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  • 40d4db9 (HEAD -> master, origin/master, origin/HEAD) 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 15:11:32 +0000;
  • f762532 (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 15:11:32 +0000;
  • 4fda1cc 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 16:03:53 +0000;
  • 1e9cf9a (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 16:03:53 +0000;
  • 43bb861 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 15:53:08 +0000;
  • 3262a4e (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 15:53:08 +0000;
  • 38f36e1 simplify email address by Michael Lawrence <michafla@gene.com> 2021-01-05 11:14:02 -0800;
  • 0a70bb8 genomeName,BiocFile() replaces other *File methods by Michael Lawrence <michafla@gene.com> 2021-01-04 13:58:36 -0800;
  • 9de3a15 Merge pull request <a href="#3">#3</a> from dpryan79/patch-1 by Michael Lawrence <michafla@gene.com> 2020-11-16 13:01:21 -0800;
  • 0d9f378 Handle platform-dependent shared library extensions by Devon Ryan <dpryan79@users.noreply.github.com> 2020-11-14 20:35:15 +0100;
  • 02e06e4 (origin/RELEASE_3_12, RELEASE_3_12) reenable maintainer mode for gstruct by Michael Lawrence <michafla@gene.com> 2020-11-06 09:06:58 -0800;
  • b2c30cb reenable maintainer mode for gstruct by Michael Lawrence <michafla@gene.com> 2020-11-05 16:12:54 -0800;
  • a7bc7ca 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 10:46:29 -0400;
  • 47ad3c2 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 10:46:29 -0400;
  • c754fa3 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 18:30:24 +0000;
  • 08251b2 (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 18:30:24 +0000;
  • b5039ae 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 13:36:17 -0400;
  • 70a270e (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 13:08:33 -0400;
  • c3db7e3 support new version of bam_tally by Michael Lawrence <michafla@gene.com> 2019-06-12 15:48:54 -0700;
  • 7cb8750 update GSTRUCT source code by Michael Lawrence <michafla@gene.com> 2019-05-22 12:39:45 -0700;
  • 41d82c7 ignore libbam.a by Michael Lawrence <michafla@gene.com> 2019-05-17 09:58:16 -0700;
  • 6d010e6 fix warning on NULL gsnap(input_b=) by Michael Lawrence <michafla@gene.com> 2019-05-09 10:18:57 -0700;
  • 095eb21 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 12:11:13 -0400;
  • 95ed5f3 (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 11:53:37 -0400;
  • 91163a4 fix Makefile for new embedded samtools source by Michael Lawrence <michafla@gene.com> 2019-03-01 11:37:40 -0800;
  • a7a458b drop binary archive by Michael Lawrence <michafla@gene.com> 2019-03-01 11:37:15 -0800;
  • 5bb21ad embed samtools sources directly, since Rsamtools has moved to htslib by Michael Lawrence <michafla@gene.com> 2019-02-11 12:33:07 -0800;
  • 7bcf7c4 (origin/RELEASE_3_8, RELEASE_3_8) version bump by Michael Lawrence <michafla@gene.com> 2019-02-05 11:13:36 -0800;
  • 3c11255 bam tally no longer crashes when NM exceeds maximum bin by Michael Lawrence <michafla@gene.com> 2019-02-05 11:11:42 -0800;
  • c9c976d bam tally no longer crashes when NM exceeds maximum bin by Michael Lawrence <michafla@gene.com> 2019-02-05 11:08:08 -0800;
  • 48bf25a version bump by Michael Lawrence <michafla@gene.com> 2018-11-20 11:08:28 -0800;
  • cd00085 cmetindex() uses default (correct) destdir by Michael Lawrence <michafla@gene.com> 2018-11-20 11:07:15 -0800;
  • 9cc44e8 version bump by Michael Lawrence <michafla@gene.com> 2018-11-20 11:02:28 -0800;
  • 6482be7 cmetindex() uses default (correct) destdir by Michael Lawrence <michafla@gene.com> 2018-11-20 10:59:59 -0800;
  • 922ee59 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;
