| HEAD | a43fa6f | Remove whitespace character preventing the removal -lrt from LDLIBS | 17 January 2024, 00:01:39 UTC |
| refs/heads/add_maj | 9917668 | restructure index sidebar and add major-allele indexes | 26 April 2019, 15:41:52 UTC |
| refs/heads/adseed | 4306fe5 | Merge branch 'master' into adseed | 28 February 2023, 16:48:35 UTC |
| refs/heads/adseed_patches | e313232 | add read get script | 03 October 2020, 14:25:44 UTC |
| refs/heads/alt_loci | ed2a0a1 | moved AlnSinkWrap::collapseAlternates definition from aln_sink.h to aln_sink.cpp | 16 May 2017, 18:34:52 UTC |
| refs/heads/batch_parsing | e54a15c | attempt at getting all the batch buffer memory allocations over with before alignment time | 28 July 2016, 18:19:24 UTC |
| refs/heads/batch_parsing_output | f424c15 | Add missing headers | 03 August 2017, 17:57:16 UTC |
| refs/heads/block_batch_parsing | ca65d91 | fixed missing init for total_read_count in PatternSource | 31 January 2017, 19:33:02 UTC |
| refs/heads/block_batch_parsing_output | a196a28 | remove compressed flag -- not supported in this branch | 03 July 2017, 15:45:43 UTC |
| refs/heads/blocked_input | c1c25df | Add missing headers | 03 August 2017, 17:57:16 UTC |
| refs/heads/blocked_input_multiout | ecfaab2 | implement --num-outputs | 16 January 2018, 03:05:18 UTC |
| refs/heads/bt2-2.3.1 | f2857aa | Update documentation for v2.3.1 | 04 March 2017, 04:26:17 UTC |
| refs/heads/bt2_cxx11 | 2ca1101 | Always use __builtin_popcountll | 04 November 2019, 20:24:52 UTC |
| refs/heads/bug_fixes | 2c91155 | Potential fix for memory leaks when processing BAM files | 27 February 2024, 18:59:08 UTC |
| refs/heads/cleaner_parsing | 525a47e | moved includes of tkt and ptl locks inside WITH_COHORT ifdef, was causing compilation issues without TBB | 04 August 2016, 15:22:02 UTC |
| refs/heads/cohort_locking_ptl_tkt | 9845c41 | merging PTL/TKT only cohort lock from cohort-lock-example from Ben | 10 January 2017, 21:29:37 UTC |
| refs/heads/cp-no-io | 8d73da7 | adding the extra no-io files | 23 June 2016, 00:00:55 UTC |
| refs/heads/feature/performance | 641021a | First try at a performance test. | 08 October 2014, 17:21:48 UTC |
| refs/heads/fix_F_clip | dea3853 | fix issue with -F mode omitting final base | 19 December 2017, 02:44:15 UTC |
| refs/heads/fix_outq_destruct | 59e9811 | Require sudo for sanitized builds | 25 January 2018, 18:11:08 UTC |
| refs/heads/haswell | d805f30 | Reformat to be similar with bowtie code. Easier to remote tinythrads code when the time will come. | 07 April 2015, 20:55:26 UTC |
| refs/heads/hints | cd4e780 | allowing hint to be anywhere in the read name | 11 August 2016, 13:24:55 UTC |
| refs/heads/issue20 | 6dd5664 | attempt at making distribution across strands more even | 15 January 2016, 21:07:38 UTC |
| refs/heads/issue56 | 3b1631b | make default local --score-min match the documentation | 01 October 2016, 18:52:32 UTC |
| refs/heads/mapq | 825ea96 | cleaning up comments | 21 April 2017, 18:27:34 UTC |
| refs/heads/master | a43fa6f | Remove whitespace character preventing the removal -lrt from LDLIBS | 17 January 2024, 00:01:39 UTC |
| refs/heads/mem_tally_ifdefed | cea21dc | put all memory tally merging into ifdef USE_MEM_TALLY | 25 August 2015, 02:50:11 UTC |
| refs/heads/no-io | 49f9b7a | adding more branches | 12 June 2016, 15:03:57 UTC |
| refs/heads/no_IO_2000seq | 59e785a | Merge branch 'no_IO_2000seq' of github.com:BenLangmead/bowtie2 into no_IO_2000seq | 04 January 2016, 19:47:34 UTC |
