| fbc6873 | Armin Toepfer | 11 June 2024, 10:45:02 UTC | Update README for v1.14.99 | 11 June 2024, 10:45:02 UTC |
| f7cbb14 | Armin Toepfer | 07 November 2023, 09:34:42 UTC | [BFX-644] Fix README | 07 November 2023, 09:34:42 UTC |
| d0838d6 | David Seifert | 02 November 2023, 09:53:24 UTC | [BFX-758] Switch to pbtestutils | 02 November 2023, 09:53:24 UTC |
| 39c263e | David Seifert | 30 October 2023, 21:49:45 UTC | [BFX-751] Switch `Cigar::ToStdString()` → `Data::ToStdString(std::span<CigarOperation>)` | 30 October 2023, 21:49:45 UTC |
| 4f18ea9 | Armin Toepfer | 25 September 2023, 14:16:57 UTC | [BFX-644] Release version 1.13.1 | 25 September 2023, 14:16:57 UTC |
| bcd99f5 | Robert Vaser | 14 August 2023, 10:28:19 UTC | [BFX-534] Update cram tests for mm2.26 | 14 August 2023, 10:51:38 UTC |
| a193c7b | Armin Toepfer | 14 August 2023, 07:34:44 UTC | [BFX-533] Update README | 14 August 2023, 07:34:44 UTC |
| 184c5ec | Armin Toepfer | 14 August 2023, 07:23:48 UTC | [BFX-533] Release version 1.13.0 | 14 August 2023, 07:27:43 UTC |
| d87a48b | Armin Toepfer | 08 August 2023, 10:06:58 UTC | [BFX-533] Sync HiFi settings with mm2 recomendations Deactivate rmt.t and best_n.t until we find better test data | 08 August 2023, 12:22:41 UTC |
| 9a20679 | Armin Toepfer | 08 August 2023, 09:43:29 UTC | [BFX-533] Update to mm2 2.26 | 08 August 2023, 12:22:40 UTC |
| c8ba5ba | Armin Toepfer | 08 August 2023, 11:26:07 UTC | [BFX-353] Do not rely in mm2 binary | 08 August 2023, 11:26:07 UTC |
| 5313e71 | Armin Toepfer | 08 August 2023, 10:25:09 UTC | [BFX-535] Add cram | 08 August 2023, 10:25:09 UTC |
| dc27bd5 | Armin Toepfer | 09 June 2023, 08:06:20 UTC | [BFX-402] Version 1.12.0 | 09 June 2023, 08:06:20 UTC |
| d25a11e | Robert Vaser | 07 June 2023, 12:20:19 UTC | [BFX-394] Set --preset CCS as default | 07 June 2023, 21:26:45 UTC |
| a4dce7d | Robert Vaser | 07 June 2023, 09:44:20 UTC | [BFX-390] Add known multithreading issues to README | 07 June 2023, 09:44:20 UTC |
| 24cb8ba | Robert Vaser | 02 June 2023, 14:45:17 UTC | [BFX-361] Fix repeated matches trimming | 06 June 2023, 08:45:55 UTC |
| ae3f174 | Robert Vaser | 05 June 2023, 12:43:04 UTC | [BFX-361] Add cram test for tag rm:i:<int> | 05 June 2023, 12:50:16 UTC |
| 1b5a417 | Armin Toepfer | 24 April 2023, 07:21:04 UTC | [BFX-258] Develop version 1.11.9 | 24 April 2023, 07:21:04 UTC |
| 531b781 | Armin Toepfer | 24 April 2023, 07:20:14 UTC | [BFX-258] Release version 1.11.0 | 24 April 2023, 07:20:14 UTC |
| 4337dfc | David Seifert | 01 April 2023, 11:10:53 UTC | [BFX-192] Update {gtest,htslib,zlib}.wrap | 01 April 2023, 11:10:53 UTC |
| 4356bbf | Armin Toepfer | 26 January 2023, 12:55:26 UTC | [BFX-50] Add new logo | 26 January 2023, 12:55:42 UTC |
| 0fb9934 | Armin Toepfer | 26 January 2023, 12:35:06 UTC | [BFX-50] Update README | 26 January 2023, 12:35:06 UTC |
| cf1a5f6 | Armin Toepfer | 26 January 2023, 12:29:37 UTC | [BFX-50] Inc develop version | 26 January 2023, 12:29:37 UTC |
