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| ### 0.1.23 minimap2 2.28 | ||
| + Fixed memory leak when not dropping mm_idx_t properly. This is done by adding in syntactic sugar in minimap2-sys @jguhlin | ||
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| ### 0.1.22 minimap2 2.28 | ||
| #### Changes | ||
| + Fixed a memory segfault when re-using a thread local buffer. Not sure why it occurs, but this fix seems to solve it. | ||
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| ### 0.1.21 minimap2 2.28 | ||
| Contributors to this release: @mbhall88 @rob-p @Sam-Sims @charlesgregory @PB-DB | ||
| #### Breaking Changes | ||
| + Map now returns Arc String's to reduce memory allocation for large and/or repetitive jobs | ||
| + map now takes an additional argument, query_name: Option<&[u8]>, possibly solves [#75](https://github.com/jguhlin/minimap2-rs/issues/75) (@rob-p @mbhall88 @jguhlin) | ||
| + Arc the Index, to prevent double-frees, solves [#71](https://github.com/jguhlin/minimap2-rs/issues/71) | ||
| + Map file now passes in query name, which should help with [#75](https://github.com/jguhlin/minimap2-rs/issues/75) | ||
| + Supplementary flag now better detected (@rob-p) | ||
| + FIX: Cigar string missing softclip operation (@Sam-Sims) | ||
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| #### Migration Guide | ||
| + Make all setting changes before calling a with_index, with_seq's function | ||
| + Change all map calls to include a query name, or None if not needed | ||
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| ### Other Changes | ||
| + Add ergonomic functions n_seq and get_seq. | ||
| + Better docs on applying presets, solves [#84](https://github.com/jguhlin/minimap2-rs/issues/84) | ||
| + Better detection of target arch c_char's and ptr's, solves [#82](https://github.com/jguhlin/minimap2-rs/issues/82) | ||
| + Support for M1 Mac compilation and addition of github workflows to test it, solving [#81](https://github.com/jguhlin/minimap2-rs/issues/81) | ||
| + Rayon test, so some support, closes [#5](https://github.com/jguhlin/minimap2-rs/issues/5) | ||
| + Static str's and now static CStr's | ||
| + FIX: memory leak due to sequences allocated by minimap2 not being freed @charlesgregory | ||
| + Add Send + Sync to Aligner, along with unit test @PB-DB | ||
| + Experimental Android support (tested on aarch64 and x86_64), solves [#66](https://github.com/jguhlin/minimap2-rs/issues/66) | ||
| + Added flag and option documents | ||
| + Added with_gap_open penalty ergonomic function | ||
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| ### 0.1.20 minimap2 2.28 | ||
| + Fix htslib errors. No update to -sys crate needed. | ||
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| ### 0.1.19 minimap2 2.28 | ||
| + Fix memory leak by @charlesgregory | ||
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| ### 0.1.18 minimap2 2.28 | ||
| + Update to minimap2 v2.28 @jguhlin | ||
| + Support for lrhqae preset @jguhlin | ||
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| ### 0.1.17 minimap2 2.27 | ||
| * Mark bam::Record objects as supplementary. #52 @PB-DB | ||
| * Only use rust-htslib/curl when curl feature is enabled. #53 @PB-DB | ||
| * Update to minimap2 v2.27 @jguhlin | ||
| * Switch to needletail for reading fast files (features map-file) @jguhlin | ||
| * Convert functions to take slices of vectors instead of refs to vecs `&[Vec<u8>]` instead of `&Vec<Vec<u8>>` @jguhlin | ||
| * _breaking_ Curl is no longer a default option for htslib, please re-enable it as needed with cargo.toml features | ||
| * _breaking_ Now using needletail for map-files, enabled by default. However, compression algorithms are disabled. Please enable with cargo.toml features | ||
| * Experimental rayon support | ||
| * aligner.with_cigar_clipping() to add soft clipping to the CIGAR vec (with_cigar() still adds to only the string, following the minimap2 outputs for PAF) | ||
| * _breaking_ .with_threads(_) is now .with_index_threads(_) to make it more clear | ||
