{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":31987083,"defaultBranch":"master","name":"diamond","ownerLogin":"bbuchfink","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2015-03-10T23:19:00.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/10001338?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1706710800.0","currentOid":""},"activityList":{"items":[{"before":"c9003f98bbb137584aa7d11058061fb7143a90cc","after":"a00d0da8081851f9423cb2168a3637af0ddd42e4","ref":"refs/heads/master","pushedAt":"2024-02-14T13:26:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Fixed taxid bug.","shortMessageHtmlLink":"Fixed taxid bug."}},{"before":"ba088282666c06db0665dafc4851df45eae701f6","after":"c9003f98bbb137584aa7d11058061fb7143a90cc","ref":"refs/heads/master","pushedAt":"2024-02-13T09:55:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Fixed crash.","shortMessageHtmlLink":"Fixed crash."}},{"before":"56f5d1403a805fe5b36985395952020052802291","after":"ba088282666c06db0665dafc4851df45eae701f6","ref":"refs/heads/master","pushedAt":"2024-01-31T13:18:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Squashed commit of the following:\n\ncommit cf66ef8a27146afe575b64e135d117b212f7bd64\nAuthor: Benjamin Buchfink \nDate: Wed Jan 31 14:04:42 2024 +0100\n\n Updated tests.\n\ncommit eae157eaae352ce9b38c268cd647ff5ffa6bdf61\nAuthor: Benjamin Buchfink \nDate: Wed Jan 31 13:57:45 2024 +0100\n\n Updated changelog.\n\ncommit 6b2f8ebc1d421cd096ee9df7c5951fc373e54982\nMerge: 8666f7e8 0c888e84\nAuthor: Benjamin Buchfink \nDate: Wed Jan 31 13:23:40 2024 +0100\n\n Merge branch 'master' into dev\n\ncommit 0c888e84367dfba1d1ab6d23a3aa663ad3c61440\nMerge: 19c730d5 56f5d140\nAuthor: Benjamin Buchfink \nDate: Wed Jan 31 13:23:25 2024 +0100\n\n Merge branch 'master' of https://github.com/bbuchfink/diamond\n\ncommit 8666f7e853efe8c8a1d7d0bdde46ad810db7475c\nAuthor: Benjamin Buchfink \nDate: Wed Jan 31 12:34:15 2024 +0100\n\n Fixed output.\n\ncommit a70a755c04135b310d119e69ab9a899a6ace94b0\nAuthor: Benjamin Buchfink \nDate: Wed Jan 31 11:09:09 2024 +0100\n\n Changed max block size for vsens mode.\n\ncommit df9be960f04c8c41b49495746790e44784e7b138\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 16:56:36 2024 +0100\n\n Fixed taxon format.\n\ncommit 565bd4fd37d4116cb6cbd147eed851fd627c81af\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 16:45:54 2024 +0100\n\n Fixed error.\n\ncommit 67df3d4af021e7d39fa559064b3122dd825ab96b\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 16:43:01 2024 +0100\n\n Added taxon lineage option.\n\ncommit e4203e82775fb50789bfe5826b0dc50aa2fc8e67\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 15:57:39 2024 +0100\n\n Added gapped seqs to help.\n\ncommit 98b64461cae30e158fbd2e27eaf9d00d9fb53a59\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 15:47:50 2024 +0100\n\n Fixed warnings.\n\ncommit ab40c4a23dc16a11c9af50657ba40bf3ea734f8d\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 15:41:20 2024 +0100\n\n Fixed warnings.\n\ncommit d9dc1ae43167fb8f496b97742e021b0300b24526\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 15:26:53 2024 +0100\n\n Fixed warnings.\n\ncommit ad6c31999575a2f0b3e84192a91a73fa0eab473e\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 15:02:00 2024 +0100\n\n Updated version.\n\ncommit 30f509a8476c8b1ed4dd1497244da554301412ae\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 14:39:42 2024 +0100\n\n Added shapes-30x10 mode.\n\ncommit dc64958415be88c5ecfbb4b47e48ad5c34f78e4d\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 14:29:17 2024 +0100\n\n Add per round cutoff options.\n\ncommit 4193abd0cf7da091bd25b794c278577075c0b9f8\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 13:43:06 2024 +0100\n\n Added setting ccd per round.\n\ncommit d78caa14b78cd8f690a02df08ef7951934486e41\nAuthor: Benjamin Buchfink \nDate: Tue Jan 30 12:59:40 2024 +0100\n\n Added shapes30x10 mode.\n\ncommit 30221fa8e1b1564fc28ab669a4f08a89da45b44b\nAuthor: Benjamin Buchfink \nDate: Mon Jan 29 16:16:44 2024 +0100\n\n Removed famsa, incremental clustering.\n\ncommit ba15651e286bfc4460343faeb5b08dd98bc97176\nAuthor: Benjamin Buchfink \nDate: Mon Jan 29 15:58:38 2024 +0100\n\n Update reassign for mutual cover.\n\ncommit cf5a84ec02058870e0c42020c66dcf423baf4383\nAuthor: Benjamin Buchfink \nDate: Mon Jan 29 15:30:01 2024 +0100\n\n Updated recluster for mutual coverage.\n\ncommit e6032ba102c805d565096b4cfc1e0c0d34ad9168\nAuthor: Benjamin Buchfink \nDate: Fri Jan 26 17:52:49 2024 +0100\n\n Update recluster for mutual cover.\n\ncommit bdee2616dfbe9195841bac59438d5cc44733a5d4\nAuthor: Benjamin Buchfink \nDate: Fri Jan 26 16:37:24 2024 +0100\n\n Fixed issue with length lookup.\n\ncommit 739be0ea92aee7d32837ab39c70efc2a792f37aa\nAuthor: Benjamin Buchfink \nDate: Fri Jan 26 11:20:14 2024 +0100\n\n Fixed issue with round values.\n\ncommit 34f0b3a73204117b41efc20883fa583e3a89339a\nAuthor: Benjamin Buchfink \nDate: Thu Jan 25 13:28:44 2024 +0100\n\n Reworked storing target ids in hits logic.\n\ncommit 76e17c7443d4362bd821f855a2e8dc8598c67710\nAuthor: Benjamin Buchfink \nDate: Wed Jan 24 18:00:39 2024 +0100\n\n Rework target ids in seed array.\n\ncommit 31f0f34a3c06e52c9a87f565260375376601553e\nAuthor: Benjamin Buchfink \nDate: Wed Jan 24 15:08:28 2024 +0100\n\n Fixed error.\n\ncommit 69680a20ad46fbc9618d5fca59cb7b76104946ca\nAuthor: Benjamin Buchfink \nDate: Wed Jan 24 13:20:32 2024 +0100\n\n Use ccd=0 in last round.