 +0000;
  • e60bea6 elementLengths was renamed -> elementNROWS in S4Vectors (new name reflects TRUE semantic, old name will be deprecated soon) by Herve Pages <hpages@fhcrc.org> 2016-01-29 01:22:03 +0000;
  • 0ba3325 Version: 4.1.13: - fixing NGSPIPE-191: removed mergeReads and peared references ; changed BioC imports ; should build on the BioC server (but cannot right now due to VariantTools::tallyVariants memory issues) by Gregoire Pau <gregoire.pau@gmail.com> 2016-01-23 08:35:18 +0000;
  • c77fa29 sync files with the new HTSeqGenie 4.0 code by Gregoire Pau <gregoire.pau@gmail.com> 2016-01-23 07:51:34 +0000;
  • 6cf242c (origin/RELEASE_3_2, RELEASE_3_2) version 3.20.1: - fixed the 'BSgenome.Hsapiens.UCSC.hg19' import warning during R CMD check phase by Gregoire Pau <gregoire.pau@gmail.com> 2016-01-18 20:55:30 +0000;
  • a66f584 checked out version 4.1.11 by Gregoire Pau <gregoire.pau@gmail.com> 2016-01-18 18:49:26 +0000;
  • 93a2903 Bumped version number of all packages after creation of 3.2 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:59:53 +0000;
  • 0b665e0 Creating branch for BioC 3.2 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:57:33 +0000;
  • ff81d47 Bumped versions of all packages prior to creating 3.2 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:36:05 +0000;
  • 611a8c6 resync with "split" methods moving from IRanges to S4Vectors by Herve Pages <hpages@fhcrc.org> 2015-10-02 19:07:22 +0000;
  • 3762b25 rtracklayer::import() has no more 'asRangedData' arg by Herve Pages <hpages@fhcrc.org> 2015-09-10 00:05:20 +0000;
  • 38a67bd Bump versions in trunk after creation of 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:02:44 +0000;
  • 55d5ba7 (origin/RELEASE_3_1, RELEASE_3_1) Creating branch for BioC 3.1 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 20:00:01 +0000;
  • 102692b Bump versions prior to creating 3.1 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-04-16 19:42:01 +0000;
  • 8ba9fbf import the exons methods from GenomicFeatures by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-03-30 21:06:35 +0000;
  • 2e30959 add RUnit to Suggests by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-01-27 19:50:05 +0000;
  • 7530c6b (origin/RELEASE_3_0) - fix bug in indel realignment step when moving bam index file - call genotypes via VariantTools controlled by config value - adapt to changes in API of VariantTools BSgenome.Hsapiens.UCSC.hg19 - use GeneGenome from gmapR to create test genomes - do some cleanup and gc during coverage computation by Jens Reeder <reeder.jens@gene.com> 2015-01-07 07:35:15 +0000;
  • abe4faf Bumping versions after creating 3.0 release branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:47:41 +0000;
  • fd8762e Creating branch for BioC 3.0 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:46:02 +0000;
  • 2c27e71 Bump package versions prior to creating the 3.0 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-10-13 21:38:33 +0000;
  • d3927ab version 3.15.3 - parallelize Indel realignment by chromosome by Gregoire Pau <gregoire.pau@gmail.com> 2014-09-24 19:49:37 +0000;
  • dfc8b93 (origin/RELEASE_2_14, RELEASE_2_14) change maintainer to Jens Reeder by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-08-26 22:41:54 +0000;
  • c6dfd55 Changed Maintainer to Jens Reeder by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-08-26 22:41:14 +0000;
  • c66a12a added HTSeqGenie/man/findVariantFile.Rd HTSeqGenie/man/isSparse.Rd by Gregoire Pau <gregoire.pau@gmail.com> 2014-07-29 18:32:10 +0000;
  • c016aad version 3.15.1 - start next dev cycle - remove count_transcripts and count_ncRNA_nongenic from QA by Gregoire Pau <gregoire.pau@gmail.com> 2014-07-17 20:53:24 +0000;
  • fb16f69 Second version bump after creating 2.14 release branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-04-11 21:21:21 +0000;
  • 6c3b593 Creating 2.14 release branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-04-11 21:17:46 +0000;
