Luis Pedro Coelho

`select()` currently supports an absolute threshold on match size, but user asks if it could support a relative one. Discussed on the mailing list: https://groups.google.com/g/ngless/c/Vq1fmnS5ZKU

The approach at https://standage.github.io/loading-paired-reads-from-position-sorted-bam-files.html should work well.

Currently, `select()` computes mapstats _only if_ there is no block.

Currently, the expectation is that the user will run `ngless` enough times, but that's not a great UI.

As it stands, references can be pre-installed, but not modules.

counts with many features/options should result in many files

1

Not clear exactly on the desired behaviour/API. But here is a proposal: counts = count(mapped, features=['A', 'B'], multiple=[{dist1}, {all1}]) write(counts, ofile='counts.{features}.{multiple}.txt') would result in 4 files: `counts.A.dist1.txt`, `counts.A.all1.txt`, `counts.B.dist1.txt`, `counts.B.all1.txt`.

Support outputting count files in binary format

1

Instead of CSV/TSV format.

stack overflow using snack on NGLess

1

I tried snack on a clean checkout of [NGLess](https://github.com/ngless-toolkit/ngless) and it first ran for a while, then it errored. From then on, running `snack build` runs for about a minute...

Explicit error if too many sequences are used

2

Right now, strobealign only supports up to 2²⁴ sequences. If the user tries more, it would silently accept it, but later crash.

ENH Fix musl64 bzip2

13

Without this patch, I get build errors related to -lbz2 not being found when building [NGLess](https://github.com/ngless-toolkit/ngless) in static mode: ``` /nix/store/xbi3yw5aj1fxf1vckmb6mf9n8k16a73y-x86_64-unknown-linux-musl-binutils-2.40/bin/x86_64-unknown-linux-musl-ld: cannot find -lbz2: No such file or directory ```