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Squashed 'lib/mmseqs/' changes from bad16c765..6a0dcee42
6a0dcee42 Update Regression test f92447d04 Rename slice to exhaustive search, add filterresult 6c2fefceb Set pca to 0.0 in expand2profile 0cc7e6748 Add unpackdb to split a database into separate files #406 877344c38 Add USE_SYSTEM_ZSTD cmake flag to use system provided zstd #411 bbd564172 Replace throw with abort in ALP again 46c26ce99 Add missing licenses and readmes for code in lib #403 20543e0aa Update ALP to 1.98 and add readme/license d5717e821 Add CDD to databases downloader #410 04b27f987 msa2profile always copies lookup/source files instead of linking them to be independent from the MSA db 2d83f5171 msa2profile/result can skip the first sequence 242a8fafe Pass threads to tar2db in databases workflow a19f5a526 Allow clustering of clustering input with set-cover or connected-component by ignoring scores/weight 39a414033 Don't set INT_MAX as --max-seqs in slice search to avoid huge allocations in prefilter 9290a2b52 Allow sequence database input in taxonomyreport #408 aaba0c7f2 Short circuit cluster-reassign if nothing can be reassigned 3822a8f56 Fix tmp files not getting removed in linclust/cluster with --remove-tmp--files 2a35e025a Fix kmermatcher setting user k-mer pattern in auto k-mer selection and breaking a1050359f Rename accelerated 2bLCA to approximate 2bLCA to be consistent with manuscript 11698a5b4 Rename LICENCE to LICENSE soedinglab/MMseqs2#402 0828d8653 Allow result database input in taxonomyreport #401 b31ebb64a Krona taxonomy report was not working if no sequence was unclassified 9f0fb3ed6 Cleanup taxonomyreport a2d9568d9 Fix wrong azure dependency b1367fc26 Make resultToBuffer buffer sizes consistent (needs further refactoring) 98f9939d0 Get rid of results temporary array in msa2result d495e0e9f Replace texlive with tectonic for userguide building e03b52576 Fix MMseqs2 Taxonomy citation 602689c11 Update examples in mmseqs (easy-)taxonomy invocation ecf152cf7 Improve (easy-)taxonomy description text by reordering parameters by importance e0b044341 Improve description of --orf-filter a7f91d46f Add warning if cluster or prefilter input is used in majoritylca with invalid --vote-mode a3399397d Update regression to include recent speedup d5da12d7a Add GTDB to databases downloader 83780f4ce Respect verbosity for rmdb calls in databases 9011c15d6 Improve output of databases list 86c03fd42 Increase buffer sizes in tar2db 2bd03c689 Fix tar directory (symlink, etc) entries causing tar2db to stop early 7bdb222da Use DBWriter to write .lookup multi-threaded in tar2db 23c9e1e75 Don't use multiple threads in tar2db when reading .tar.gz/.tgz as nearly all the time is spent inside zlib 2e128d4f8 Increase zlib buffer in tar2db to speedup reading c19118935 Fix multiple locations where Util::checkAllocation would never be called as the preceding allocation would already terminate on failure 1f302134a Fix two compilation failures revealed by Debian 5b03cdff7 Another instance of the same warning 3fda449b6 Fix compile warning 3b0197afa Encode species names in taxonomy blocklist to make sure we don't block random nodes in non-NCBI taxonomies (e.g. GTDB) ab2426f89 Fix String MultiParameter (e.g. sub matrices) breaking if filenames contain whitespaces e8de35071 Encode whitespace containing parameters as base64 to better deal with shell word splitting in workflows c7a7c366f Add instructions to simd.h 6672bbc9d Fix missing newline in log message 84034a527 Remove useless taxonomy ancestor warning 6609c6cd5 Fix invalid taxonomy output mode being set 441c52cf5 Fix taxpercontig not working with easy-taxonomy 4ce381092 lca is not computed by easy-taxonomy anymore 9d631c16a Fix cleanup of taxonomy intermediate files d0f596f56 taxonomyreport and addtaxonomy output is now adjustable in easy-taxonomy 6bfd08d54 Cleanup default set parameters in easy-taxonomy afcade163 Improve default taxonomy parameter lists shown (without -h) fc126b3e1 Improve error messages when something is wrong with the input/output paths 3b49310f5 Improve unrecognized parameter message 83b9e9a18 Remove useless missing tmp dir warning d0a9b79f1 Fix typo 48f9737a8 Add ORF filter parameters only to taxonomy for now a60689753 Disable unfinished ORF filter in search 336d9d04b Add taxonomy citation f7fde6fef Reduce binary taxonomy dump memory requirements slightly eff61cfef Add \0 byte after serialization 7e63e1ea7 Fix typo in Parameters.h 019de271a Add vector of predefined substitution matrices 34b3a5396 Merge pull request #389 from mr-c/simde_v0.7.0 74724b3ae Cleanup headers in kmermatcher 73fd5cfa6 Update xxhash to v0.8.0 8dd192c00 Don't create false _has_{builtin,attribute} 062ef9953 Merge commit 'c2d60348af5c036eb2cbc7974d84065e16ab4096' into simde_v0.7.0 c2d60348a Squashed 'lib/simde/simde/' changes from f2257f11..b6c9c964 git-subtree-dir: lib/mmseqs git-subtree-split: 6a0dcee42f77d10756cd03dee095b7aaafb5a444
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