| 086d7b6 | Robert Vaser | 25 January 2023, 12:33:22 UTC | [BFX-12] Strip hifi kinetic tags | 25 January 2023, 21:14:23 UTC |
| 0bc7f84 | Armin Töpfer | 02 January 2023, 22:12:49 UTC | [TAG-5920] Release version 1.10.0 | 02 January 2023, 22:12:49 UTC |
| 6f08701 | Armin Toepfer | 28 December 2022, 09:01:42 UTC | [TAG-5913] Store number of mismatches, tag NM | 28 December 2022, 09:06:21 UTC |
| 97c0369 | Armin Toepfer | 27 December 2022, 09:33:12 UTC | [TAK-1796] Do not allow overwriting input files | 27 December 2022, 10:13:22 UTC |
| 22e594c | Armin Töpfer | 25 December 2022, 15:18:30 UTC | [TAG-5905] Add cram test for unaligned RC input | 25 December 2022, 15:18:30 UTC |
| 0ce09a4 | Armin Töpfer | 25 December 2022, 15:18:30 UTC | [TAG-5905] Create unaligned copy, if input is unaligned RC | 25 December 2022, 15:18:30 UTC |
| cab4123 | Armin Toepfer | 22 December 2022, 15:02:41 UTC | [SL-8906] Allow infix, not flanking, spaces in sample name | 22 December 2022, 15:26:42 UTC |
| 49830d0 | Armin Töpfer | 21 December 2022, 22:18:02 UTC | [TAG-5905] Fix RC input unaligned BAM | 21 December 2022, 22:18:02 UTC |
| 8781a39 | Ivan Sovic | 02 October 2022, 16:21:41 UTC | [TAG-5853] Implemented a fix which relabels a supplementary alignment if a primary does not exist. | 04 October 2022, 15:52:59 UTC |
| aeac828 | David Seifert | 24 September 2022, 10:03:26 UTC | [TAK-1737] Fix `-Wstrict-prototypes` | 24 September 2022, 10:03:26 UTC |
| 6176486 | David Seifert | 19 September 2022, 19:58:41 UTC | [TAK-1729] Remove ${SAMTOOLS} | 19 September 2022, 19:58:41 UTC |
| 3eb4d3d | David Seifert | 19 September 2022, 19:58:41 UTC | [TAK-1737] Use POSIX `grep` * GNU grep 3.8 considers `egrep` and `fgrep` obsolescent and throws warnings: https://lists.gnu.org/archive/html/info-gnu/2022-09/msg00001.html | 19 September 2022, 19:58:41 UTC |
| 8e37c29 | David Seifert | 27 August 2022, 10:55:20 UTC | [TAK-1730] Port from deprecated pbbam API | 27 August 2022, 10:55:20 UTC |
| 04c3a64 | David Seifert | 25 August 2022, 14:54:20 UTC | [TAK-1729] Consistent `constexpr` variable naming | 25 August 2022, 14:54:20 UTC |
| c88156a | David Seifert | 25 August 2022, 14:54:20 UTC | [TAK-1729] `BOOST_ASSERT_MSG(...)` -> `assert(...)` | 25 August 2022, 14:54:20 UTC |
| bec8e28 | Nathaniel Echols | 09 June 2022, 02:48:17 UTC | [SL-8138] add optional mapping stats report json output | 09 June 2022, 02:48:17 UTC |
| 6db6b76 | Darien Pardinas Diaz | 10 May 2022, 19:20:29 UTC | [TAK-1672] Fix for undefined behaviour when assigning nanoseconds to int 32 | 10 May 2022, 19:20:51 UTC |
| dd14425 | Armin Töpfer | 19 April 2022, 10:31:25 UTC | [TAG-5624] Version 1.9.0 | 19 April 2022, 10:32:11 UTC |
| 8a0bf2d | Chris Saunders | 14 March 2022, 23:59:07 UTC | [TAK-1659] Update meson build for macOS/arm64 | 14 March 2022, 23:59:53 UTC |
| 6175573 | Darien Pardinas Diaz | 10 March 2022, 14:16:05 UTC | [TAG-5552] Make g_is_by_qname atomic | 10 March 2022, 14:16:05 UTC |
| 6e48c1f | Armin Töpfer | 04 March 2022, 14:32:23 UTC | [TAK-1649] Use pbcopper's Stopwatch | 04 March 2022, 14:32:23 UTC |
