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  • 0b6a8e3 (HEAD -> master, origin/master, origin/HEAD) avoid integer overflow in countFastq by Martin Morgan <Martin.Morgan@RoswellPark.org> 2022-11-16 04:57:29 -0800;
  • e5758ff (origin/RELEASE_3_16, RELEASE_3_16) avoid integer overflow in countFastq by Martin Morgan <Martin.Morgan@RoswellPark.org> 2022-11-16 04:57:29 -0800;
  • c1fee50 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 11:03:51 -0400;
  • df25d08 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 11:03:51 -0400;
  • e3eaa06 Merge branch 'HenrikBengtsson-master' by Martin Morgan <Martin.Morgan@RoswellPark.org> 2022-10-20 16:15:22 -0400;
  • d6e9ad7 version bump by Martin Morgan <Martin.Morgan@RoswellPark.org> 2022-10-20 16:13:59 -0400;
  • a0785ac HELP: Clarify note on the OpenMP-implementation causing issues when run in parallel [#7] by Henrik Bengtsson <hb@aroma-project.org> 2022-10-20 11:21:26 -0700;
  • 2b693a1 add URL: and BugReports:, use Authors@R in DESCRIPTION by Martin Morgan <Martin.Morgan@RoswellPark.org> 2022-10-16 15:10:17 -0400;
  • cca7724 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 15:01:12 +0000;
  • a1082a3 (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 15:01:12 +0000;
  • 252de6a Get ShortRead ready for the switch to virtual DataFrame (in S4Vectors package) by Hervé Pagès <hpages.on.github@gmail.com> 2021-11-15 22:01:25 -0800;
  • 938fd77 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 15:52:20 +0000;
  • 4d7304d (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 15:52:20 +0000;
  • fb8723c 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 15:40:52 +0000;
  • 31dea4d (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 15:40:52 +0000;
  • f5a6503 don't segfault on re-serialized FastqStreamer / FastqSampler by Martin Morgan <Martin.Morgan@RoswellPark.org> 2021-05-17 05:49:19 -0400;
  • d6e893d no more hot fix by Hervé Pagès <hpages.on.github@gmail.com> 2021-02-03 11:10:45 -0800;
  • e2eb649 version bump by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-12-10 15:19:31 -0500;
  • ee71f25 add names (id()) to QualityScaledXStringSet coercion by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-12-10 15:18:48 -0500;
  • adf4a49 add as(ShortRead(), "DNAStringSet") method by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-12-10 15:17:29 -0500;
  • aa07f35 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 10:33:27 -0400;
  • ba44cd2 (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 10:33:27 -0400;
  • 187835a missing header file for countFastq by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-05-27 05:24:05 -0400;
  • 3616077 Merge remote-tracking branch 'refs/remotes/upstream/master' by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-05-23 17:40:33 -0400;
  • 3e7a6c0 remove coercion to defunct RangedData by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-05-23 17:37:00 -0400;
  • 2fc1782 add countFastq for fast counting of fastq records by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-05-23 17:27:06 -0400;
  • b88ccd3 Remove coercion from AlignedRead to RangedData by Hervé Pagès <hpages@fredhutch.org> 2020-05-01 23:54:36 -0700;
  • f6eeedc 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 18:17:12 +0000;
  • 7b25d95 (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 18:17:12 +0000;
  • d57c778 version bump by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-03-18 16:03:16 -0400;
  • c7c30d1 update code for stringsAsFactors by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-03-18 16:00:26 -0400;
  • c71d447 Changes made to fix tests in test_AlignedRead.R by Kayla-Morrell <Kayla.Morrell@roswellpark.org> 2020-03-18 14:57:46 -0400;
  • 63324b6 Merge branch 'RELEASE_3_10' by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-02-03 15:40:50 -0500;
  • d97933c (origin/RELEASE_3_10) update unit test by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-02-03 15:39:26 -0500;