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| ### 0.1.16 minimap2 2.26 | ||
| * Much better cross compilation support thanks to @Adoni5 | ||
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| ### 0.1.15 minimap2 2.26 | ||
| * Compilation on aarch64 thanks to @leiste375 | ||
| * README corrections thanks to @wdecoster | ||
| * Better support for static builds / linking | ||
| * Update fffx to a version that uses bytelines without tokio. Drastically reduces compile times and dependency tree. | ||
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| ### 0.1.14 minimap2 2.26 | ||
| * Memory leak fixed by @Adoni5 | ||
| * Updated deps | ||
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| ### 0.1.13 minimap2 2.26 | ||
| * Add with_seq to support indexing a single sequence (as per mappy: https://github.com/lh3/minimap2/blob/master/python/mappy.pyx#L115) | ||
| * minimap2-rs: update rust-htslib deps | ||
| * simdutf8 now optional dependency requiring map-file feature to be enabled | ||
| * Support soft-clipping string in CIGAR. WARNING: Does not support hard clipping. Please open an issue if you need this. | ||
| * Update minimap to 2.26 | ||
| * Not convinced SSE41/SSE2 are working properly. Recommend simde. | ||
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| ### 0.1.11 | ||
| * HTS lib: add support for optional quality scores by @eharr | ||
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| ### 0.1.10 | ||
| * HTS lib support by @eharr | ||
| * HTS lib: Output sam/bam files by @eharr | ||
| * More tests by @eharr | ||
| * Display impl for Strand thanks to @ahcm | ||
| * Update minimap2-sys to latest version by @jguhlin | ||
| * -sys crate mm2fast added as additional backend by @jguhlin | ||
| * zlib dep changes by @jguhlin (hopefully now it is more portable and robust) | ||
| * -sys crate now supports SIMDe | ||
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| ## 0.1.9 | ||
| * Thanks for @Adoni5 for switching to builder pattern, and @eharr for adding additional fields to alignment. | ||
| * Do not require libclang for normal compilation. | ||
| ## 0.1.8 | ||
| * Multithreading support (use less raw pointers, and treat more like rust Struct's) | ||
| ## 0.1.7 | ||
| * use libc instead of std:ffi::c_int as well | ||
| ## 0.1.6 | ||
| * Support slightly older versions of rustc by using libc:: rather than std::ffi for c_char (Thanks dwpeng!) | ||
| * Use fffx module for fasta/q parsing |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| [package] | ||
| name = "minimap2" | ||
| version = "0.1.22+minimap2.2.28" | ||
| version = "0.1.23+minimap2.2.28" | ||
| edition = "2021" | ||
| authors = ["Joseph Guhlin <[email protected]>"] | ||
| license = "MIT OR Apache-2.0" | ||
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@@ -31,14 +31,14 @@ libc = "0.2" | |
| needletail = { version = "0.6", optional = true, default-features = false} | ||
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| # Dep for development | ||
| minimap2-sys = { path = "./minimap2-sys" } #, version = "0.1.20+minimap2.2.28" } | ||
| minimap2-sys = { path = "./minimap2-sys" , version = "0.1.20+minimap2.2.28" } | ||
| # minimap2-sys = "0.1.19" | ||
| rust-htslib = { version = "0.48", default-features = false, optional = true } | ||
| rust-htslib = { version = "0.49", default-features = false, optional = true } | ||
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| [dev-dependencies] | ||
| rayon = "1.10" | ||
| crossbeam = "0.8.4" | ||
| clap = { version = "4.5.21", features = ["derive"] } | ||
| clap = { version = "4.5.23", features = ["derive"] } | ||
| needletail = { version = "0.6", default-features = false} | ||
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| # The end-user should decide this... | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| [package] | ||
| name = "minimap2-sys" | ||
| version = "0.1.20+minimap2.2.28" | ||
| version = "0.1.21+minimap2.2.28" | ||
| edition = "2021" | ||
| links = "libminimap2" | ||
| authors = ["Joseph Guhlin <[email protected]>"] | ||
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