  • 19a2eb1 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;
  • 4aae21b replace BiocInstaller biocLite mentions with BiocManager by LiNk-NY <mramos09@gmail.com> 2018-08-30 13:49:42 -0400;
  • cda7c25 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;
  • e2621b2 (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 10:35:25 -0400;
  • c087114 follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12 by Hervé Pagès <hpages@fredhutch.org> 2018-01-21 16:24:43 -0800;
  • c67b519 The path() generic has moved from Rsamtools to BiocGenerics by LiNk-NY <mramos09@gmail.com> 2017-12-20 15:04:28 -0500;
  • 99ba020 version bump by Michael Lawrence <michafla@gene.com> 2017-11-14 15:02:49 -0800;
  • 1cb2c80 export and document cmetindex command by Michael Lawrence <michafla@gene.com> 2017-11-14 14:43:33 -0800;
  • 910550c add as.character,GmapGenomeDirectory by Michael Lawrence <michafla@gene.com> 2017-11-14 14:42:56 -0800;
  • 433a26b bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:52:20 -0400;
  • e20d214 (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 12:39:47 -0400;
  • 071760a fixes for keep_ref=TRUE by Michael Lawrence <michafla@gene.com> 2017-09-14 11:30:38 -0700;
  • 5824b72 GMAP alignment categories seemed to have changed by Michael Lawrence <michafla@gene.com> 2017-09-14 11:30:22 -0700;
  • faf50b5 allow omitting gmap arg suboptimal_score, and make that the default by Michael Lawrence <michafla@gene.com> 2017-08-29 15:10:50 -0700;
  • a31ec5d Merge pull request <a href="#1">#1</a> from alexandremkuhn/whichAsGRangesList by Michael Lawrence <lawremi@gmail.com> 2017-09-12 09:27:21 -0700;
  • 979ba54 corrected BamTallyParam-class.Rd by alexandremkuhn <akuhn@devfrt01.vital-it.ch> 2017-09-12 15:06:36 +0000;
  • 4e51e3d Merge branch 'master' into whichAsGRangesList by alexandremkuhn <akuhn@frt.vital-it.ch> 2017-08-31 13:18:39 +0000;
  • 1c40485 'which' is a GenomicRanges_OR_GRangesList by alexandremkuhn <akuhn@frt.vital-it.ch> 2017-08-31 13:00:25 +0000;
  • 13fdf50 defined 'which' as GenomicRanges_OR_GRangesList by alexandremkuhn <akuhn@frt.vital-it.ch> 2017-08-31 12:51:24 +0000;
  • 4bc5367 allow omitting gmap arg suboptimal_score, and make that the default by Michael Lawrence <michafla@gene.com> 2017-08-29 15:10:50 -0700;
  • 8ec8fe1 version bump by Michael Lawrence <lawremi@iastate.edu> 2017-05-18 22:47:55 +0000;
  • 7545fca normalize path to fasta file for gmap_build by Michael Lawrence <lawremi@iastate.edu> 2017-05-18 22:47:22 +0000;
  • 3854987 vectorize over 'output' by Michael Lawrence <lawremi@iastate.edu> 2017-05-17 20:11:24 +0000;
  • 4f2f27e support character which to getSeq,GmapGenome by Michael Lawrence <lawremi@iastate.edu> 2017-05-17 19:50:56 +0000;
  • 69da1e1 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;
  • a1356a8 (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;
  • 38b3975 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;
  • e1b17d3 follow renaming of union classes in S4Vectors by Herve Pages <hpages@fhcrc.org> 2017-02-01 13:23:02 +0000;
  • 32a9b51 start on C-level interface to IIT files by Michael Lawrence <lawremi@iastate.edu> 2016-12-14 18:20:54 +0000;
  • 0771cfd be more flexible when getting genome name by Michael Lawrence <lawremi@iastate.edu> 2016-12-14 18:20:28 +0000;
  • 4c32b1b GSTRUCT build script updates by Michael Lawrence <lawremi@iastate.edu> 2016-11-14 22:02:59 +0000;
  • 1f2284f readd maintainer mode control to GSTRUCT by Michael Lawrence <lawremi@iastate.edu> 2016-11-14 22:00:33 +0000;
  • 15c3d79 disable maintainer mode for GSTRUCT by Michael Lawrence <lawremi@iastate.edu> 2016-11-14 21:57:42 +0000;
