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CHANGELOG.md

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0.1.23 minimap2 2.28

  • Functions to set flag opts for MapOpt and IdxOpt @dwpeng
  • Fixed memory leak when not dropping mm_idx_t properly. This is done by adding in syntactic sugar in minimap2-sys @jguhlin

0.1.22 minimap2 2.28

  • Fixed a memory segfault when re-using a thread local buffer. Not sure why it occurs, but this fix seems to solve it.

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 (@rob-p @mbhall88 @jguhlin)
  • Arc the Index, to prevent double-frees, solves #71
  • Map file now passes in query name, which should help with #75
  • Supplementary flag now better detected (@rob-p)
  • FIX: Cigar string missing softclip operation (@Sam-Sims)

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

Other Changes

  • Add ergonomic functions n_seq and get_seq.
  • Better docs on applying presets, solves #84
  • Better detection of target arch c_char's and ptr's, solves #82
  • Support for M1 Mac compilation and addition of github workflows to test it, solving #81
  • Rayon test, so some support, closes #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
  • Added flag and option documents
  • Added with_gap_open penalty ergonomic function

0.1.20 minimap2 2.28

  • Fix htslib errors. No update to -sys crate needed.

0.1.19 minimap2 2.28

  • Fix memory leak by @charlesgregory

0.1.18 minimap2 2.28

  • Update to minimap2 v2.28 @jguhlin
  • Support for lrhqae preset @jguhlin

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

0.1.16 minimap2 2.26

  • Much better cross compilation support thanks to @Adoni5

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.

0.1.14 minimap2 2.26

  • Memory leak fixed by @Adoni5
  • Updated deps

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.

0.1.11

  • HTS lib: add support for optional quality scores by @eharr

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

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