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commit 1c07e03013ddf80c01b78419c98fde60122a65da Author: Benjamin Buchfink <[email protected]> Date: Thu Feb 16 16:41:35 2023 +0100 Updated version. commit d655b42d095fd5fc187b7734a17b360b897e63dd Author: Benjamin Buchfink <[email protected]> Date: Thu Feb 16 12:22:35 2023 +0100 Use linsearch for backmapping. commit 330becf3ffca6bbef91c33490dbb2c55adb5379c Author: Benjamin Buchfink <[email protected]> Date: Thu Feb 16 10:17:38 2023 +0100 Added linsearch option. commit c7d7cffa920950a6927a91ff1903cb795076f104 Author: Benjamin Buchfink <[email protected]> Date: Wed Feb 15 20:51:35 2023 +0100 Allow lin suffix. commit b7e01fc21aa2adee3a6f8d08a59c828e2d0c74c1 Author: Benjamin Buchfink <[email protected]> Date: Wed Feb 15 10:19:52 2023 +0100 Use linear clustering only for linclust. commit 2e82ce30f52bc4d76a02290c3641e9f1761f15a8 Author: Benjamin Buchfink <[email protected]> Date: Tue Feb 14 16:49:58 2023 +0100 Added check. commit 46966470bf2e2bd6ba4e5fce9a6f73fb4ee53007 Author: Benjamin Buchfink <[email protected]> Date: Tue Feb 14 16:02:42 2023 +0100 Added linear search to --iterate. commit 746d8a4addc0c9b5357c120f1768368380181140 Author: Benjamin Buchfink <[email protected]> Date: Tue Feb 14 12:39:31 2023 +0100 Fixed timer. commit 30233debd687e414d51e5f1bc904648b5540f06f Author: Benjamin Buchfink <[email protected]> Date: Tue Feb 14 11:15:01 2023 +0100 Added linear stage for targets. commit 1c9bf349fb07ba92b46a1f7ab719d54fb81e8b11 Author: Benjamin Buchfink <[email protected]> Date: Mon Feb 13 16:51:30 2023 +0100 No extra for lin-stage1 option. commit 190cef799c9877603f3f86b62515090323c3b909 Author: Benjamin Buchfink <[email protected]> Date: Mon Feb 13 16:34:00 2023 +0100 Added linclust command. commit fa888a19422daea83e8124ea3092aa7c3d0b180e Author: Benjamin Buchfink <[email protected]> Date: Mon Feb 13 14:59:01 2023 +0100 Fixed linclust bug. commit 20a9bd2efe2a78f4c24cbd9317b4537c7d292dc5 Author: Benjamin Buchfink <[email protected]> Date: Mon Feb 13 13:33:01 2023 +0100 Add tests to cmake. commit a95bfc459b79ddd42911f0df7ac6441d1d7961e5 Author: Benjamin Buchfink <[email protected]> Date: Mon Feb 13 13:11:17 2023 +0100 Added ctest file. commit c73bc9d8c1f6648e350c5e81b7b43048c3715f63 Merge: d8475271 1de45b3 Author: Benjamin Buchfink <[email protected]> Date: Mon Feb 13 13:10:04 2023 +0100 Merge branch 'master' into dev commit d847527139fcbb9a63ebb35a8a80586d4ef7f937 Merge: 06361689 579b497 Author: Benjamin Buchfink <[email protected]> Date: Mon Feb 13 10:36:45 2023 +0100 merged w/master commit 06361689da3aab9cbb094559e990c1e508e5e8dc Author: Benjamin Buchfink <[email protected]> Date: Mon Feb 13 10:30:58 2023 +0100 Fixed macos errors. commit 65911a2cc276db2f50dbbdc55ea1a37dcf1ff325 Author: Benjamin Buchfink <[email protected]> Date: Fri Feb 10 17:26:36 2023 +0100 Use temp files for db blocks. commit 5350c59abf3d2e5be661edc56f0fa33d5ab0d1dd Author: Benjamin Buchfink <[email protected]> Date: Fri Feb 10 15:16:10 2023 +0100 Fixed -k for view. commit f6cc746b206be49939eef8c339448d0c8b220c2b Author: Benjamin Buchfink <[email protected]> Date: Fri Feb 10 15:13:23 2023 +0100 Added merge-daa command. commit fb573774f12267218e80d2691bbbc8843b93dfa1 Author: Benjamin Buchfink <[email protected]> Date: Fri Feb 10 15:03:34 2023 +0100 Fixed config, commit 0da23199907de5f01abeb453a17e34d4d7903d31 Author: Benjamin Buchfink <[email protected]> Date: Fri Feb 10 14:42:03 2023 +0100 Added merge-daa command. commit de5db9380d527cfaeb63cc729389070fedf94e1d Author: Benjamin Buchfink <[email protected]> Date: Fri Feb 10 14:22:56 2023 +0100 Fixed error in view. commit 3e265c1b226020aa3c18e326de726730246b55e3 Author: Benjamin Buchfink <[email protected]> Date: Fri Feb 10 13:59:45 2023 +0100 Added option to turn off avx2.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,9 @@ | ||
