initial GPU support for monomer search #391
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9c102e13 MathUtil squaredist (#910) c2c3ad9c result2profile can print frequencies in tsv format (#907) 747c64cc Remove translatenucs from more parameter lists a0dad1eb Disable GPU SW for unsupported parameters d595aa41 Remove brew dependency causing issues 6e18b99e Next try to fix mac arm CI issue 71ccd5ad Force install brew in mac arm CI b0519d6e Merge branch 'master' of https://github.com/soedinglab/mmseqs2 1e5d1803 Add background and lambda to all PAM and blosum 753e1c6c Remove useless assignment 0310e6b5 Merge branch 'skip_orf' 266c894c Update regression for prev commit bug fix dc7f8adb Reapply "Make sure last position is properly evaluated in Prefilter" 0889c78b Error out in various search modes without GPU support c3aa34aa Add GPU support to easy-rbh 41c7eeaa Check that GPU binary doesn't use too new glibc 75a0d7c2 Remove GPU param for workflows that don't support GPU 93d74798 Try to solve issue with GLIBC_PRIVATE symbols 562a47f3 Update docker metadata-action to support onlatest 37729f0d Typo 0468de18 Next try to get docker images 89ec0906 Don't compile with WERROR on GCC 4.9 82840b84 Fix docker workflow 8616910b Build docker gpu image 3740224d Add GPU paper citation 23503f3b Forgot to actually upload the gpu binaries da84100c Add build-* to gitignore b315b1f5 Add link to precompiled GPU binary 34fef192 Fix macos build dc739581 Typo 73a81278 Try building precompiled binaries for GPU b63668c3 Fix warnings bd53fe32 Try to work around GCC 4.9 issue 3ebb8568 Fix unused warning e98df764 Merge commit 'be62ab5252176867a3b47f18883ba2719ab01fa2' be62ab52 Squashed 'lib/libmarv/' changes from 444c7dfe..ca62422d e6ff82c7 Fix warnings c16181c8 Squashed 'lib/libmarv/' changes from 6f933d6b..444c7dfe 776ac3ba Merge commit 'c16181c8723b9d79ed4cab8523c609c7d826490b' into relicense 2b55efb6 Remove chat badge a66ad0c2 Allow easy-search to work with --gpu 1 81171a53 Error if GPU modules are used with non-gpu dbs 6750af34 Update README fc068137 Squashed 'lib/libmarv/' content from commit 6f933d6b 1cdfdd77 Merge commit 'fc068137ba5c464116bde4588f589b675cb4fb85' as 'lib/libmarv' 7a347087 Fix tantan in makepaddedseqdb cf585a2f MMseqs2-GPU fc28a05e Complete relicensing to MIT with permission from all relevant contributors 1fecf667 Refactor RMQ 28910844 Update license header 93b2d94c Disable custom substitution matrices for now 111d893a Remove gzstream 22a232de Further rework dependencies 3ba8036a Rework apply 6cf95a2a Revert "Make sure last position is properly evaluated in Prefilter" 799f0daf Fix tantan flags fa12ab2b Fix tantan test b2fe0a2a Merge branch 'master' of https://github.com/soedinglab/mmseqs2 06f74297 Make sure last position is properly evaluated in Prefilter 0f567986 Remove parallel stl sort and revert to std++11 54f8983e Add priority sort to filterdb 7c8c4a66 Remove omptl, switch to c++17 and use parallel stl 3e53eee8 Update tantan a804518b make full frame mode available through --translation-mode 964bfaa2 change extracframes to have same output with extractframes+tranlatenucs 94eae3ae add PARAM_TRANSLATE into extractframes 88b36705 add translation in extract frames 2c1f500c make sure translated_search with skip_orf option (extractorfs->extractframes & translatenucs) works b1e51399 fix error with DB key 87e7103d Switch to github hosted mac arm runner for testing 9dce49a7 change extractframes function to consider multiple frames in forward/reverse a035b87e add ORF_SKIP option in translated_search 3263e9da Merge branch 'soedinglab:master' into master 88d102d9 Merge pull request #878 from Woosub-Kim/tmp b59ad53c fix createclusearchdb ordering issue 8ef39f41 Merge pull request #872 from leejoey0921/fix/prefilter_segfault a64d60a4 fix: safe check ef2ebe9c fix: seq len underflow 4c6f74f2 delete unused variable 02840924 recover longest orf after fragment elimination git-subtree-dir: lib/mmseqs git-subtree-split: 9c102e1390e908b70c08d462a0fb2870de4a0d58
59016d25 Merge commit '6d20adb7043719912b7ac51e8b3e90722c6140c0' 6d20adb7 Squashed 'lib/libmarv/' changes from ca62422d..d0a20cbc git-subtree-dir: lib/mmseqs git-subtree-split: 59016d25aaa5ce476852c2a33ad4f9070e4c3d94
ddc19be54 Remove libgcc_s as a dependency when trying to compile static binaries git-subtree-dir: lib/mmseqs git-subtree-split: ddc19be546230aceb027bb0f9ef16a81a5b36fe6
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Default initialize all members of complexfiltercriteria
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7f5c0003 Fix memory issue b80ce103 Fix issues in masksequence a2d01d01 Rework masking and add N repeat masking e3b16faf Fix issue soedinglab/MMseqs2#916 git-subtree-dir: lib/mmseqs git-subtree-split: 7f5c0003a9135add5a2b6f14ab822e527b3df547
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