\n\ncommit a428f0d9dfcd3225ec34bb358984ac1c6a2e4cd0\nAuthor: Benjamin Buchfink \nDate: Wed Jan 24 13:07:51 2024 +0100\n\n Added round approx id setting.\n\ncommit 261cf75522b9a703644329bfb24164d53d126e84\nAuthor: Benjamin Buchfink \nDate: Wed Jan 24 12:49:19 2024 +0100\n\n Fixed error.\n\ncommit 1f3f8a7acd480f4814f5a0f9eaee5b17630c7b11\nAuthor: Benjamin Buchfink \nDate: Mon Jan 22 17:00:42 2024 +0100\n\n Rework round coverage option\n\ncommit fb55d8eba76e8726b241d3f4fee81e73922af753\nAuthor: Benjamin Buchfink \nDate: Mon Jan 22 15:55:01 2024 +0100\n\n Apply evalue max in cascaded clustering.\n\ncommit ab498d0bbffe523b4e3087149cd7b6be5c29b096\nAuthor: Benjamin Buchfink \nDate: Mon Jan 22 15:25:31 2024 +0100\n\n Apply coverage increment.\n\ncommit f5dd1367549c7932185c78218b0eb6c4618e7e01\nAuthor: Benjamin Buchfink \nDate: Fri Jan 19 16:49:23 2024 +0100\n\n Fixed evalue calculation.\n\ncommit 87aff2d0eab54fc4440a5046f8d06f12440fec1b\nAuthor: Benjamin Buchfink \nDate: Fri Jan 12 12:26:15 2024 +0100\n\n Added shapes.\n\ncommit a49026b0319b04675ac3fa65c851bb116f792c43\nAuthor: Benjamin Buchfink \nDate: Thu Jan 11 14:52:17 2024 +0100\n\n Added new weight 10 modes.\n\ncommit 590e1756fd198b288b4010414010d8b9baed089a\nAuthor: Vincent Spath <90271444+v-spath@users.noreply.github.com>\nDate: Wed Nov 29 17:24:01 2023 +0100\n\n DNA only mapping (#18)\n\n * seed repetition cutoff\n\n * remove overhead\n\n * back to array\n\n * test\n\n * repetitive filter\n\n * changed float to double for parser\n\n * fixed count typo\n\n * removed io header\n\n * min heap seed filtering\n\n * fix heap\n\n * filter multithreaded\n\n * multithreaded optimized\n\n * locked guard\n\n * test new multithreading filter\n\n * filter multithreaded optimized\n\n * pass thread index during creation of thread\n\n * check smallest element before adding to queue\n\n * remove unordered set, replace by checking against cutoff value\n\n * refactor\n\n * new heuristics\n\n * add ungapped extension to set\n\n * new timer\n\n * temp\n\n * new timer\n\n * ssh\n\n * d\n\n * Delete Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.gz\n\n * new timer\n\n * timer\n\n * remove timer\n\n * temp\n\n * Delete Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.gz\n\n * temp\n\n * Delete Arabidopsis_thaliana.TAIR10.dna.chromosome.Pt.fa.gz\n\n * temp\n\n * Delete Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz\n\n * refactor\n\n * seed filter\n\n * target filter\n\n * target filter\n\n * target filter\n\n * revert\n\n * r_ungapped to score\n\n * fix\n\n * wfadaptive\n\n * setheuristicnone\n\n * remove ungapped eval\n\n * repetition cutoff 0\n\n * fix filter for small index\n\n * backup chaining and apple specifics\n\n * revert\n\n * test ksw2 for mac\n\n * chaining and bug fixes and apple specifics\n\n * backtracking\n\n * backup chaining, with old out commented code, 1 bug left\n\n * working_chaining\n\n * add dna chaining condition\n\n * basic chaining\n\n * Delete src/align/align.cpp.save\n\n * repetition-cutoff into WITH_DNA\n\n * Delete libwfa2cpp.a\n\n * add fast approximation of log2\n\n * Delete setup.cpp.save\n\n * delete binary obj\n\n * remove key in RepetitiveCounter\n\n * removed vector of priority_queues as class member\n\n * Update dna_index.cpp\n\n check size repetitive before adding to queue\n\n * extended struct SeedMatch\n\n * fixed bug 100 % ungapped score\n\n * struct for data an chain\n\n * removed std output\n\n * update chain.cpp\n\n * change built queue\n\n * add sorting before chaining\n\n * chaining only for one target at a time\n\n * head\n\n * comments\n\n * include wfa2 in comment\n\n * include wfa comment\n\n * Update log2_fast.h\n\n * chain_end two parameters\n\n * fixed bug backtrack\n\n * make variables const if possible\n\n * parameters struct\n\n * struct anchor data\n\n * update documentation\n\n * backtrack simplification\n\n * update backtrack\n\n * delete wrong commit\n\n * map hsp\n\n * remove RepetitiveCounter struct\n\n * updated chain struct\n\n * construction Chain Object\n\n * chain Standard Komparator\n\n * use iterator\n\n * mapping\n\n * correction syntax\n\n * update indices\n\n * mapping quality\n\n * fixed index t_id\n\n * mapping output includes n_anchors (cm)\n\n * remove redundancy\n\n * fixed bug match build\n\n * primary computation for all targets\n\n * overlap percentage of shorter chain\n\n * fix compile error\n\n * dna extension\n\n * with dna compile\n\n * debug test\n\n * Update extension.cpp\n\n * fix segmentation fault\n\n * test why slow\n\n * test only map best\n\n * test map percentage\n\n * test 1\n\n * sort score\n\n * todo\n\n * move semantics\n\n * forward/reverse together\n\n * test seed lookup\n\n * Update extension.cpp\n\n * add chaining penalties\n\n * new primary chain computation\n\n * Update extension.cpp\n\n * Update extension.cpp\n\n * simplify chain structure\n\n * use PAF when only mapping\n\n * Update config.cpp\n\n * compile error on mac\n\n * Merge branch 'personal_dev' into dev\n\n # Conflicts:\n #\tsrc/basic/config.cpp\n #\tsrc/run/config.cpp\n #\tsrc/run/double_indexed.cpp\n #\tsrc/search/stage0.cpp\n\n * Todo: align long reads\n\n * basic chaining alignment\n\n * fix bug short reads reverse (now correct)\n\n * chain alignment\n\n * integrate ksw2 correctly\n\n * update WFA\n\n * corrected anchor alignment\n\n * fixed residue matches mapping\n\n * change semantics\n\n * refacator chain alignment\n\n * integrate WFA\n\n * correct primary computation\n\n * Update extension.h\n\n * chaining penalties scaling factors\n\n * correction chain alignment\n\n * compute correct alignment score\n\n * correct paf format DNA\n\n * clean up includes\n\n * filter chains\n\n * comments\n\n * wfa low memory mode\n\n * filter chains with lower bound\n\n ---------\n\n Co-authored-by: Dimi \n Co-authored-by: Dimitrios Koutsogiannis \n Co-authored-by: Dimi99 <73211787+Dimi99@users.noreply.github.com>\n Co-authored-by: vinceaps <90271444+vinceaps@users.noreply.github.com>\n Co-authored-by: Benjamin Buchfink \n\ncommit b8f12f41864bc2c2795bcf9ed22b867d717bc5da\nAuthor: Benjamin Buchfink \nDate: Wed Nov 22 10:52:38 2023 +0100\n\n Add cmake flag for famsa.