| 49de465 | Armin Töpfer | 04 March 2022, 13:49:50 UTC | [TAK-1649] Fix include order | 04 March 2022, 14:16:04 UTC |
| 5f62f04 | Armin Toepfer | 04 March 2022, 13:30:02 UTC | Pull request #171: [TAG-5045] Unaligned MAPQ to 0 Merge in SAT/pbmm2 from feature/TAG-5045-unaligned-flag to develop * commit 'f98719d57cffd7e942fb15c78f500774188af5e5': [TAG-5045] Unaligned MAPQ to 0 | 04 March 2022, 13:30:02 UTC |
| f98719d | Armin Töpfer | 04 March 2022, 11:50:36 UTC | [TAG-5045] Unaligned MAPQ to 0 | 04 March 2022, 12:03:49 UTC |
| 389f613 | Armin Toepfer | 04 March 2022, 09:23:49 UTC | Pull request #170: [TAG-5520] Print dependency versions Merge in SAT/pbmm2 from feature/TAG-5520-versioning to develop * commit '0b39dd9da7deeaa384796c5edc71e230c2c70db5': [TAG-5520] Print dependency versions | 04 March 2022, 09:23:49 UTC |
| 0b39dd9 | Armin Töpfer | 04 March 2022, 09:03:01 UTC | [TAG-5520] Print dependency versions | 04 March 2022, 09:10:24 UTC |
| a4a25ef | Darien Diaz | 02 March 2022, 17:26:39 UTC | Pull request #169: Update htslib wrap to version 1.15 Merge in SAT/pbmm2 from feature/TAG-5458-htslib-1.15-update to develop * commit '4cb2497169b3bf87f239c0868c47357cba9d3086': [TAG-5458] updating meson wraps to the latest versions | 02 March 2022, 17:26:39 UTC |
| 4cb2497 | Darien Pardinas Diaz | 02 March 2022, 15:32:34 UTC | [TAG-5458] updating meson wraps to the latest versions | 02 March 2022, 15:32:34 UTC |
| 1b58ce0 | Darien Diaz | 01 March 2022, 14:17:18 UTC | Pull request #168: [TAG-5374] update clang formatting Merge in SAT/pbmm2 from feature/TAG-5374-update-clang-format to develop * commit '89eed8d95b7d75a8f2c5136a46daebf9621e22de': [TAG-5374] update clang formatting | 01 March 2022, 14:17:18 UTC |
| 89eed8d | Darien Pardinas Diaz | 01 March 2022, 12:43:43 UTC | [TAG-5374] update clang formatting | 01 March 2022, 12:43:43 UTC |
| aad7e6b | Christopher Dunn | 04 February 2022, 15:05:05 UTC | Pull request #167: Update README: --num-threads Merge in SAT/pbmm2 from bugfix/TAK-1547-j-bamboo-build to develop * commit '8ca041f294dedaa88490684c4f47ee83e50ce5fa': Update README: --num-threads | 04 February 2022, 15:05:05 UTC |
| 8ca041f | Christopher Dunn | 01 June 2021, 22:06:18 UTC | Update README: --num-threads Was `--alignment-threads`. This is the same as `-j`, and it is provided by **pbcopper**. * https://github.com/PacificBiosciences/pbbioconda/issues/407 Note that the README in our GH repo, https://github.com/PacificBiosciences/pbmm2/ does not necessarily match what is released in Bioconda. And Bioconda is actually several releases old now (1.4.0 from September 2020). So we need to push to GH for this update, but we also need a need Bioconda release in general. TAK-1547 | 04 February 2022, 14:08:30 UTC |
| 6bc6a5f | Herb Maeder | 26 January 2022, 20:53:47 UTC | Merge HEAD of release/prep to develop postbranch, end-of-sprint 2022.01 (01/26/2022) | 26 January 2022, 20:53:47 UTC |
