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‎CHANGELOG.md‎

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### 0.1.23 minimap2 2.28
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+ Fixed memory leak when not dropping mm_idx_t properly. This is done by adding in syntactic sugar in minimap2-sys @jguhlin
3+
4+
### 0.1.22 minimap2 2.28
5+
#### Changes
6+
+ Fixed a memory segfault when re-using a thread local buffer. Not sure why it occurs, but this fix seems to solve it.
7+
8+
### 0.1.21 minimap2 2.28
9+
Contributors to this release: @mbhall88 @rob-p @Sam-Sims @charlesgregory @PB-DB
10+
#### Breaking Changes
11+
+ Map now returns Arc String's to reduce memory allocation for large and/or repetitive jobs
12+
+ 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)
13+
+ Arc the Index, to prevent double-frees, solves [#71](https://github.com/jguhlin/minimap2-rs/issues/71)
14+
+ Map file now passes in query name, which should help with [#75](https://github.com/jguhlin/minimap2-rs/issues/75)
15+
+ Supplementary flag now better detected (@rob-p)
16+
+ FIX: Cigar string missing softclip operation (@Sam-Sims)
17+
18+
#### Migration Guide
19+
+ Make all setting changes before calling a with_index, with_seq's function
20+
+ Change all map calls to include a query name, or None if not needed
21+
22+
### Other Changes
23+
+ Add ergonomic functions n_seq and get_seq.
24+
+ Better docs on applying presets, solves [#84](https://github.com/jguhlin/minimap2-rs/issues/84)
25+
+ Better detection of target arch c_char's and ptr's, solves [#82](https://github.com/jguhlin/minimap2-rs/issues/82)
26+
+ Support for M1 Mac compilation and addition of github workflows to test it, solving [#81](https://github.com/jguhlin/minimap2-rs/issues/81)
27+
+ Rayon test, so some support, closes [#5](https://github.com/jguhlin/minimap2-rs/issues/5)
28+
+ Static str's and now static CStr's
29+
+ FIX: memory leak due to sequences allocated by minimap2 not being freed @charlesgregory
30+
+ Add Send + Sync to Aligner, along with unit test @PB-DB
31+
+ Experimental Android support (tested on aarch64 and x86_64), solves [#66](https://github.com/jguhlin/minimap2-rs/issues/66)
32+
+ Added flag and option documents
33+
+ Added with_gap_open penalty ergonomic function
34+
35+
### 0.1.20 minimap2 2.28
36+
+ Fix htslib errors. No update to -sys crate needed.
37+
38+
### 0.1.19 minimap2 2.28
39+
+ Fix memory leak by @charlesgregory
40+
41+
### 0.1.18 minimap2 2.28
42+
+ Update to minimap2 v2.28 @jguhlin
43+
+ Support for lrhqae preset @jguhlin
44+
45+
### 0.1.17 minimap2 2.27
46+
* Mark bam::Record objects as supplementary. #52 @PB-DB
47+
* Only use rust-htslib/curl when curl feature is enabled. #53 @PB-DB
48+
* Update to minimap2 v2.27 @jguhlin
49+
* Switch to needletail for reading fast files (features map-file) @jguhlin
50+
* Convert functions to take slices of vectors instead of refs to vecs `&[Vec<u8>]` instead of `&Vec<Vec<u8>>` @jguhlin
51+
* _breaking_ Curl is no longer a default option for htslib, please re-enable it as needed with cargo.toml features
52+
* _breaking_ Now using needletail for map-files, enabled by default. However, compression algorithms are disabled. Please enable with cargo.toml features
53+
* Experimental rayon support
54+
* 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)
55+
* _breaking_ .with_threads(_) is now .with_index_threads(_) to make it more clear
56+
57+
### 0.1.16 minimap2 2.26
58+
* Much better cross compilation support thanks to @Adoni5
59+
60+
### 0.1.15 minimap2 2.26
61+
* Compilation on aarch64 thanks to @leiste375
62+
* README corrections thanks to @wdecoster
63+
* Better support for static builds / linking
64+
* Update fffx to a version that uses bytelines without tokio. Drastically reduces compile times and dependency tree.
65+
66+
### 0.1.14 minimap2 2.26
67+
* Memory leak fixed by @Adoni5
68+
* Updated deps
69+
70+
### 0.1.13 minimap2 2.26
71+
* Add with_seq to support indexing a single sequence (as per mappy: https://github.com/lh3/minimap2/blob/master/python/mappy.pyx#L115)
72+
* minimap2-rs: update rust-htslib deps
73+
* simdutf8 now optional dependency requiring map-file feature to be enabled
74+
* Support soft-clipping string in CIGAR. WARNING: Does not support hard clipping. Please open an issue if you need this.
75+
* Update minimap to 2.26
76+
* Not convinced SSE41/SSE2 are working properly. Recommend simde.
77+
78+
### 0.1.11
79+
* HTS lib: add support for optional quality scores by @eharr
80+
81+
### 0.1.10
82+
* HTS lib support by @eharr
83+
* HTS lib: Output sam/bam files by @eharr
84+
* More tests by @eharr
85+
* Display impl for Strand thanks to @ahcm
86+
* Update minimap2-sys to latest version by @jguhlin
87+
* -sys crate mm2fast added as additional backend by @jguhlin
88+
* zlib dep changes by @jguhlin (hopefully now it is more portable and robust)
89+
* -sys crate now supports SIMDe
90+
91+
## 0.1.9
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* Thanks for @Adoni5 for switching to builder pattern, and @eharr for adding additional fields to alignment.
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* Do not require libclang for normal compilation.
94+
## 0.1.8
95+
* Multithreading support (use less raw pointers, and treat more like rust Struct's)
96+
## 0.1.7
97+
* use libc instead of std:ffi::c_int as well
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## 0.1.6
99+
* Support slightly older versions of rustc by using libc:: rather than std::ffi for c_char (Thanks dwpeng!)
100+
* Use fffx module for fasta/q parsing