\n\ncommit 7fdecdb2879997b6b6a1079ed28ee2ecacf25229\nAuthor: Benjamin Buchfink \nDate: Wed Nov 15 16:52:41 2023 +0100\n\n Added hit culling.\n\ncommit e3eadb911af4df39aa08bf0f560ec1068d4f5211\nAuthor: Benjamin Buchfink \nDate: Thu Nov 9 17:02:54 2023 +0100\n\n Fixed non x86 compile.\n\ncommit b258c2f5be5421c5c80e44b77b4870d24ac6c603\nAuthor: Benjamin Buchfink \nDate: Thu Nov 9 16:58:40 2023 +0100\n\n Fixed non x86 compile.\n\ncommit e055ce95c60e769da4f496232108b3968d0c4bf9\nAuthor: Vincent Spath <90271444+v-spath@users.noreply.github.com>\nDate: Tue Nov 7 15:59:40 2023 +0100\n\n DNA chaining (#17)\n\n * seed repetition cutoff\n\n * remove overhead\n\n * back to array\n\n * test\n\n * repetitive filter\n\n * changed float to double for parser\n\n * fixed count typo\n\n * removed io header\n\n * min heap seed filtering\n\n * fix heap\n\n * filter multithreaded\n\n * multithreaded optimized\n\n * locked guard\n\n * test new multithreading filter\n\n * filter multithreaded optimized\n\n * pass thread index during creation of thread\n\n * check smallest element before adding to queue\n\n * remove unordered set, replace by checking against cutoff value\n\n * refactor\n\n * new heuristics\n\n * add ungapped extension to set\n\n * new timer\n\n * temp\n\n * new timer\n\n * ssh\n\n * d\n\n * Delete Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.gz\n\n * new timer\n\n * timer\n\n * remove timer\n\n * temp\n\n * Delete Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.gz\n\n * temp\n\n * Delete Arabidopsis_thaliana.TAIR10.dna.chromosome.Pt.fa.gz\n\n * temp\n\n * Delete Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz\n\n * refactor\n\n * seed filter\n\n * target filter\n\n * target filter\n\n * target filter\n\n * revert\n\n * r_ungapped to score\n\n * fix\n\n * wfadaptive\n\n * setheuristicnone\n\n * remove ungapped eval\n\n * repetition cutoff 0\n\n * fix filter for small index\n\n * backup chaining and apple specifics\n\n * revert\n\n * test ksw2 for mac\n\n * chaining and bug fixes and apple specifics\n\n * backtracking\n\n * backup chaining, with old out commented code, 1 bug left\n\n * working_chaining\n\n * add dna chaining condition\n\n * basic chaining\n\n * Delete src/align/align.cpp.save\n\n * repetition-cutoff into WITH_DNA\n\n * Delete libwfa2cpp.a\n\n * add fast approximation of log2\n\n * Delete setup.cpp.save\n\n * delete binary obj\n\n * remove key in RepetitiveCounter\n\n * removed vector of priority_queues as class member\n\n * Update dna_index.cpp\n\n check size repetitive before adding to queue\n\n * extended struct SeedMatch\n\n * fixed bug 100 % ungapped score\n\n * struct for data an chain\n\n * removed std output\n\n * update chain.cpp\n\n * change built queue\n\n * add sorting before chaining\n\n * chaining only for one target at a time\n\n * head\n\n * comments\n\n * include wfa2 in comment\n\n * include wfa comment\n\n * Update log2_fast.h\n\n * chain_end two parameters\n\n * fixed bug backtrack\n\n * make variables const if possible\n\n * parameters struct\n\n * struct anchor data\n\n * update documentation\n\n * backtrack simplification\n\n * update backtrack\n\n * delete wrong commit\n\n * remove RepetitiveCounter struct\n\n * updated chain struct\n\n * construction Chain Object\n\n * chain Standard Komparator\n\n * use iterator\n\n * correction syntax\n\n * fixed index t_id\n\n * move semantics\n\n ---------\n\n Co-authored-by: Dimi \n Co-authored-by: Dimitrios Koutsogiannis \n Co-authored-by: Dimi99 <73211787+Dimi99@users.noreply.github.com>\n Co-authored-by: vinceaps <90271444+vinceaps@users.noreply.github.com>\n Co-authored-by: Benjamin Buchfink \n\ncommit 19c730d59620efa02e9b7a6928283962767a64c3\nAuthor: Benjamin Buchfink \nDate: Tue Nov 7 15:54:53 2023 +0100\n\n Add output field for lineage.\n\ncommit 7cb96085fa2950f0d500e468331d0f7a8367c182\nAuthor: Benjamin Buchfink \nDate: Tue Nov 7 10:48:11 2023 +0100\n\n Check for identical block.\n\ncommit 8438e3387278dad3405ed9c2f7b1b6a29be94407\nAuthor: Benjamin Buchfink \nDate: Thu Oct 26 14:23:56 2023 +0200\n\n remove alignment computation.\n\ncommit 52649efac7cc76c4ab7822c7848cd74763582c07\nAuthor: Benjamin Buchfink \nDate: Wed Oct 25 17:35:38 2023 +0200\n\n Filter by mutual coverage.\n\ncommit 1bfa4e2a82e52fb91241c48eeb349a29f7dbed53\nAuthor: Benjamin Buchfink \nDate: Wed Oct 25 17:08:11 2023 +0200\n\n Added alignment.\n\ncommit 1149045d6c55fcf40604248e57c8c93b3ddbd4ab\nAuthor: Benjamin Buchfink \nDate: Wed Oct 25 12:55:15 2023 +0200\n\n Fix centroid lookup.\n\ncommit dcef57b958768f36c69dc6a1c19527082a043f9e\nAuthor: Benjamin Buchfink \nDate: Tue Oct 24 16:35:01 2023 +0200\n\n Added parallel processing.