minimap2-rs

minimap2-rs copied to clipboard

Bug(s?): Soft clipping in cigar outputs

6

Hello, I came across an issue with soft clipping results in the output. I think at least one of these is probably a bug, the other I'm not sure if...

holtjma

FEATURE: Make work with rayon

5

jguhlin

Test crashes with strlen out of bounds

2

https://asan.saethlin.dev/ub?crate=minimap2&version=0.1.14%2Bminimap2.2.26 ``` ==15122==ERROR: AddressSanitizer: global-buffer-overflow on address 0x55f1867e33ba at pc 0x55f184e15219 bp 0x7feb520f2f60 sp 0x7feb520f2728 READ of size 283 at 0x55f1867e33ba thread T31 #0 0x55f184e15218 in strlen /rustc/llvm/src/llvm-project/compiler-rt/lib/asan/../sanitizer_common/sanitizer_common_interceptors.inc:390:5 #1 0x55f18614e561...

riking

Dear @jguhlin, I really think the minimap2-rs is something big and bring mappers to rust. In a similarly wrapper around another widely used software hmmer, hmmer-rs (https://github.com/wwood/hmmer-rs), I think the...

jianshu93

open syncmer version of minimap2?

1

Dear @jguhlin, I think there is a open syncmer (not minimzer) as seed (https://github.com/lh3/minimap2/blob/c2f07ff2ac8bdc5c6768e63191e614ea9012bd5d/sketch.c#L145-L192), but not sure whether the rust version provided the interface to use it. Thanks, Jianshu

jianshu93

Invalid cast (on arm64?)

2

Within minimap2-rs, I'm getting [the following error](https://app.circleci.com/pipelines/github/bioconda/bioconda-recipes/126266/workflows/797d75f4-c39a-4b40-9135-2e867aaeb2de/jobs/204317?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-checks-link&utm_content=summary&invite=true#step-107-531504_105) when building on bioconda for an arm64 linux machine: ``` 19:11:58 BIOCONDA INFO (OUT) | 19:11:58 BIOCONDA INFO (OUT) 856 | self.idx.as_ref().unwrap() as...

rob-p

Difficulty building on M1 mac

2

Hi @jguhlin, I encounter the following error when attempting to include the minimap2-rs crate when building on OSX on an M1 Mac (MacOS 13.4): ``` = note: ld: warning: directory...

rob-p

This PR adds a function `map_with_name` which allows resolving https://github.com/jguhlin/minimap2-rs/issues/75. Specifically, it passes the query name (which must be `\0` terminated) to the map function, which allows the internal minimap2...

rob-p

Very subtle differences from minimap2

3

I'm just trying to track down the very subtle differences in aligning a dataset between the minimap2-rs bindings and what is output by the reference minimap2 implementation. Mostly everything is...

rob-p

cross compiling to linux android

9

Hi @jguhlin, I am not sure whether this is interesting to others but I want to report here. I was trying to import and compile many Rust software packages to...

jianshu93