| /**** | ||
| DIAMOND protein aligner | ||
| Copyright (C) 2013-2018 Benjamin Buchfink <[email protected]> | ||
| Copyright (C) 2016-2023 Max Planck Society for the Advancement of Science e.V. | ||
| Benjamin Buchfink | ||
| Code developed by Benjamin Buchfink <[email protected]> | ||
| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
|
|
@@ -66,6 +69,7 @@ vector<SuperBlockId> cluster(shared_ptr<SequenceFile>& db, const shared_ptr<BitV | |
| config.self = true; | ||
| config.iterate.unset(); | ||
| config.mapany = false; | ||
| config.linsearch = false; | ||
| tie(config.chunk_size, config.lowmem_) = block_size(Util::String::interpret_number(config.memory_limit.get(DEFAULT_MEMORY_LIMIT)), config.sensitivity, config.lin_stage1); | ||
|
|
||
| shared_ptr<Callback> callback(new Callback); | ||
|
|
@@ -99,10 +103,10 @@ static pair<vector<SuperBlockId>, BitVector> update_clustering(const BitVector& | |
| return { current_centroids, oid_filter }; | ||
| } | ||
|
|
||
| vector<SuperBlockId> cascaded(shared_ptr<SequenceFile>& db) { | ||
| vector<SuperBlockId> cascaded(shared_ptr<SequenceFile>& db, bool linear) { | ||
| if (db->sequence_count() > (int64_t)numeric_limits<SuperBlockId>::max()) | ||
| throw runtime_error("Workflow supports a maximum of " + to_string(numeric_limits<SuperBlockId>::max()) + " input sequences."); | ||
| const auto steps = cluster_steps(config.approx_min_id); | ||
| const auto steps = cluster_steps(config.approx_min_id, linear); | ||
| shared_ptr<BitVector> oid_filter(new BitVector); | ||
| int64_t cluster_count = db->sequence_count(); | ||
| vector<SuperBlockId> centroids(cluster_count); | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,9 @@ | ||
| /**** | ||
| DIAMOND protein aligner | ||
| Copyright (C) 2013-2018 Benjamin Buchfink <[email protected]> | ||
| Copyright (C) 2016-2023 Max Planck Society for the Advancement of Science e.V. | ||
| Benjamin Buchfink | ||
| Code developed by Benjamin Buchfink <[email protected]> | ||
| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
|
|
@@ -30,8 +33,8 @@ struct Cascaded : public ClusteringAlgorithm { | |
| } | ||
| }; | ||
|
|
||
| std::vector<SuperBlockId> cascaded(std::shared_ptr<SequenceFile>& db); | ||
| std::vector<std::string> cluster_steps(double approx_id); | ||
| std::vector<SuperBlockId> cascaded(std::shared_ptr<SequenceFile>& db, bool linear); | ||
| std::vector<std::string> cluster_steps(double approx_id, bool linear); | ||
|
|
||
| struct Callback : public Consumer { | ||
| using Edge = Util::Algo::Edge<SuperBlockId>; | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,37 @@ | ||
| /**** | ||
| DIAMOND protein aligner | ||
| Copyright (C) 2019-2023 Max Planck Society for the Advancement of Science e.V. | ||
| Code developed by Benjamin Buchfink <[email protected]> | ||
| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
| the Free Software Foundation, either version 3 of the License, or | ||
| (at your option) any later version. | ||
| This program is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU General Public License for more details. | ||
| You should have received a copy of the GNU General Public License | ||
| along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| ****/ | ||
|
|
||
| #include "cascaded.h" | ||
|
|
||
| using std::string; | ||
| using std::vector; | ||
|
|
||
| namespace Cluster { | ||
|
|
||
| vector<string> cluster_steps(double approx_id) { | ||
| vector<string> cluster_steps(double approx_id, bool linear) { | ||