  • 55d77a1 update to latest GSTRUCT by Michael Lawrence <lawremi@iastate.edu> 2016-11-14 21:54:30 +0000;
  • 28abe94 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;
  • dba7a31 (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;
  • e945492 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;
  • aba57c5 bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
  • ca9cadb (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;
  • 3748356 Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
  • eb2c4af one more adjustment in response to the 'vals' -> 'filter' renaming in GenomicFeatures by Herve Pages <hpages@fhcrc.org> 2016-04-05 23:53:00 +0000;
  • 8b7fd7a adjustments in response to the vals -> filter renaming in GenomicFeatures by Herve Pages <hpages@fhcrc.org> 2016-04-05 22:55:27 +0000;
  • c3d54b8 move Rsamtools to Depends to avoid masking of bamPaths() by Michael Lawrence <lawremi@iastate.edu> 2016-03-12 19:23:55 +0000;
  • 12074fe stream past XS counts for indels (even when XS counting is disabled) by Michael Lawrence <lawremi@iastate.edu> 2016-02-01 20:11:05 +0000;
  • d92a799 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;
  • 4f3d48a re-enable maintainer mode toggling in gmap by Michael Lawrence <lawremi@iastate.edu> 2015-12-07 19:55:43 +0000;
  • d36ac68 make seqinfo setting robust to missing seqlevels by Michael Lawrence <lawremi@iastate.edu> 2015-12-07 03:40:40 +0000;
  • cb7ab58 fix single output case for GMAP by Michael Lawrence <lawremi@iastate.edu> 2015-12-05 15:00:00 +0000;
  • 4a648a5 regenerate autotools stuff by Michael Lawrence <lawremi@iastate.edu> 2015-12-05 14:42:50 +0000;
  • 676579c re-add maintainer mode support to gstruct by Michael Lawrence <lawremi@iastate.edu> 2015-12-05 14:39:13 +0000;
  • ff0b3d9 disable maintainer mode for gsnap by Michael Lawrence <lawremi@iastate.edu> 2015-12-05 14:20:35 +0000;
  • 8db42dc So let's try to support gmapR again on Mac. See: by Herve Pages <hpages@fhcrc.org> 2015-12-05 00:34:38 +0000;
  • f053c5f general cleanup and fixes, doc updates by Michael Lawrence <lawremi@iastate.edu> 2015-12-03 21:11:09 +0000;
  • 5659f09 add raw total count statistic to tallies (everything else now qual filtered) by Michael Lawrence <lawremi@iastate.edu> 2015-11-24 22:19:59 +0000;
  • ead94b3 add ability to call GMAP by Michael Lawrence <lawremi@iastate.edu> 2015-11-23 23:25:34 +0000;
  • b8e2b22 let users pass a 'param' when building a GmapGenome from a FaFile by Michael Lawrence <lawremi@iastate.edu> 2015-11-20 12:24:09 +0000;
  • 2332d26 add untested support for FaFile=>GmapGenome by Michael Lawrence <lawremi@iastate.edu> 2015-11-19 18:51:30 +0000;
  • 38518dd fixes for bam_tally update by Michael Lawrence <lawremi@iastate.edu> 2015-11-13 22:40:27 +0000;
  • 685d60e work towards supporting new bam_tally; drops quality info (now cutoff based), adds xs/nm/del and codon-level counts by Michael Lawrence <lawremi@iastate.edu> 2015-11-13 21:50:11 +0000;
  • f18ff85 more robust check for empty read pos breaks by Michael Lawrence <lawremi@iastate.edu> 2015-11-02 22:42:05 +0000;
  • bfeb9ea fix forwarding args to TallyIIT by Michael Lawrence <lawremi@iastate.edu> 2015-11-02 21:40:00 +0000;
  • a5e0518 various hacks to get the source code updater to work for me by Michael Lawrence <lawremi@iastate.edu> 2015-10-28 20:56:15 +0000;
  • f51bc89 Update gstruct (bam_tally) by Michael Lawrence <lawremi@iastate.edu> 2015-10-28 20:55:30 +0000;
  • a49cb8d Makefile cleanup by Michael Lawrence <lawremi@iastate.edu> 2015-10-28 20:53:26 +0000;
  • 8418591 resurrect improvements that we reverted before the April release, expect breakage for a while by Michael Lawrence <lawremi@iastate.edu> 2015-10-28 18:51:00 +0000;