\n\ncommit c0ebcc97a3f0201ca5a271199795a144f97c49c5\nAuthor: Benjamin Buchfink \nDate: Tue Oct 24 13:48:51 2023 +0200\n\n Fixed bug.\n\ncommit ff8b053116a7df875e59fafff7e933da10c2bddf\nAuthor: Benjamin Buchfink \nDate: Tue Oct 24 13:43:18 2023 +0200\n\n Check for indirection.\n\ncommit 539416b50a933cde0594c9a110b4945d6c366d57\nAuthor: Benjamin Buchfink \nDate: Tue Oct 24 12:33:32 2023 +0200\n\n Write output.\n\ncommit 0fdfe23a8695efeb8e824fb07e79a959e5ce317a\nAuthor: Benjamin Buchfink \nDate: Mon Oct 23 16:59:07 2023 +0200\n\n Process alignments.\n\ncommit 83b0442e0efc20f28e703d16ebf52503015189d0\nMerge: 8d0ce419 5171828f\nAuthor: Benjamin Buchfink \nDate: Sat Oct 21 14:39:44 2023 +0200\n\n Merge branch 'dev' of https://github.com/bbuchfink/diamond_dev into dev\n\ncommit 8d0ce419c8bf9c835403ca1afd1ee0b8be5d4b5e\nAuthor: Benjamin Buchfink \nDate: Sat Oct 21 14:39:34 2023 +0200\n\n Fixed error.\n\ncommit 5171828faf97348653d5447f4765e8c041075c58\nAuthor: Benjamin Buchfink \nDate: Fri Oct 20 14:50:12 2023 +0200\n\n Fixed error.\n\ncommit 367ac23fc68acbb4c195d6136f5d83d2e24a9770\nAuthor: Benjamin Buchfink \nDate: Thu Oct 19 17:38:31 2023 +0200\n\n Added profile alignment.\n\ncommit 03b51a98073196fb03494979fa03ee917448b376\nMerge: 13a3e512 6096ef28\nAuthor: Benjamin Buchfink \nDate: Wed Oct 18 16:26:27 2023 +0200\n\n Merge branch 'dev' of https://github.com/bbuchfink/diamond_dev into dev\n\ncommit 13a3e512efd362d6746359fd17580fc4dfee6908\nAuthor: Benjamin Buchfink \nDate: Wed Oct 18 16:26:08 2023 +0200\n\n Fixed blastdb.\n\ncommit 6096ef2841d6e0c87d58292b4238eb9ce3d6b17d\nAuthor: Benjamin Buchfink \nDate: Tue Oct 17 16:53:37 2023 +0200\n\n Added local alignment of profiles.\n\ncommit 8a5eca0d72348012775177f929447ddcfd5db0a7\nAuthor: Benjamin Buchfink \nDate: Fri Oct 13 15:32:15 2023 +0200\n\n Fix leak.\n\ncommit d2563fd8c85c6891064ce2a8010a5c38e94c63b9\nAuthor: Benjamin Buchfink \nDate: Fri Oct 13 15:04:16 2023 +0200\n\n Added profile-recluster workflow.\n\ncommit d4b638e4fee52ae4024d35e109e81bed1f9ee32d\nAuthor: Benjamin Buchfink \nDate: Thu Oct 12 17:03:33 2023 +0200\n\n Added MSA computation.\n\ncommit a7e375040af808cdea6ae2bfc9a43b2fb285b1db\nAuthor: Benjamin Buchfink \nDate: Thu Oct 12 14:24:55 2023 +0200\n\n Added FAMSA.\n\ncommit 88119a03726d7288c406237d0b975c1ad304c426\nAuthor: Benjamin Buchfink \nDate: Wed Sep 27 16:52:47 2023 +0200\n\n Use letter count of subdb in clustering.\n\ncommit bed1a484f7f28beb654d12817431c8a7610faca0\nAuthor: Benjamin Buchfink \nDate: Wed Sep 27 16:28:07 2023 +0200\n\n Added length lookup.\n\ncommit 81843d6fa42081219f89d0833838b8d481dfec23\nAuthor: Benjamin Buchfink \nDate: Tue Sep 26 13:54:08 2023 +0200\n\n Use coverage increment in earlier rounds.\n\ncommit 53a20c61e5f4e68b41505bc08dcb776070cbca35\nAuthor: Benjamin Buchfink \nDate: Tue Sep 26 13:40:00 2023 +0200\n\n Use ccd=0 in linear stages.\n\ncommit e5699a10fb0b8da76f1152ac5773d3cafdb304a1\nAuthor: Benjamin Buchfink \nDate: Mon Sep 18 16:52:45 2023 +0200\n\n Use median sequence.\n\ncommit da749bc1fb1826bebbeadd80ad8a46adc70dc118\nMerge: eb336685 a1c35d03\nAuthor: Benjamin Buchfink \nDate: Mon Sep 18 11:44:00 2023 +0200\n\n Merge branch 'dev' of https://github.com/bbuchfink/diamond_dev into dev\n\ncommit eb33668574a28a84ec585613c8d31de644d89ff6\nAuthor: Benjamin Buchfink \nDate: Mon Sep 18 11:43:25 2023 +0200\n\n Fixed subject source range.\n\ncommit a1c35d03f4ba0f4a56461d431df6dbde277b85eb\nAuthor: Benjamin Buchfink \nDate: Mon Sep 11 14:50:49 2023 +0200\n\n Auto set min length ratio.\n\ncommit 612df402ca9fafc2c5cfed2d54b62354041edb8f\nAuthor: Benjamin Buchfink \nDate: Mon Sep 11 13:43:35 2023 +0200\n\n Added mutual cover clustering.\n\ncommit c909a44381fa52d6a359d44b607fedc59690eeff\nAuthor: Benjamin Buchfink \nDate: Fri Sep 8 11:15:33 2023 +0200\n\n Added connected component depth.\n\ncommit b613c12c6d4f5abaa9914075626414f39392b7b0\nAuthor: Benjamin Buchfink \nDate: Wed Sep 6 16:58:28 2023 +0200\n\n Added cc clustering.\n\ncommit abd593504534f23632b98787f5053d5d93d23dc4\nAuthor: Benjamin Buchfink \nDate: Tue Sep 5 17:04:45 2023 +0200\n\n Added callback for bidirectional clustering.\n\ncommit 76b222058f50e2fee6664159e0df47cb518b667b\nAuthor: Benjamin Buchfink \nDate: Tue Sep 5 15:46:27 2023 +0200\n\n Added --no-reassign to gvc.\n\ncommit 268090426a40c2b22f04b8a0ced5101b6195ba5d\nAuthor: Benjamin Buchfink \nDate: Tue Sep 5 10:31:51 2023 +0200\n\n Fixed approx_id for anchored swipe.\n\ncommit 4acb106d2495d0cd67481567607c81184081fbf9\nAuthor: Benjamin Buchfink \nDate: Mon Aug 28 14:56:25 2023 +0200\n\n Fixed bug.\n\ncommit ccae0326a15e745e07c54edced47e3284b92c949\nAuthor: Benjamin Buchfink \nDate: Mon Aug 28 13:26:12 2023 +0200\n\n Added length ratio filter.\n\ncommit 43eb577fd11eca0a84901b558013a409edcfd5c6\nMerge: 49c3fffb 7d89b2b0\nAuthor: Benjamin Buchfink \nDate: Fri Aug 25 16:04:42 2023 +0200\n\n Merge branch 'dev' of https://github.com/bbuchfink/diamond_dev into dev\n\ncommit 49c3fffb58f22405b1496b2f18fe8c04e35298b2\nAuthor: Benjamin Buchfink \nDate: Fri Aug 25 16:03:43 2023 +0200\n\n Added len ratio filter.\n\ncommit 7d89b2b0197901a8727e2814ea35605e2cf5cdaf\nAuthor: Benjamin Buchfink \nDate: Thu Jul 20 16:12:54 2023 +0200\n\n Fixed warning.\n\ncommit 6c4c4d7994f80f8603027cabf1d966ead048b428\nAuthor: Benjamin Buchfink \nDate: Thu Jul 20 16:02:58 2023 +0200\n\n Added sorting.