| if (!config.cluster_steps.empty()) | ||
| return config.cluster_steps; | ||
| vector<string> v = { "faster_lin", "fast" }; | ||
| vector<string> v = { "faster_lin" }; | ||
| if (linear) | ||
| return v; | ||
| v.push_back("fast"); | ||
| if (approx_id < 90) | ||
| v.push_back("default"); | ||
| if (approx_id < 50) | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,23 @@ | ||
| /**** | ||
| DIAMOND protein aligner | ||
| Copyright (C) 2019-2023 Max Planck Society for the Advancement of Science e.V. | ||
| Code developed by Benjamin Buchfink <[email protected]> | ||
| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
| the Free Software Foundation, either version 3 of the License, or | ||
| (at your option) any later version. | ||
| This program is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU General Public License for more details. | ||
| You should have received a copy of the GNU General Public License | ||
| along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| ****/ | ||
|
|
||
| #include <numeric> | ||
| #include "cascaded.h" | ||
| #include "../data/fasta/fasta_file.h" | ||
|
|
@@ -26,16 +46,18 @@ namespace Cluster { | |
|
|
||
| struct Config { | ||
| Config(shared_ptr<SequenceFile>& db) : | ||
| linclust(config.command == ::Config::LINCLUST), | ||
| message_stream(true), | ||
| verbosity(1), | ||
| sens(from_string<Sensitivity>(rstrip(cluster_steps(config.approx_min_id).back(), "_lin"))), | ||
| sens(from_string<Sensitivity>(rstrip(cluster_steps(config.approx_min_id, linclust).back(), "_lin"))), | ||
| output_format(init_output(-1)), | ||
| centroids(new FastaFile("", true, FastaFile::WriteAccess())), | ||
| seqs_processed(0), | ||
| letters_processed(0), | ||
| oid_to_centroid_oid(new File(Schema{ Type::INT64, Type::INT64 }, "", Flags::TEMP)) | ||
| { | ||
| } | ||
| bool linclust; | ||
| MessageStream message_stream; | ||
| int verbosity; | ||
| Sensitivity sens; | ||
|
|
@@ -78,7 +100,15 @@ static vector<SuperBlockId> search_vs_centroids(shared_ptr<FastaFile>& super_blo | |
| config.query_cover = config.member_cover; | ||
| config.subject_cover = 0; | ||
| config.query_or_target_cover = 0; | ||
| config.iterate = vector<string>(); | ||
| if (cfg.linclust) { | ||
| config.iterate.unset(); | ||
| config.linsearch = true; | ||
| } | ||
| else { | ||
| config.iterate = vector<string>(); | ||
| config.linsearch = false; | ||
| } | ||
| config.lin_stage1 = false; | ||
| tie(config.chunk_size, config.lowmem_) = block_size(Util::String::interpret_number(config.memory_limit.get(DEFAULT_MEMORY_LIMIT)), cfg.sens, false); | ||
| cfg.centroids->set_seqinfo_ptr(0); | ||
| shared_ptr<BestCentroid> best_centroid(new BestCentroid(super_block->sequence_count())); | ||
|
|
@@ -119,7 +149,7 @@ void Cascaded::run() { | |
| unique_ptr<Util::Tsv::File> out(open_out_tsv()); | ||
|
|
||
| if (block_size >= (double)db->letters() && db->sequence_count() < numeric_limits<SuperBlockId>::max()) { | ||
| const auto centroids = cascaded(db); | ||
| const auto centroids = cascaded(db, config.command == ::Config::LINCLUST); | ||
| timer.go("Generating output"); | ||
| output_mem<SuperBlockId>(*out, *db, centroids); | ||
| } | ||
|
|
@@ -159,7 +189,7 @@ void Cascaded::run() { | |
| seqs.reset(); | ||
| timer.finish(); | ||
| } | ||
| const vector<SuperBlockId> clustering = cascaded(unaligned_db); | ||
| const vector<SuperBlockId> clustering = cascaded(unaligned_db, cfg.linclust); | ||
| timer.go("Updating clustering"); | ||
| vector<SuperBlockId> centroids; | ||
| for (SuperBlockId i = 0; i < (SuperBlockId)unaligned.size(); ++i) { | ||
|
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||
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