| refs/heads/parallelized_indexbuild | 646a5ed | Parallelized three time-consuming steps of the index building, with the option, --threads | 19 December 2015, 18:13:25 UTC |
| refs/heads/pre_batch_parsing_master | 9e9624b | finishing up test infrastructure readme | 02 October 2016, 01:54:30 UTC |
| refs/heads/rail_load_balancing | 6d01f37 | merging Merge branch 'master' into rail_load_balancing | 18 July 2017, 15:02:27 UTC |
| refs/heads/rel2.3 | 06899ce | Fix to resolve failures when creating packages on Windows | 22 December 2016, 17:09:14 UTC |
| refs/heads/rel2.3.2 | 72d5487 | Update documentation for release v2.3.2 | 06 May 2017, 01:49:33 UTC |
| refs/heads/sra | 057fbc2 | Add support for SRA reads in simple tests | 09 March 2019, 04:34:53 UTC |
| refs/heads/stack_threadsafe | b989f0f | put shared_ back in the conditions | 20 April 2017, 20:50:05 UTC |
| refs/heads/tbb_threads_with_delay | 8a1afe0 | first commit of tbb::threads + 10ms delay | 17 March 2017, 22:12:25 UTC |
| refs/heads/tbb_tts_lock | 0463546 | replaced all ThreadSafe calls with queue locks (scoped_lock) | 10 December 2015, 18:55:28 UTC |
| refs/heads/testing_suite | 824acd7 | changed comment | 18 May 2017, 21:43:36 UTC |
| refs/heads/th_scaling | 6ce19d7 | Added the data set used for our testing. | 29 May 2015, 19:25:52 UTC |
| refs/heads/v2.0.6_thread_profiling | 0ac3e7b | added from current master thread profiling for v206 | 24 September 2015, 21:25:55 UTC |
| refs/heads/v2.2 | 05b9706 | fix failure to fully sort diff cov sample | 08 June 2017, 20:10:16 UTC |
| refs/heads/v206_no_IO_2000seq | e9d73f7 | back ported the no_IO code to v206 | 24 September 2015, 22:14:20 UTC |
| refs/heads/v229_withq | 8e3f064 | remove heap allocation for ThreadSafe | 19 October 2017, 14:25:47 UTC |
| refs/heads/website-1kgmaj-2021 | e93634f | remove statement about chain files | 05 June 2021, 14:10:54 UTC |
| refs/heads/website-updates | af010cc | fix source for canfam4 | 01 October 2020, 17:01:10 UTC |
| refs/tags/rlb_v1 | 49a6a48 | added working version of load balancing for Rail in EMR, note hardcoded pid_dir and thread_ceiling is set to ncpus-2 | 19 February 2016, 02:47:59 UTC |
| refs/tags/rlb_v1a | e0959b8 | applying the latest bug fix from the fix_parallel_build_support_for_tbb branch | 19 February 2016, 02:55:03 UTC |
| refs/tags/v2.3.4 | cdf70d7 | Remove unmatched parenthesis in Makefile | 29 December 2017, 16:08:31 UTC |
| refs/tags/v2.3.4-alpha | 9076f1d | Potential fix for issues #155 and #158 | 03 December 2017, 01:05:39 UTC |
| refs/tags/v2.3.4.1 | 80edefe | Update release date and generate MANUAL and manual.html from markdown file | 03 February 2018, 12:57:06 UTC |
| refs/tags/v2.3.4.1-beta | 59e9811 | Require sudo for sanitized builds | 25 January 2018, 18:11:08 UTC |
| refs/tags/v2.3.4.2-alpha | 863d9c8 | Attempt at solving travis LSAN failures | 15 June 2018, 15:43:42 UTC |
| refs/tags/v2.3.4.2-alpha.2 | 6e1657f | Address feature request: trim reads exceeding a given length #191 | 13 July 2018, 03:27:09 UTC |
| refs/tags/v2.3.4.3 | f5d794d | Update version to 2.3.4.3 | 17 September 2018, 04:22:55 UTC |
| refs/tags/v2.4.4 | e20d2c9 | Remove smart filter when running pandoc in HBB container | 23 May 2021, 23:17:26 UTC |
| refs/tags/v2.5.0 | f06cad5 | Adjust release date | 01 November 2022, 01:53:08 UTC |
| refs/tags/v2.5.1 | 04a2ecd | Make cross-compiling a bit easier | 17 January 2023, 16:37:37 UTC |
| refs/tags/v2.5.2 | 04ec2d4 | Add more semi-colons | 13 October 2023, 23:19:48 UTC |
| refs/tags/v2.5.3 | a43fa6f | Remove whitespace character preventing the removal -lrt from LDLIBS | 17 January 2024, 00:01:39 UTC |
