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lines changed- .github/workflows/ci.yml+102
- .github/workflows/release.yml+133
- Cargo.lock+596-1.0k
- Cargo.toml+21-37
- README.md+50-35
- conda/LICENSE-21
- conda/build.sh-6
- conda/meta.yaml-32
- crates/api/Cargo.toml+6-5
- crates/api/example/Cargo.toml+1-1
- crates/api/example/src/main.rs+94-61
- crates/api/src/lib.rs+97-23
- crates/assembler/Cargo.toml+15-13
- crates/assembler/src/lib.rs+86-66
- crates/assembler/src/pipeline/build_unitigs.rs-27
- crates/assembler/src/pipeline/compute_matchtigs.rs+1-3
- crates/assembler/src/pipeline/hashes_sorting.rs+2-2
- crates/assembler/src/pipeline/maximal_unitig_links.rs+4-4
- crates/assembler/src/pipeline/maximal_unitig_links/mappings_loader.rs+1-1
- crates/assembler/src/pipeline/maximal_unitig_links/maximal_unitig_index.rs+22-2
- crates/assembler_kmers_merge/Cargo.toml+10-9
- crates/assembler_kmers_merge/src/final_executor.rs+1-1
- crates/assembler_kmers_merge/src/lib.rs+2-4
- crates/assembler_minimizer_bucketing/Cargo.toml+2-2
- crates/assembler_minimizer_bucketing/src/lib.rs+1-1
- crates/capi/Cargo.toml+2-2
- crates/capi/ggcat-cpp-api/example/main.cc+40
- crates/capi/ggcat-cpp-api/include/ggcat-cpp-bindings.hh+6-1
- crates/capi/ggcat-cpp-api/include/ggcat.hh+61-2
- crates/capi/ggcat-cpp-api/src/ggcat-cpp-bindings.hh+10-1
- crates/capi/ggcat-cpp-api/src/ggcat.cc+26-1
- crates/capi/src/lib.rs+82-6
- crates/cmdline/Cargo.toml+28-24
- crates/cmdline/src/main.rs+67-59
- crates/colors/Cargo.toml+18-16
- crates/colors/src/colors_manager.rs+2-2
- crates/colors/src/colors_memmap_writer.rs+4-4
- crates/colors/src/managers/multiple.rs+36-14
- crates/colors/src/managers/single.rs+11-4
- crates/colors/src/non_colored.rs+12-5
- crates/colors/src/storage/deserializer.rs+44-14
- crates/colors/src/storage/roaring.rs+2-2
- crates/colors/src/storage/run_length.rs+2-2
- crates/colors/src/storage/serializer.rs+27-8
- crates/config/Cargo.toml+2-1
- crates/dumper/Cargo.toml+12-10
- crates/dumper/src/lib.rs+26-9
- crates/dumper/src/pipeline.rs+1
- crates/dumper/src/pipeline/dumper_colormap_querying.rs+61
- crates/dumper/src/pipeline/dumper_colormap_reading.rs+8-3
- crates/dumper/src/pipeline/dumper_minimizer_bucketing.rs+1-1
- crates/hashes/Cargo.toml+3-3
- crates/hashes/src/lib.rs+4-4
- crates/io/Cargo.toml+12-9
- crates/io/src/concurrent/structured_sequences.rs+40-3
- crates/io/src/concurrent/structured_sequences/fasta.rs+23-11
- crates/io/src/concurrent/structured_sequences/gfa.rs+153
- crates/io/src/concurrent/structured_sequences/stream_finish.rs+65
- crates/io/src/lib.rs+6-4
- crates/io/src/lines_reader.rs+4-4
- crates/io/src/sequences_stream/fasta.rs+5-3
- crates/io/src/sequences_stream/general.rs+2-2
- crates/kmers_transform/Cargo.toml+12-11
- crates/kmers_transform/src/debug_bucket_stats.rs+3-3
- crates/kmers_transform/src/lib.rs+1-1
- crates/kmers_transform/src/processor.rs+1-1
- crates/kmers_transform/src/reader.rs+4-4
- crates/logging/Cargo.toml+7
- crates/logging/src/lib.rs+79
- crates/minimizer_bucketing/Cargo.toml+6-5
- crates/minimizer_bucketing/src/counters_analyzer.rs+5-5
- crates/minimizer_bucketing/src/lib.rs+2-2
- crates/querier/Cargo.toml+12-10
- crates/querier/src/lib.rs+6-6
- crates/querier/src/pipeline/colored_query_output.rs+6-3
- crates/querier/src/pipeline/colormap_reading.rs+9-5
- crates/querier/src/pipeline/querier_minimizer_bucketing.rs+1-1
- crates/structs/Cargo.toml+4-4
- crates/utils/Cargo.toml+2-2
- libs-crates/instrumenter-rs+1-1
- libs-crates/mt-debug-counters-rs+1-1
- libs-crates/nightly-quirks-rs+1-1
- libs-crates/papi-bindings-rs+1-1
- libs-crates/parallel-processor-rs+1-1
- libs-crates/streaming-libdeflate-rs+1-1
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