| 1b5e5a0 | Herb Maeder | 26 January 2022, 16:59:41 UTC | Rhino Release branch, develop to release/prep, end-of-sprint 2022.01 01/26/2022 @ smrtlink-incremental_11.0.0.SNAPSHOT140070 (RBS-DEVSMRTLINKINC-49213) @ sequel-pac_11.0.0.SNAPSHOT140025 (IRP-SPR-2504) @ engui-11_0_0_snapshot140012 (MANU-ENGUIDEV-643) @ chemistry-pb-11.0.0.SNAPSHOT139970 (IRP-CHEM-442) @ pa-common-0.0.0.SNAPSHOT96166 (DEP-PD-36) @ pa-thirdparty_bid53 (SEQ-PAV-53) | 26 January 2022, 16:59:41 UTC |
| fbb6bf0 | Armin Toepfer | 10 January 2022, 15:46:36 UTC | Pull request #166: [TAG-5379] Switch to C++20 Merge in SAT/pbmm2 from feature/TAG-5379-cpp20 to develop * commit 'a8663638aa0757eb3def9d29c3fc0087ad3fd36b': [TAG-5379] Switch to C++20 | 10 January 2022, 15:46:36 UTC |
| a866363 | David Seifert | 10 January 2022, 15:09:28 UTC | [TAG-5379] Switch to C++20 | 10 January 2022, 15:09:28 UTC |
| 1ff519e | David Seifert | 12 December 2021, 11:26:40 UTC | Pull request #165: Feature/TAG-5277 cpp20 Merge in SAT/pbmm2 from feature/TAG-5277-cpp20 to develop * commit 'a75c081710c04ee9bd8a3e57354d9241b4470576': [TAG-5277] `b_ndebug=if-release` [TAG-5277] Switch to C17 [TAG-5277] Switch to C++17 [TAG-5277] `ExternalProgram.path()` -> `ExternalProgram.full_path()` [TAG-5277] `meson.build_root()` -> `meson.project_build_root()` [TAG-5277] `meson.source_root()` -> `meson.project_source_root()` | 12 December 2021, 11:26:40 UTC |
| a75c081 | David Seifert | 12 December 2021, 11:16:50 UTC | [TAG-5277] `b_ndebug=if-release` | 12 December 2021, 11:16:50 UTC |
| 7e384bc | David Seifert | 12 December 2021, 11:16:50 UTC | [TAG-5277] Switch to C17 | 12 December 2021, 11:16:50 UTC |
| 3d18f80 | David Seifert | 12 December 2021, 11:16:49 UTC | [TAG-5277] Switch to C++17 | 12 December 2021, 11:16:49 UTC |
| c3eac62 | David Seifert | 12 December 2021, 11:16:48 UTC | [TAG-5277] `ExternalProgram.path()` -> `ExternalProgram.full_path()` | 12 December 2021, 11:16:48 UTC |
| 1b5b6c3 | David Seifert | 12 December 2021, 11:16:48 UTC | [TAG-5277] `meson.build_root()` -> `meson.project_build_root()` | 12 December 2021, 11:16:48 UTC |
| 358b0eb | David Seifert | 12 December 2021, 11:16:47 UTC | [TAG-5277] `meson.source_root()` -> `meson.project_source_root()` | 12 December 2021, 11:16:47 UTC |
| e0b626a | Herb Maeder | 02 October 2021, 14:23:33 UTC | Merge HEAD of release/prep to develop, mid-sprint 2021.19 (10/02/2021) | 02 October 2021, 14:23:33 UTC |
| 3c16a4d | Herb Maeder | 23 September 2021, 09:22:28 UTC | Quokka Release branch (smrtlink-only), for final Quokka/10.2.0 release, develop to release/prep, end-of-sprint 2021.18 09/22/2021 @ smrtlink-incremental_10.2.0.SNAPSHOT130530 (RBS-DEVSMRTLINKINC-45227) | 23 September 2021, 09:22:28 UTC |
| d9e67d4 | Derek Barnett | 21 September 2021, 20:57:30 UTC | Pull request #164: Version 1.8.0 Merge in SAT/pbmm2 from feature/TAG-5095-bump-version to develop * commit 'd1071feb5b10f01c4eb5168095cd48c282d140ed': Version 1.8.0 | 21 September 2021, 20:57:30 UTC |
| d1071fe | Derek Barnett | 21 September 2021, 18:54:49 UTC | Version 1.8.0 | 21 September 2021, 18:54:49 UTC |