  • d30c4f4 Merge branch 'RELEASE_3_10' -- readFastq qualityType = "Auto" by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-01-30 17:56:15 -0500;
  • 39e9755 readFastq argument qualityType = "Auto" detects SFastqQuality correctly by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-01-30 17:54:13 -0500;
  • 6bbf239 Merge branch 'RELEASE_3_10' (bugfix: internal: avoid lenght > 1 logical test) by Martin Morgan <Martin.Morgan@RoswellPark.org> 2019-12-19 11:53:21 -0500;
  • a5041a8 bugfix: internal: avoid length > 1 logical test by Martin Morgan <Martin.Morgan@RoswellPark.org> 2019-12-19 11:52:09 -0500;
  • 07cb63f 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 13:34:49 -0400;
  • fbefabe 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 13:07:56 -0400;
  • f3718cb Merge branch 'kasperdanielhansen-master' by Martin Morgan <martin.morgan@roswellpark.org> 2019-09-10 13:44:27 -0400;
  • a0f3dac Using Rs CFLAGS and LDFLAGS by Kasper Daniel Hansen <kasperdanielhansen@gmail.com> 2019-09-09 11:24:52 -0400;
  • f95f223 Use is(x, "DataFrame") instead of class(x) == "DataFrame" by Hervé Pagès <hpages@fredhutch.org> 2019-08-16 19:34:12 -0700;
  • 3d4f5a4 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 12:10:47 -0400;
  • daa2576 (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 11:53:10 -0400;
  • b695537 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:27 -0400;
  • 0cbe4b6 (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 11:41:44 -0400;
  • 4525ba1 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:37 -0400;
  • e9498f0 (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 10:35:09 -0400;
  • be12ac5 Use get_List_elementType() instead of get_XStringSet_xsbaseclassname() by Hervé Pagès <hpages@fredhutch.org> 2018-03-15 18:54:35 -0700;
  • 3a60b21 change location of sread(), id() docs by Martin Morgan <martin.morgan@roswellpark.org> 2018-03-06 15:52:37 -0500;
  • 176c34e (origin/RELEASE_3_6, RELEASE_3_6) (port) FastqQuality unit test update by Martin Morgan <martin.morgan@roswellpark.org> 2018-02-21 05:40:48 -0500;
  • eb44527 one more documentation update by Martin Morgan <martin.morgan@roswellpark.org> 2018-02-21 06:01:03 -0500;
  • eaec3c7 version bump and NEWS entry by Martin Morgan <martin.morgan@roswellpark.org> 2018-02-21 05:59:25 -0500;
  • 674ba00 documentation and other clean-up by Martin Morgan <martin.morgan@roswellpark.org> 2018-02-21 05:58:49 -0500;
  • b221ec9 countLines() supports more than 2^31-1 records by Martin Morgan <martin.morgan@roswellpark.org> 2018-02-21 05:41:38 -0500;
  • 63cf6f0 FastqQuality unit test update by Martin Morgan <martin.morgan@roswellpark.org> 2018-02-21 05:40:48 -0500;
  • 45506e5 silence compiler warning by Martin Morgan <martin.morgan@roswellpark.org> 2018-02-21 05:31:31 -0500;
  • c36d34b (port) FastqQuality should include '~' by Martin Morgan <martin.morgan@roswellpark.org> 2018-02-20 17:17:06 -0500;
  • 02b197b FastqQuality should include '~' by Martin Morgan <martin.morgan@roswellpark.org> 2018-02-20 17:17:06 -0500;
  • 3ea9ecb follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12 by Hervé Pagès <hpages@fredhutch.org> 2018-01-21 16:31:32 -0800;
  • c262505 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:52:08 -0400;
  • 2d15caf 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 12:39:23 -0400;
  • 25daac6 (origin/RELEASE_3_5, RELEASE_3_5) fix BiocGenerics version requirement by Hervé Pagès <hpages@fredhutch.org> 2017-10-06 21:51:04 -0700;
  • 75582cb Apply "hotfix 73465" to FastqFileList(), FastqStreamerList(), and FastqSamplerList() generics (see file R/hotfix73465.R in package BiocGenerics for more information). by Hervé Pagès <hpages@fredhutch.org> 2017-10-06 19:12:10 -0700;
  • 5620ac4 Apply "hotfix 73465" to FastqFileList(), FastqStreamerList(), and FastqSamplerList() generics (see file R/hotfix73465.R in package BiocGenerics for more information). by Hervé Pagès <hpages@fredhutch.org> 2017-10-06 19:12:10 -0700;