‎Cargo.toml‎

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@@ -1,6 +1,6 @@
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[package]
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name = "minimap2"
3-
version = "0.1.22+minimap2.2.28"
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version = "0.1.23+minimap2.2.28"
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edition = "2021"
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authors = ["Joseph Guhlin <[email protected]>"]
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license = "MIT OR Apache-2.0"
@@ -31,14 +31,14 @@ libc = "0.2"
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needletail = { version = "0.6", optional = true, default-features = false}
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# Dep for development
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minimap2-sys = { path = "./minimap2-sys", version = "0.1.20+minimap2.2.28" }
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minimap2-sys = { path = "./minimap2-sys" , version = "0.1.20+minimap2.2.28" }
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# minimap2-sys = "0.1.19"
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rust-htslib = { version = "0.48", default-features = false, optional = true }
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rust-htslib = { version = "0.49", default-features = false, optional = true }
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[dev-dependencies]
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rayon = "1.10"
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crossbeam = "0.8.4"
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clap = { version = "4.5.21", features = ["derive"] }
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clap = { version = "4.5.23", features = ["derive"] }
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needletail = { version = "0.6", default-features = false}
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# The end-user should decide this...
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[features]
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default = ["map-file"]
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map-file = ["needletail"] #, "simdutf8"]
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map-file = ["needletail"]
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htslib = ['rust-htslib']
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simde = ["minimap2-sys/simde"]
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zlib-ng = ["minimap2-sys/zlib-ng"]