| 5b07aa1 | Armin Toepfer | 16 September 2021, 11:00:36 UTC | Pull request #163: [SL-7144] recognize fsa extension (required by NCBI) Merge in SAT/pbmm2 from bugfix/SL-7144-change-final-mapping-to-use-rotated-final-assembly to develop * commit 'dcf94b07516775450f017456880e69f8918fe38f': [SL-7144] remove .fsa.gz support [SL-7144] also test index mode [SL-7144] add cram test | 16 September 2021, 11:00:36 UTC |
| dcf94b0 | Nathaniel Echols | 15 September 2021, 15:22:36 UTC | [SL-7144] remove .fsa.gz support | 15 September 2021, 15:22:36 UTC |
| 3f15d3f | Nathaniel Echols | 14 September 2021, 18:24:47 UTC | [SL-7144] also test index mode | 14 September 2021, 18:24:47 UTC |
| b44573e | Nathaniel Echols | 14 September 2021, 14:36:10 UTC | [SL-7144] add cram test | 14 September 2021, 14:36:10 UTC |
| 8a3638f | Herb Maeder | 17 August 2021, 16:32:34 UTC | Merge HEAD of release/prep to develop, mid-sprint 2021.16 (08/17/2021) | 17 August 2021, 16:32:34 UTC |
| e50ac3a | Herb Maeder | 11 August 2021, 22:27:22 UTC | Quokka Release branch (smrtlink-only), for Pangolin Early Access release, develop to release/prep, end-of-sprint 2021.15 08/11/2021 @ smrtlink-incremental_10.2.0.SNAPSHOT127627 (RBS-DEVSMRTLINKINC-44009) | 11 August 2021, 22:27:22 UTC |
| ab8ac6a | Armin Toepfer | 09 August 2021, 12:57:13 UTC | Pull request #162: Bump to version 1.7.0 Merge in SAT/pbmm2 from feature/TAG-5045-bump-version to develop * commit '5c4f52d91a0182710727ac3352d5d8500246e4d2': Bump to version 1.7.0 | 09 August 2021, 12:57:13 UTC |
| 5c4f52d | Armin Töpfer | 09 August 2021, 12:50:29 UTC | Bump to version 1.7.0 | 09 August 2021, 12:50:29 UTC |
| 4e5ebb6 | David Seifert | 02 June 2021, 13:14:16 UTC | Pull request #161: Ensure one newline between CLI help footer and RUO disclaimer Merge in SAT/pbmm2 from bugfix/TAK-1545-unsmoosh-license to develop * commit 'e920454fb3f3d1d0ba958d798a2bb0527259ffc4': Ensure one newline between CLI help footer and RUO disclaimer | 02 June 2021, 13:14:16 UTC |
| e920454 | David Seifert | 02 June 2021, 13:10:13 UTC | Ensure one newline between CLI help footer and RUO disclaimer | 02 June 2021, 13:10:13 UTC |
| 2a62858 | David Seifert | 17 May 2021, 09:52:26 UTC | Pull request #159: Fix spacing before RUO-disclaimer Merge in SAT/pbmm2 from bugfix/TAK-1498-disclaimer-spacing to develop * commit '056bc523915c51787f26b2aab174c905377bb545': Fix spacing before RUO-disclaimer | 17 May 2021, 09:52:26 UTC |
| 056bc52 | David Seifert | 17 May 2021, 09:47:55 UTC | Fix spacing before RUO-disclaimer | 17 May 2021, 09:47:55 UTC |
| 0fe15a2 | David Seifert | 11 May 2021, 10:05:38 UTC | Pull request #158: Ignore disclaimer in tests Merge in SAT/pbmm2 from feature/TAK-1498-boilerplate-fix to develop * commit '4e3d809ea627a01e33163ebfec9795063c287164': Ignore disclaimer in tests | 11 May 2021, 10:05:38 UTC |
| 4e3d809 | David Seifert | 11 May 2021, 10:02:57 UTC | Ignore disclaimer in tests | 11 May 2021, 10:02:57 UTC |