\n\ncommit 97c350241a5b309b3fc1862b3666365834cfbe39\nAuthor: Benjamin Buchfink \nDate: Wed Jul 19 11:23:49 2023 +0200\n\n Fixed full_qqual field.\n\ncommit 4ba1920cbe2d4ed3cb45d803126296a2bcc1a775\nAuthor: Benjamin Buchfink \nDate: Tue Jul 18 18:50:34 2023 +0200\n\n Add len-ratio filter.\n\ncommit 58bf56ec153b9f5944b672db9f136aec0e1af705\nAuthor: Benjamin Buchfink \nDate: Tue Jul 18 16:19:29 2023 +0200\n\n Added symmetric option to gvc.\n\ncommit 4d8f6d6aee2d895d7a62ace47689432dc31e6de3\nAuthor: Benjamin Buchfink \nDate: Mon Jul 17 16:43:32 2023 +0200\n\n Added mutual cov lin-stage1.\n\ncommit 6693d01a2004346cd35f209f448aa5803a347737\nAuthor: Benjamin Buchfink \nDate: Fri Jul 14 16:59:11 2023 +0200\n\n Added linclust stage with mutual cov.\n\ncommit dd3fb04acc23760257664ea6c4f6127dd576f8c6\nAuthor: Benjamin Buchfink \nDate: Fri Jul 14 12:41:03 2023 +0200\n\n Added mutual coverage.\n\ncommit 97c1e2e54dd5a540800b022a7e3bb513ae5da429\nAuthor: Benjamin Buchfink \nDate: Wed Jul 12 15:55:04 2023 +0200\n\n Fixed sam query field.\n\ncommit 2af1fa4028f30bbb9da4363d80f268ead311e3f5\nMerge: e1d1c047 23a1ba79\nAuthor: Benjamin Buchfink \nDate: Wed Jul 12 15:54:11 2023 +0200\n\n Merge branch 'master' into dev\n\ncommit e1d1c047d6459ced42b85ce897a5d42a7640714e\nAuthor: Benjamin Buchfink \nDate: Fri Jun 23 15:11:53 2023 +0200\n\n Added length ratio filter.\n\ncommit 59a52cd0bcf1458bc311b36ba3911fd00bee1319\nMerge: 561b9632 af4fc648\nAuthor: Benjamin Buchfink \nDate: Fri Jun 23 14:24:04 2023 +0200\n\n Merge branch 'master' into dev\n\ncommit 561b96324e32731019b3e3ca7d3df5b54caa9217\nMerge: 70409de0 749de49c\nAuthor: Dimi99 <73211787+Dimi99@users.noreply.github.com>\nDate: Wed Jun 21 14:21:55 2023 +0200\n\n Merge pull request #12 from Dimi99/dev\n\n Add the WFA Extension-Option\n\ncommit 749de49c7d90b6fee3c331bd009fb86dfcce4557\nMerge: 141f517e 52cdcbae\nAuthor: Dimi \nDate: Wed Jun 21 14:13:18 2023 +0200\n\n Merge branch 'dev' of github.com:Dimi99/diamond_dev into dev\n\ncommit 141f517ee52480501ac3a79b72be8ca05818cde0\nAuthor: Dimi \nDate: Wed Jun 21 14:13:09 2023 +0200\n\n changes\n\ncommit 52cdcbae9023e38c94235778a33abb4542425b6a\nMerge: c6c9bfff 70409de0\nAuthor: Dimi99 <73211787+Dimi99@users.noreply.github.com>\nDate: Wed Jun 21 12:35:12 2023 +0200\n\n Merge branch 'dev' into dev\n\ncommit c6c9bfff21d275992a55da542553120d6af0231a\nAuthor: Dimi \nDate: Wed Jun 21 12:31:25 2023 +0200\n\n cmake\n\ncommit 9a19d041c72f09aca50a41913b2adb8e4f10eae8\nAuthor: Dimi \nDate: Wed Jun 21 12:30:59 2023 +0200\n\n cmake\n\ncommit 5dd3ac5e6cd6db4062e2da9b726d155ba2f823e6\nAuthor: Dimi \nDate: Wed Jun 21 12:23:41 2023 +0200\n\n timer","shortMessageHtmlLink":"Squashed commit of the following:"}},{"before":"dd435198140ea95c8c28f9790c78f3485a7900b9","after":"56f5d1403a805fe5b36985395952020052802291","ref":"refs/heads/master","pushedAt":"2024-01-31T12:22:42.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Add NEON implementation for `armv7` and `aarch64` platforms (#615)\n\n* Configure build system to compile arch-specific extension for Arm NEON\r\n\r\n* Add NEON implementation for `util/simd/vector.h`\r\n\r\n* Add `tranpose16x16` implementation with NEON\r\n\r\n* Fix wrong macro used in dynamic dispatch with NEON enabled\r\n\r\n* Add NEON implementation of score vectors in `score_vector_int8.h`\r\n\r\n* Enable `benchmark_transpose` when compiled with NEON support\r\n\r\n* Add NEON implementation in `score_vector_int16.h`\r\n\r\n* Implement `SwipeProfile` with NEON in `swipe.h`\r\n\r\n* Add remaining unimplemented code in `score_vector.h`\r\n\r\n* Enable SIMD swipe and benchmarks when compiling for NEON\r\n\r\n* Add guards to compile NEON code on Armv7 platforms\r\n\r\n* Add NEON horizontal sums implementations using `vpadalq` cascades\r\n\r\n* Add fallback `ScoreVector::cmp_mask` implementation for Armv7 NEON\r\n\r\n* Add NEON support to `finger_print.h` and `hash_set.h`\r\n\r\n* Enable NEON architecture in `banded_3frame_swipe.cpp`\r\n\r\n* Add remaining benchmarks for which there exist a NEON implementation\r\n\r\n* List NEON in compile-time and runtime feature lists\r\n\r\n* Update define macros for compilation of NEON architecture library\r\n\r\n* Fix some define guards in `util/simd` headers\r\n\r\n* Fix define guards in `ungapped_simd` when compiling for Aarch64\r\n\r\n* Fix `cmp_mask` implementations for NEON `ScoreVector` instantiations\r\n\r\n* Rewrite NEON `transpose` without Aarch64-specific instructions\r\n\r\n* Use Arm NEON include guards instead of architecture for banded swipe code\r\n\r\n* Add `expand_from_8bit` implementation for Armv7 NEON\r\n\r\n* Rewrite 16x16 NEON transpose without `vst1q_s8_x4` for Armv7 compatibility\r\n\r\n* Benchmark scalar 16x16 transpose to compare to vectorized code\r\n\r\n* Fix include guards in `swipe_wrapper.cpp` preventing the use of NEON vectors\r\n\r\n* Remove `Deque::Iterator::operator-` when compiling for Arm for `armv7` compatibility\r\n\r\n* Fix `benchmark_transpose` not using a valid scalar implementation\r\n\r\n* Refactor `cmp_mask` implementation into common inline function for NEON\r\n\r\n* Add Arm NEON implementation to `sse_dist.h`\r\n\r\n* Add Arm NEON implementation of `BitVector::one_count` using `vcntq_u8` intrinsic\r\n\r\n* Fix `reduce_seq_aarch64` definition in `sse_dist.h`\r\n\r\n* Implement `ScoreVector(unsigned, Register)` for NEON\r\n\r\n* Fix