  • e99671a First version bump prior to creating 2.14 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2014-04-11 21:07:21 +0000;
  • b6526a3 version 3.13.13: - removed the "no job lefts" tests in test.sclapply() by Gregoire Pau <gregoire.pau@gmail.com> 2014-04-09 00:17:12 +0000;
  • a7935ee version 3.13.12: - now uses TP53Which() (instead of which.rds) for variant calling tests - now builds in BioC by Gregoire Pau <gregoire.pau@gmail.com> 2014-03-28 21:46:35 +0000;
  • e6ea13d version 3.13.11: - now use TxDb.Hsapiens.UCSC.hg19.knownGene's version number in the TP53 genomic feature cache file, to avoid bugs when updating TxDb.Hsapiens.UCSC.hg19.knownGene by Gregoire Pau <gregoire.pau@gmail.com> 2014-03-24 06:16:45 +0000;
  • 85a11e4 modify to new biocViews to DESCRIPTION file by Sonali Arora <sarora@fhcrc.org> 2014-03-04 22:12:21 +0000;
  • f0dcb06 version 3.13.8: - fixed the "as.vector(x, mode) : invalid 'mode' argument" bug by adding the "importFrom(BiocGenerics,table)" NAMESPACE directive by Gregoire Pau <gregoire.pau@gmail.com> 2014-02-27 02:44:48 +0000;
  • 0c13100 version 3.13.2 - activate read trimming for illumina 1.5 quality using the 'B' as qual indicator by Gregoire Pau <gregoire.pau@gmail.com> 2014-01-03 21:27:56 +0000;
  • 38b0852 bump version after release branch has been created by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-10-14 21:47:19 +0000;
  • 03da120 (origin/RELEASE_2_13, RELEASE_2_13) Creating branch for BioC 2.13 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-10-14 21:43:43 +0000;
  • a47133f bump versions prior to creating BioC 2.13 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-10-14 21:29:21 +0000;
  • 800aee7 version 3.11.10 - vignette updated to build on BioC dev by Gregoire Pau <gregoire.pau@gmail.com> 2013-09-30 22:33:23 +0000;
  • 6cba4af version 3.11.10 - vignette updated to build on BioC dev by Gregoire Pau <gregoire.pau@gmail.com> 2013-09-30 21:52:39 +0000;
  • 64bc57d version 3.11.10 - vignette updated to build on BioC dev by Gregoire Pau <gregoire.pau@gmail.com> 2013-09-30 21:06:26 +0000;
  • 94ba646 version 3.11.9 - TP53GenomicFeatures() now uses the same temp dir as TP53Genome(), to fix a build issues on BioC servers by Gregoire Pau <gregoire.pau@gmail.com> 2013-09-28 00:58:06 +0000;
  • 95dac1b version 3.11.8 -choice of VT filters configurable via config by Gregoire Pau <gregoire.pau@gmail.com> 2013-09-26 22:20:44 +0000;
  • 9c8f549 Use GAlignments, new name for GappedAlignments. by Herve Pages <hpages@fhcrc.org> 2013-04-10 23:54:34 +0000;
  • 821e30b Bump y in version x.y.z to odd number in devel by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-04-03 22:06:11 +0000;
  • 0ad1fca (origin/RELEASE_2_12, RELEASE_2_12) Creating branch for BioC 2.12 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-04-03 21:56:22 +0000;
  • 884c8b5 bump y of x.y.z version number for BioC 2.12 release by Dan Tenenbaum <dtenenba@fhcrc.org> 2013-04-03 21:32:27 +0000;
  • a1c457f version 3.9.25: - VariantTools "analyzeVariants.indels" are OK by Gregoire Pau <gregoire.pau@gmail.com> 2013-04-03 19:02:34 +0000;
  • 283bba3 version 3.9.22 - removed the dependency towards the "logging" package by Gregoire Pau <gregoire.pau@gmail.com> 2013-03-29 22:55:17 +0000;
  • 41b9381 version 3.9.20: - preparation to BioC submission - now using detectRRNA.do: FALSE in default-config.txt by Gregoire Pau <gregoire.pau@gmail.com> 2013-03-27 06:13:50 +0000;
  • 8a129ab bump package versions after creating 2.11 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-10-01 22:43:56 +0000;
  • 2141f5e (origin/RELEASE_2_11, RELEASE_2_11) Creating branch for BioC 2.11 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-10-01 22:37:11 +0000;
  • ba98449 Bump all packages before creating 2.11 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-10-01 22:16:24 +0000;
  • 9ccd3ac mark as unsupported on mac and windows since it depends on gmapR by Dan Tenenbaum <dtenenba@fhcrc.org> 2012-09-29 18:08:07 +0000;