‎README.md‎

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2020
## Minimap2 Version Table
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| minimap2-rs | minimap2 |
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|-------------|----------|
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| 0.1.23 | 2.28 |
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| 0.1.22 | 2.28 |
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| 0.1.21 | 2.28 |
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| 0.1.20 | 2.28 |
@@ -334,103 +335,7 @@ See [customization](#customization) for how to use these.
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| `MM_I_NO_NAME` | `4` | Do not store sequence names in the index. |
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# Changelog
337-
### 0.1.22 minimap2 2.28
338-
#### Changes
339-
+ Fixed a memory segfault when re-using a thread local buffer. Not sure why it occurs, but this fix seems to solve it.
340-
341-
### 0.1.21 minimap2 2.28
342-
Contributors to this release: @mbhall88 @rob-p @Sam-Sims @charlesgregory @PB-DB
343-
#### Breaking Changes
344-
+ Map now returns Arc String's to reduce memory allocation for large and/or repetitive jobs
345-
+ 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)
346-
+ Arc the Index, to prevent double-frees, solves [#71](https://github.com/jguhlin/minimap2-rs/issues/71)
347-
+ Map file now passes in query name, which should help with [#75](https://github.com/jguhlin/minimap2-rs/issues/75)
348-
+ Supplementary flag now better detected (@rob-p)
349-
+ FIX: Cigar string missing softclip operation (@Sam-Sims)
350-
351-
#### Migration Guide
352-
+ Make all setting changes before calling a with_index, with_seq's function
353-
+ Change all map calls to include a query name, or None if not needed
354-
355-
### Other Changes
356-
+ Add ergonomic functions n_seq and get_seq.
357-
+ Better docs on applying presets, solves [#84](https://github.com/jguhlin/minimap2-rs/issues/84)
358-
+ Better detection of target arch c_char's and ptr's, solves [#82](https://github.com/jguhlin/minimap2-rs/issues/82)
359-
+ Support for M1 Mac compilation and addition of github workflows to test it, solving [#81](https://github.com/jguhlin/minimap2-rs/issues/81)
360-
+ Rayon test, so some support, closes [#5](https://github.com/jguhlin/minimap2-rs/issues/5)
361-
+ Static str's and now static CStr's
362-
+ FIX: memory leak due to sequences allocated by minimap2 not being freed @charlesgregory
363-
+ Add Send + Sync to Aligner, along with unit test @PB-DB
364-
+ Experimental Android support (tested on aarch64 and x86_64), solves [#66](https://github.com/jguhlin/minimap2-rs/issues/66)
365-
+ Added flag and option documents
366-
+ Added with_gap_open penalty ergonomic function
367-
368-
### 0.1.20 minimap2 2.28
369-
+ Fix htslib errors. No update to -sys crate needed.
370-
371-
### 0.1.19 minimap2 2.28
372-
+ Fix memory leak by @charlesgregory
373-
374-
### 0.1.18 minimap2 2.28
375-
+ Update to minimap2 v2.28 @jguhlin
376-
+ Support for lrhqae preset @jguhlin
377-
378-
### 0.1.17 minimap2 2.27
379-
* Mark bam::Record objects as supplementary. #52 @PB-DB
380-
* Only use rust-htslib/curl when curl feature is enabled. #53 @PB-DB
381-
* Update to minimap2 v2.27 @jguhlin
382-
* Switch to needletail for reading fast files (features map-file) @jguhlin
383-
* Convert functions to take slices of vectors instead of refs to vecs `&[Vec<u8>]` instead of `&Vec<Vec<u8>>` @jguhlin
384-
* _breaking_ Curl is no longer a default option for htslib, please re-enable it as needed with cargo.toml features
385-
* _breaking_ Now using needletail for map-files, enabled by default. However, compression algorithms are disabled. Please enable with cargo.toml features
386-
* Experimental rayon support
387-
* 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)
388-
* _breaking_ .with_threads(_) is now .with_index_threads(_) to make it more clear
389-
390-
### 0.1.16 minimap2 2.26
391-
* Much better cross compilation support thanks to @Adoni5
392-
393-
### 0.1.15 minimap2 2.26
394-
* Compilation on aarch64 thanks to @leiste375
395-
* README corrections thanks to @wdecoster
396-
* Better support for static builds / linking
397-
* Update fffx to a version that uses bytelines without tokio. Drastically reduces compile times and dependency tree.
398-
399-
### 0.1.14 minimap2 2.26
400-
* Memory leak fixed by @Adoni5
401-
* Updated deps
402-
403-
### 0.1.13 minimap2 2.26
404-
* Add with_seq to support indexing a single sequence (as per mappy: https://github.com/lh3/minimap2/blob/master/python/mappy.pyx#L115)
405-
* minimap2-rs: update rust-htslib deps
406-
* simdutf8 now optional dependency requiring map-file feature to be enabled
407-
* Support soft-clipping string in CIGAR. WARNING: Does not support hard clipping. Please open an issue if you need this.
408-
* Update minimap to 2.26
409-
* Not convinced SSE41/SSE2 are working properly. Recommend simde.
410-
411-
### 0.1.11
412-
* HTS lib: add support for optional quality scores by @eharr
413-
414-
### 0.1.10
415-
* HTS lib support by @eharr
416-
* HTS lib: Output sam/bam files by @eharr
417-
* More tests by @eharr
418-
* Display impl for Strand thanks to @ahcm
419-
* Update minimap2-sys to latest version by @jguhlin
420-
* -sys crate mm2fast added as additional backend by @jguhlin
421-
* zlib dep changes by @jguhlin (hopefully now it is more portable and robust)
422-
* -sys crate now supports SIMDe
423-
424-
## 0.1.9
425-
* Thanks for @Adoni5 for switching to builder pattern, and @eharr for adding additional fields to alignment.
426-
* Do not require libclang for normal compilation.
427-
## 0.1.8
428-
* Multithreading support (use less raw pointers, and treat more like rust Struct's)
429-
## 0.1.7
430-
* use libc instead of std:ffi::c_int as well
431-
## 0.1.6
432-
* Support slightly older versions of rustc by using libc:: rather than std::ffi for c_char (Thanks dwpeng!)
433-
* Use fffx module for fasta/q parsing
338+
See [CHANGELOG.md](CHANGELOG.md)
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# Funding
436341
![Genomics Aotearoa](info/genomics-aotearoa.png)

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