Unify API with mappy?

[kyleabeauchamp]

This is a nice project, but it would be really cool if mappy/minimap2 and bwapy happened to share the same python api.

[kyleabeauchamp]

I wonder if @lh3 would be interested if the build system, packaging, and API were consistent with mappy.

[cjw85]

This package uses CFFI for creating the python extension whilst mappy uses cython. Creating and including libbwa.a here was simply the easiest thing to do (rather than listing all the source files in the python extension build). I think switching making the builds equivalent would amount to a rewrite.

The API here was chosen simply to mirror that of bwa mem with minimal fuss, albeit creating python objects. I think @lh3 has done pretty much the same in his mappy.

We had a short-lived minimappy project before @lh3 released his python binding. My understanding is @lh3 considers minimap2 to make bwa mem obsolete.

[lh3]

My understanding is @lh3 considers minimap2 to make bwa mem obsolete.

For long reads, minimap2 should be mostly better than bwa-mem. I wouldn't recommend to use bwa for long reads these days. I thought to replace bwa-mem for short reads, too, but it turns out that bwa-mem is still better at relatively noisy Illumina reads, so bwa-mem will stay for short reads.

[kyleabeauchamp]

All sgtm. My only idea was a "standard" set of functions and classes for I'll interoperability.

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On Mon, Apr 2, 2018, 6:43 AM Heng Li ***@***.***> wrote: My understanding is @lh3 <https://github.com/lh3> considers minimap2 to make bwa mem obsolete. For long reads, minimap2 should be mostly better than bwa-mem. I wouldn't recommend to use bwa for long reads these days. I thought to replace bwa-mem for short reads, too, but it turns out that bwa-mem is still better at relatively noisy Illumina reads, so bwa-mem will stay for short reads. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABz_q_7fUpTMBWo7_CyeSwPavT3ZHAecks5tkisKgaJpZM4TDITB> .

[cjw85]

@lh3 Thanks for your clarifying blogpost.