potential overflow in NEON code of `BitVector::one_count`\r\n\r\n* Fix `CMakeLists.txt` and `simd.h` to only build NEON on `armv7` with build support\r\n\r\n* Setup runtime detection of `NEON` for `armv7` in `simd.cpp`\r\n\r\n* Setup dispatch for NEON in `dispatch.h`\r\n\r\n* Fix scope of NEON helpers in `simd.h`\r\n\r\n* Change NEON architecture ID in `CMakeLists.txt` to avoid conflict with AVX512\r\n\r\n* Fix remaining use of `::SIMD` namespace in NEON code\r\n\r\n* Fix NEON `letter_mask` not disabling sequence mask based on macros\r\n\r\n* Revert back commented code in `deque.h`\r\n\r\n* Fix iteration in `hauser_correction.cpp`\r\n\r\n* Use compile-time macro to avoid `Deque::Iterator::operator-` overload\r\n\r\n* Fix benchmarks not running properly for NEON\r\n\r\n* Fix `armv7l` implementation of `vmaskq_s8`\r\n\r\n* Fix `table.h` for 32-bit platforms","shortMessageHtmlLink":"Add NEON implementation for armv7 and aarch64 platforms (#615)"}},{"before":"e336e5405403778fc219a6acd02b972d71678cc8","after":"dd435198140ea95c8c28f9790c78f3485a7900b9","ref":"refs/heads/master","pushedAt":"2024-01-08T13:51:26.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Fix build with clang 17 (#771)\n\nThe build was fixed by adding the -= operator to Deque's random access\r\niterator.","shortMessageHtmlLink":"Fix build with clang 17 (#771)"}},{"before":"a81a7471efda635dcc26dda3669469b90cb6b860","after":"e336e5405403778fc219a6acd02b972d71678cc8","ref":"refs/heads/master","pushedAt":"2023-10-09T10:29:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"23a1ba79f20b79a92eeda4721c90d2db136f92e9","after":"a81a7471efda635dcc26dda3669469b90cb6b860","ref":"refs/heads/master","pushedAt":"2023-09-20T09:18:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"af4fc6484250c497c6b1f1a08f734764dc5d2ed4","after":"23a1ba79f20b79a92eeda4721c90d2db136f92e9","ref":"refs/heads/master","pushedAt":"2023-07-12T13:47:57.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"util/string: Allow T/G/M/K size suffixes (#724)\n\n* util/string: Allow T/G/M/K size suffixes\r\n\r\nThis patch allows one to specify sizes to diamond (e.g. for memory usage\r\nin deepclust) using T/G/M/K suffixes, rather than only using a G suffix.\r\n\r\n* Match tab indendation","shortMessageHtmlLink":"util/string: Allow T/G/M/K size suffixes (#724)"}},{"before":"194e174e5ea3e7a37821d8b30d1cfc8666591975","after":"af4fc6484250c497c6b1f1a08f734764dc5d2ed4","ref":"refs/heads/master","pushedAt":"2023-06-20T10:46:23.306Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Fixed test.","shortMessageHtmlLink":"Fixed test."}},{"before":"03e7f4a77b36e7500f6856cd15a05771c1c731fb","after":"194e174e5ea3e7a37821d8b30d1cfc8666591975","ref":"refs/heads/master","pushedAt":"2023-06-20T07:56:44.108Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Fixed issues.","shortMessageHtmlLink":"Fixed issues."}},{"before":"14f355071e5c8627fd6ab5b795cacfc91cb5a215","after":"03e7f4a77b36e7500f6856cd15a05771c1c731fb","ref":"refs/heads/master","pushedAt":"2023-06-20T07:27:16.839Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Squashed commit of the following:\n\ncommit 70409de0e2af0a16a7136bab31086ef7eab04d9b\nAuthor: Benjamin Buchfink \nDate: Tue Jun 20 09:25:18 2023 +0200\n\n Updated version.\n\ncommit 4099a6d4e2d61fa0ca32e1ea2935bf7fda871601\nAuthor: Benjamin Buchfink \nDate: Mon Jun 19 17:03:26 2023 +0200\n\n Added alias taxid.\n\ncommit 38b77f968b2013944480e4c855be7ee8f6fe6c57\nAuthor: Benjamin Buchfink \nDate: Mon Jun 19 16:10:41 2023 +0200\n\n Added qlen for sam format.\n\ncommit 9db6be8ccd7293d501f4640cf317c72c0532c926\nAuthor: Benjamin Buchfink \nDate: Tue Jun 13 16:57:07 2023 +0200\n\n Delete iostream\n\ncommit f91883fac79b43c29989b3091dec6d981457164b\nAuthor: Benjamin Buchfink \nDate: Tue Jun 13 12:53:17 2023 +0200\n\n Use array for root.\n\ncommit 2d9667af766c8379b1f734fd6263ab8ece2efd2a\nAuthor: Benjamin Buchfink \nDate: Tue Jun 13 12:53:10 2023 +0200\n\n Use array as root.\n\ncommit 95023132611bf4dfa2667ea172a2aa5542a7cabe\nAuthor: emile151 <83399151+emile151@users.noreply.github.com>\nDate: Tue Jun 13 12:25:34 2023 +0200\n\n Dev (#15)\n\n * json format reworked in blast_tab\n\n * json format reworked in blast_tab\n\n * json format reworked in blast_tab\n\n * json format reworked in blast_tab\n\n * json format reworked in blast_tab\n\n * json format reworked in blast_tab\n\n * json format reworked in blast_tab (comments fixed)\n\n * json format reworked in blast_tab (comments fixed)\n\n * json format reworked in blast_tab (comments fixed)\n\n * json format reworked in blast_tab (comments fixed)\n\n * json format reworked in blast_tab (comments fixed)\n\n * json format reworked in blast_tab (comments fixed)\n\n * json format reworked in blast_tab (comments fixed)\n\n * json format reworked in blast_tab (comments fixed)\n\n * Merge conflcit resolved\n\n * json format reworked in blast_tab (comments fixed)\n\ncommit 608bc06a082c528eecdb2642205208906f1a756d\nAuthor: Benjamin Buchfink \nDate: Tue Jun 13 11:23:31 2023 +0200\n\n Added seed masking for --algo 1.\n\ncommit aac15b8ba2489c76c8810714ae572f3e3278a1d8\nAuthor: Benjamin Buchfink \nDate: Mon Jun 12 17:23:31 2023 +0200\n\n Filter low complex seeds in enum_seeds.