expose more fai stuff? (and some slowness with Fai.get()) about hts-nim HOT 4 CLOSED

That's great to hear that it's getting use!
Just yesterday, I added fai.chrom_len() which exposes faidx_seq_len and I just now pushed a way to expose faidx_iseq by using []. You can see the tests in the commit for an example.

with these changes you can write something like:

for x in 0..fai.len-1:
  var L = fai.chrom_len(fai[i])
  ...

For why/how it is slow, can you show an example so I can test? It should be similar speed to pysam, but it does have to make a copy of the string because (as you know) a cstring is not the same as a string in nim.

Please let me know any additional issues you encounter.

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and also re the performance, you are compiling with -d:release yes?

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Thanks I just saw the chrom_len() after I posted. My test was just chr1 from GRCh38 (https://api.gdc.cancer.gov/data/62f23fad-0f24-43fb-8844-990d531947cf). so fa.get("chr1") in nim and fa.fetch(region="chr1") in pysam...

Ok after doing a much better "test" i actually see similar stats:

• python: 169.11user 41.20system 3:30.34elapsed 99%CPU (0avgtext+0avgdata 990340maxresident)k

import pysam

fa = pysam.FastaFile("/mnt/SCRATCH/refdata/GRCh38.d1.vd1.fa")

for i in range(100):
    seq = fa.fetch(region="chr1")

fa.close()

• nim: 168.89user 17.64system 3:06.55elapsed 99%CPU (0avgtext+0avgdata 493344maxresident)k

import hts

when isMainModule:
  var
    fafil = "/mnt/SCRATCH/refdata/GRCh38.d1.vd1.fa"
    fa: Fai
    chrom = "chr1"

  discard open(fa, fafil)
  for i in 0..<100:
    var bases = fa.get(chrom)

So, I think you can ignore that statement

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great! let me know if you hit any more issues.

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