  • 8bace57 version bump by Martin Morgan <martin.morgan@roswellpark.org> 2017-08-30 16:29:50 -0400;
  • 795fe19 feature: increase max. read length to 2M bases by Martin Morgan <martin.morgan@roswellpark.org> 2017-08-30 16:27:30 -0400;
  • 19fccae version bump by Martin Morgan <martin.morgan@roswellpark.org> 2017-08-30 16:28:50 -0400;
  • c4fa5ca feature: increase max. read length to 2M bases by Martin Morgan <martin.morgan@roswellpark.org> 2017-08-30 16:27:30 -0400;
  • 1455abd use pruning.mode="coarse" instead of force=TRUE when calling seqlevels() setter by Herve Pages <hpages@fhcrc.org> 2017-04-29 21:21:50 +0000;
  • 6143088 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;
  • 7713cdb Creating branch for BioC 3.5 release by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:45:44 +0000;
  • c2eca7c 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;
  • 88d2396 (origin/RELEASE_3_4, RELEASE_3_4) Bump versions of all packages that define "c" methods by Herve Pages <hpages@fhcrc.org> 2017-03-16 02:03:50 +0000;
  • 447f2d8 some tweaks in reponse to latest changes in S4Vectors C interface by Herve Pages <hpages@fhcrc.org> 2017-01-23 05:56:48 +0000;
  • ca1d3c7 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;
  • 69a0a28 Creating branch for BioC 3.4 release by Herve Pages <hpages@fhcrc.org> 2016-10-17 19:00:47 +0000;
  • 82f2b69 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;
  • 39bc39d Need to define the left() and right() generics here now that they've been removed from GenomicAlignments. by Herve Pages <hpages@fhcrc.org> 2016-07-10 08:46:24 +0000;
  • da712b8 bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
  • 638e879 (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;
  • 79ed22b Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
  • 9462d14 typo in man page example by Martin Morgan <mtmorgan@fhcrc.org> 2016-03-15 21:59:45 +0000;
  • 71b9efc cleanup: rename readInfo as readIntensityInfo by Martin Morgan <mtmorgan@fhcrc.org> 2016-03-13 12:15:11 +0000;
  • 0ddc0fd cleanup: cast Qseq filter to vector before applying by Martin Morgan <mtmorgan@fhcrc.org> 2016-03-13 12:11:59 +0000;
  • a5eceb2 bugfix: resolve malloc & friends to std:: namespace in C++ code by Martin Morgan <mtmorgan@fhcrc.org> 2016-03-09 16:52:54 +0000;
  • 47b7e45 cleanup: lengths() instead of elementLengths() by Martin Morgan <mtmorgan@fhcrc.org> 2016-01-23 17:31:44 +0000;
  • 7204c53 .gitignore by Martin Morgan <mtmorgan@fhcrc.org> 2016-01-23 17:31:29 +0000;
  • 8f4ca20 unname colClasses in read.table by Martin Morgan <mtmorgan@fhcrc.org> 2015-10-25 06:13:12 +0000;
  • 80010fd 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;
  • 7ca6850 (origin/RELEASE_3_2, RELEASE_3_2) Creating branch for BioC 3.2 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:57:33 +0000;
  • eb6d3f8 Bumped versions of all packages prior to creating 3.2 branch. by Dan Tenenbaum <dtenenba@fhcrc.org> 2015-10-13 19:36:05 +0000;
  • 2b77b84 implement [<,ShortReadQ-method by Martin Morgan <mtmorgan@fhcrc.org> 2015-07-01 13:08:43 +0000;
  • 9a81def vignette typo (from Jonathan van Eyll) by Martin Morgan <mtmorgan@fhcrc.org> 2015-05-18 11:50:46 +0000;
  • f1394dc use makeTxDbFromUCSC() instead of makeTranscriptDbFromUCSC() by Herve Pages <hpages@fhcrc.org> 2015-05-03 19:31:29 +0000;
  • f54fc3e missing(...) replaces length(list(...)) == 0 by Martin Morgan <mtmorgan@fhcrc.org> 2015-05-02 22:10:24 +0000;
  • e568bf4 resync with major refactoring of C-level Auto-Extending buffers in S4Vectors by Herve Pages <hpages@fhcrc.org> 2015-04-30 00:03:48 +0000;
  • b167201 unnecessary Suggests: removed by Martin Morgan <mtmorgan@fhcrc.org> 2015-04-21 23:53:28 +0000;
  • 50a6484 update NEWS and version bump by Martin Morgan <mtmorgan@fhcrc.org> 2015-04-21 23:51:47 +0000;