\n\ncommit ddca6fa9cce1eb65d17893930d969b8bd6228e1c\nMerge: 5c10a7dd 14f35507\nAuthor: Benjamin Buchfink \nDate: Wed Jun 7 09:33:45 2023 +0200\n\n Merge branch 'master' into dev","shortMessageHtmlLink":"Squashed commit of the following:"}},{"before":"c0a759de9959e96ab4ef99ab69e9ea20f5fac8fa","after":"14f355071e5c8627fd6ab5b795cacfc91cb5a215","ref":"refs/heads/master","pushedAt":"2023-05-31T08:47:15.892Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Fixed tests.","shortMessageHtmlLink":"Fixed tests."}},{"before":"c7b19e96b7b49075cf667bd6a88d5306ae6961a7","after":"c0a759de9959e96ab4ef99ab69e9ea20f5fac8fa","ref":"refs/heads/master","pushedAt":"2023-05-30T15:54:00.506Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Squashed commit of the following:\n\ncommit 5c10a7ddd2e443a85bfca2418c2f4d9da2a606e7\nAuthor: Benjamin Buchfink \nDate: Tue May 30 17:48:52 2023 +0200\n\n Updated changelog.\n\ncommit 253ddffe7fba443ddd0e7390bd49156c0e82169e\nAuthor: Benjamin Buchfink \nDate: Tue May 30 16:33:29 2023 +0200\n\n Updated version.\n\ncommit 67e9ea316f89df8605fe5c019d1e09be647e531e\nAuthor: Benjamin Buchfink \nDate: Tue May 30 16:16:57 2023 +0200\n\n Fixed CLI.\n\ncommit 5b94bd8edea81f20b3c963e99fe2be8ca66d7ae5\nAuthor: Benjamin Buchfink \nDate: Fri May 26 17:01:36 2023 +0200\n\n CLI.\n\ncommit 910d2971d9b7cf9bfc342047586c0ab260f2b326\nAuthor: Benjamin Buchfink \nDate: Wed May 24 12:05:37 2023 +0200\n\n Added tantan license.\n\ncommit 916c9a26c2df0ee7641f0e4e8a4668c981500f29\nAuthor: Benjamin Buchfink \nDate: Tue May 23 16:55:12 2023 +0200\n\n Fixed changelog.\n\ncommit a99803c54dda3af26280c52a15ffb41037d04899\nAuthor: Benjamin Buchfink \nDate: Tue May 23 15:28:43 2023 +0200\n\n Fixed message.\n\ncommit 0470b1655dbdc4c2820302ade7f84dd8115f9e46\nMerge: dae33fc2 c7b19e96\nAuthor: Benjamin Buchfink \nDate: Tue May 23 15:28:31 2023 +0200\n\n Merged w/master.\n\ncommit dae33fc29827c2abe70b2dcfa096d29a1f45129a\nAuthor: Benjamin Buchfink \nDate: Tue May 23 15:05:21 2023 +0200\n\n Fixed message.\n\ncommit da332d2315409df89d9179ab5c97f9d065ec6ca6\nAuthor: emile151 <83399151+emile151@users.noreply.github.com>\nDate: Wed May 10 10:27:32 2023 +0200\n\n Dev (#13)\n\n * Created Documentation function:\n Selects the corresponding possible options depending on the mode selected\n\n * Arranged print Doc\n\n * Changed the print_help function to print only possible modes\n\n * Changed the print_help function to print only possible modes\n\n * Fixed remarks, prints Documentation when two arguments\n\n * print_documentation adjusted\n\ncommit 504540eb3328423c77215728965b9ed19086fea1\nMerge: ac48249f 83cc65a5\nAuthor: Benjamin Buchfink \nDate: Tue May 2 09:52:18 2023 +0200\n\n Merge branch 'dev' of https://github.com/bbuchfink/diamond_dev into dev\n\ncommit ac48249f477d3ac6a3d6cf3d58acdbbb292a920c\nAuthor: Benjamin Buchfink \nDate: Mon May 1 21:43:50 2023 +0200\n\n Added model-seqs command.\n\ncommit 83cc65a569b86afc2cc0cebf17f46d7258d2cab9\nAuthor: Benjamin Buchfink \nDate: Thu Apr 27 17:12:03 2023 +0200\n\n Added stats for accession parsing.\n\ncommit 77c2ffc5cf4bfc207e6df68e4689bbdd5193038b\nAuthor: Benjamin Buchfink \nDate: Thu Apr 27 16:18:50 2023 +0200\n\n Allow `--tmpdir` for other workflows.\n\ncommit 9db87473bf9dc4a07285b6459420dfbb7ceca983\nAuthor: Benjamin Buchfink \nDate: Thu Apr 13 10:13:51 2023 +0200\n\n Fixed error.\n\ncommit 27bdbeddcbf323f6e591b8ef34dee4a7f641b857\nAuthor: Benjamin Buchfink \nDate: Thu Apr 13 10:13:13 2023 +0200\n\n Fixed errors.\n\ncommit c1676e276f6a78345b607a61144e0552fb7ae1fe\nAuthor: Benjamin Buchfink \nDate: Thu Apr 13 09:14:24 2023 +0200\n\n Updated changelog.\n\ncommit 168a21e1120f263e35959c787f61ad09151667d9\nAuthor: Benjamin Buchfink \nDate: Wed Apr 12 11:11:48 2023 +0200\n\n Added tests.\n\ncommit 9ab6a5d09c0894c81ea2ab21f55183920a9cce26\nAuthor: Benjamin Buchfink \nDate: Tue Apr 4 16:58:26 2023 +0200\n\n Updated test script.\n\ncommit 98ecdfbc3cc4215e667254cae772d5ae0daec5ed\nAuthor: Benjamin Buchfink \nDate: Tue Apr 4 09:30:33 2023 +0200\n\n Added test script.\n\ncommit c475d4b5ea487d089b502e6bbf91747f216b3e9b\nAuthor: Benjamin Buchfink \nDate: Fri Mar 31 17:15:24 2023 +0200\n\n Implemented tokenizers for fasta and fastq.\n\ncommit ba34eb0186a1fa366e863544a9f158c2d0411c13\nMerge: 9542bcaa 82e9959f\nAuthor: Benjamin Buchfink \nDate: Fri Mar 31 15:02:53 2023 +0200\n\n Merge branch 'master' into dev","shortMessageHtmlLink":"Squashed commit of the following:"}},{"before":"a6f429d523e80b939880bdcb48a920eb3369401c","after":"c7b19e96b7b49075cf667bd6a88d5306ae6961a7","ref":"refs/heads/master","pushedAt":"2023-04-24T13:29:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Added `--no-parse-seqids` option.","shortMessageHtmlLink":"Added --no-parse-seqids option."}},{"before":"82e9959fa5a811a21d03904e229776cba666f2e2","after":"a6f429d523e80b939880bdcb48a920eb3369401c","ref":"refs/heads/master","pushedAt":"2023-04-24T13:23:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Added `--no-parse-seqids` option.","shortMessageHtmlLink":"Added --no-parse-seqids option."}},{"before":"75c825047ce92041b17fdef819db1a9caa826fb7","after":"82e9959fa5a811a21d03904e229776cba666f2e2","ref":"refs/heads/master","pushedAt":"2023-03-31T12:20:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Fixed crash for --target-indexed.","shortMessageHtmlLink":"Fixed crash for --target-indexed."