| f4b5ceb | Armin Toepfer | 16 April 2021, 06:26:57 UTC | Merge pull request #156 in SAT/pbmm2 from feature/TAK-1435-trim-edge-indels to develop * commit '7718e4b24bdbca255ead7d4d42f6327042668946': Trim I/D/X from cigar flanks Update README | 16 April 2021, 06:26:57 UTC |
| 7718e4b | Armin Töpfer | 14 April 2021, 13:50:41 UTC | Trim I/D/X from cigar flanks | 15 April 2021, 15:08:07 UTC |
| e6d9f59 | Armin Töpfer | 15 April 2021, 09:20:07 UTC | Update README | 15 April 2021, 09:20:07 UTC |
| d685f19 | Armin Toepfer | 24 March 2021, 16:16:35 UTC | Merge pull request #155 in SAT/pbmm2 from TAK-1323-TLEN to develop * commit 'd49d8613b5e6dcdee667a39a0a5365fdc24bef9f': A quick check for TLEN Set TLEN as length of query in reference Mention TLEN in README | 24 March 2021, 16:16:35 UTC |
| d49d861 | Christopher Dunn | 23 March 2021, 15:46:29 UTC | A quick check for TLEN TAK-1323 | 24 March 2021, 15:57:49 UTC |
| 3c6754b | Christopher Dunn | 24 February 2021, 18:48:02 UTC | Set TLEN as length of query in reference TAK-1323 | 26 February 2021, 14:30:51 UTC |
| 9e17a80 | Christopher Dunn | 24 February 2021, 18:51:00 UTC | Mention TLEN in README | 26 February 2021, 14:19:10 UTC |
| e740eb8 | Armin Toepfer | 17 February 2021, 15:41:34 UTC | Merge pull request #153 in SAT/pbmm2 from feature/TAG-4776-make-SA-cigar-long to develop * commit '053e66831466cd38d189f2017ea7ceca6482f44f': Use long SA cigars by default,add --short-sa-cigar | 17 February 2021, 15:41:34 UTC |
| 053e668 | Armin Töpfer | 15 February 2021, 12:10:42 UTC | Use long SA cigars by default,add --short-sa-cigar | 15 February 2021, 12:38:08 UTC |
| db74edd | Nathaniel Echols | 02 February 2021, 15:11:39 UTC | Merge pull request #152 in SAT/pbmm2 from bugfix/ITG-1667-fix-pbmm2-hq-mode to develop * commit '8d3abaa7f776b7ba4b35d1c4d8e28ccdf4c2cb95': [ITG-1667] skip reads with zero-length HQregion | 02 February 2021, 15:11:39 UTC |
| 8d3abaa | Nathaniel Echols | 02 February 2021, 00:30:37 UTC | [ITG-1667] skip reads with zero-length HQregion | 02 February 2021, 00:30:37 UTC |
| 8b8111a | Armin Toepfer | 01 February 2021, 09:51:07 UTC | Merge pull request #151 in SAT/pbmm2 from bugfix/TAG-4771-matching-sample-names to develop * commit '241ed58ea745dd87e014c6e5ac2d2e4f8ba352f4': Use -j 1 for tests Parallelize tests Convert filename infix whitespace to underscore Run cram tests in parallel Remove whitespace warning BAM is primary source of truth for biosample names Sanitize sample names for split BAM headers Use fallback variable instead of string Inc version | 01 February 2021, 09:51:07 UTC |
| 241ed58 | Armin Töpfer | 01 February 2021, 09:10:55 UTC | Use -j 1 for tests | 01 February 2021, 09:35:06 UTC |
| a22a506 | Armin Töpfer | 01 February 2021, 08:50:55 UTC | Parallelize tests | 01 February 2021, 09:35:05 UTC |
| 7722d1b | Armin Töpfer | 01 February 2021, 08:50:38 UTC | Convert filename infix whitespace to underscore | 01 February 2021, 09:35:04 UTC |
| 745f9cb | Armin Töpfer | 29 January 2021, 15:02:43 UTC | Run cram tests in parallel | 01 February 2021, 09:35:03 UTC |