}},{"before":"d700d155f9aa0af60158efa60329f4ad09c2f373","after":"75c825047ce92041b17fdef819db1a9caa826fb7","ref":"refs/heads/master","pushedAt":"2023-03-28T12:57:29.763Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"0540f86d3d5965cf9a6ef8871068999ef61211dc","after":"d700d155f9aa0af60158efa60329f4ad09c2f373","ref":"refs/heads/master","pushedAt":"2023-03-27T09:42:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Fixed bug for loading taxon names.","shortMessageHtmlLink":"Fixed bug for loading taxon names."}},{"before":"21a32fc57d66f6679a2ab3a0d302700de899753d","after":"0540f86d3d5965cf9a6ef8871068999ef61211dc","ref":"refs/heads/master","pushedAt":"2023-03-18T10:20:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Squashed commit of the following:\n\ncommit 9542bcaa9036f585f56048cb12c4eee8d12319c0\nAuthor: Benjamin Buchfink \nDate: Sat Mar 18 11:17:52 2023 +0100\n\n Fixed PAF bug.\n\ncommit e6563b3dd023bd7bd4c81c7bce8ba7b655a635f0\nAuthor: Benjamin Buchfink \nDate: Sat Mar 18 10:47:09 2023 +0100\n\n Fixed unaligned bug.\n\ncommit 285afd5f33b8a58eb2d1d2cf3afff08063446f94\nAuthor: Benjamin Buchfink \nDate: Sat Mar 18 10:16:15 2023 +0100\n\n Fixed macOS compiler error.\n\ncommit 7dd350e04eb5626090313fe1af6d79e73711c6cc\nAuthor: Benjamin Buchfink \nDate: Thu Mar 16 09:35:22 2023 +0100\n\n Added switch to disable tls.\n\ncommit 39c80484883ccbc31c439da1f37f5ef6dedb42f3\nMerge: a11f8eda 21a32fc5\nAuthor: Benjamin Buchfink \nDate: Wed Mar 15 11:50:28 2023 +0100\n\n Merge branch 'master' into dev\n\ncommit a11f8eda395a1d7055d243346c1d786572c9343e\nAuthor: Benjamin Buchfink \nDate: Wed Mar 15 11:49:23 2023 +0100\n\n Disable sse for building blast.\n\ncommit 857e96f539089474a66b37e35033ffcabd3bb8b3\nAuthor: Benjamin Buchfink \nDate: Tue Mar 14 12:54:52 2023 +0100\n\n Fixed error.\n\ncommit f8b3c28075c6a7a0bf2764389696de372dd8aa59\nAuthor: Benjamin Buchfink \nDate: Tue Mar 14 12:52:36 2023 +0100\n\n Removed iostream includes.\n\ncommit 24c930eed464fe08be2ab61f93042ce1a0fc804c\nAuthor: Benjamin Buchfink \nDate: Tue Mar 14 11:29:03 2023 +0100\n\n Added new dispatch code.\n\ncommit b18d9e16043fc57122c095c91b29c0dcbf5f4b69\nAuthor: Benjamin Buchfink \nDate: Tue Mar 14 10:57:10 2023 +0100\n\n Added new dispatch code.\n\ncommit f1b05d05d0948f99f30c3e854b522546940d115e\nAuthor: Benjamin Buchfink \nDate: Mon Mar 13 17:22:15 2023 +0100\n\n Added new dispatch code.\n\ncommit 8c66829f0df52eabaffe58215c730dae2af8b521\nAuthor: Benjamin Buchfink \nDate: Mon Mar 13 12:25:46 2023 +0100\n\n Added new dispatch code.\n\ncommit edb9ede545536c05ec47c16734a67a7c68b38033\nMerge: 6b1658e2 c71b49c6\nAuthor: Benjamin Buchfink \nDate: Mon Mar 13 09:55:35 2023 +0100\n\n Merge branch 'dev' of https://github.com/bbuchfink/diamond_dev into dev\n\ncommit c71b49c6d16f6134b7068aa896be7961de02bce3\nAuthor: Benjamin Buchfink \nDate: Fri Mar 10 15:23:18 2023 +0100\n\n Handle non-x86 case.","shortMessageHtmlLink":"Squashed commit of the following:"}},{"before":"124725341168ab34d67d7f1e3580349370164a5c","after":"21a32fc57d66f6679a2ab3a0d302700de899753d","ref":"refs/heads/master","pushedAt":"2023-03-10T08:34:43.847Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Fix msvc issues.","shortMessageHtmlLink":"Fix msvc issues."}},{"before":"40e440f05742ced1c39debc983298abda7c302a8","after":"124725341168ab34d67d7f1e3580349370164a5c","ref":"refs/heads/master","pushedAt":"2023-03-09T19:15:34.717Z","pushType":"push","commitsCount":1,"pusher":{"login":"bbuchfink","name":"Benjamin Buchfink","path":"/bbuchfink","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10001338?s=80&v=4"},"commit":{"message":"Squashed commit of the following:\n\ncommit 6b1658e2764e4c1e31afe9d35a7a805fb6596a6b\nMerge: 2f1bafe4 40e440f0\nAuthor: Benjamin Buchfink \nDate: Thu Mar 9 20:08:58 2023 +0100\n\n Merge branch 'master' into dev\n\ncommit 2f1bafe4b5cda4195fe344c3ef5d37ce825d6509\nAuthor: Benjamin Buchfink \nDate: Thu Mar 9 20:05:33 2023 +0100\n\n Updated version.\n\ncommit f6cdba737cd926945ed0623cb855fca599aa01f1\nAuthor: Benjamin Buchfink \nDate: Thu Mar 9 17:17:50 2023 +0100\n\n Mem use for extend stage.\n\ncommit b0d8841d46dcca30fd712c2ab27b7af67decfad9\nAuthor: Benjamin Buchfink \nDate: Thu Mar 9 15:16:06 2023 +0100\n\n Changed estimate for minimizers.\n\ncommit 1ee97297be8a63fd9e51ae08e071ffe00e15117e\nAuthor: Benjamin Buchfink \nDate: Wed Mar 8 18:41:41 2023 +0100\n\n Added memory for extend stage.\n\ncommit 33de8f8c61c058c92ead3c2de5b8646c6accd0da\nAuthor: Benjamin Buchfink \nDate: Wed Mar 8 17:06:01 2023 +0100\n\n Remove capping of chunk size.\n\ncommit 0fa174446118484f7f49c3e3fc25782449f3221d\nAuthor: Benjamin Buchfink \nDate: Tue Mar 7 17:06:08 2023 +0100\n\n Fixed translation bug.\n\ncommit 76fa63ee6dc542c7a0fdbaadc21b67e7e59e551a\nAuthor: Benjamin Buchfink \nDate: Tue Mar 7 15:34:12 2023 +0100\n\n Added heartbeat option.\n\ncommit e556f044cb82e44bb23b621169926b2163e35077\nAuthor: Benjamin Buchfink \nDate: Tue Mar 7 13:27:34 2023 +0100\n\n Disabled rounding.\n\ncommit e1993c244388b964f17bf07a387bde8bd15f11b9\nAuthor: Benjamin Buchfink \nDate: Tue Mar 7 11:48:27 2023 +0100\n\n Use variable super block sizes.\n\ncommit 724f0489077165feb11bd32c6248e9c3b4cb01af\nAuthor: Benjamin Buchfink \nDate: Mon Mar 6 14:01:12 2023 +0100\n\n Fixed issues in gvc.\n\ncommit e397ebd7fbf98e575c001467519999ebe0a0e6cf\nAuthor: Benjamin Buchfink \nDate: Mon Mar 6 12:24:53 2023 +0100\n\n Removed register declarations.","shortMessageHtmlLink":"Squashed commit of the following:"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAD-pIWSwA","startCursor":null,"endCursor":null}},"title":"Activity ยท bbuchfink/diamond"}