brentp / bigwig-nim Goto Github PK

bwtool might be available on conda (if it's the same tool) - if you're interested.

https://anaconda.org/pwwang/bwtool

Thanks for your new contribution, we need tools to work on bigwig since it's an important quantitative and very fast track for genome browsers. Especially for RNA-seq, methylation (including from Oxford Nanopore - where your bed-> bigwig will be most useful) and ChIP-seq.

mosdepth outputs 0 coverage intervals and these get added to the bigwig, but this affects the coverage stat. need to look into this more.

and output BED format.

• bigwig view:
  • analog to samtools/bcftools view
  • defaults to bed(graph) output
  • -O b|w|z|g for bed/wig/beg.gz/bigwig
  • -o = /dev/stdout
  • -r/--region

for comments / feedback.
see:

• pybigwig
• bw-python

var bw: BigWig
bw.open(path, fmRead)

# avoid allocating when possible
var values: seq[float32]
bw.values(values, "chr1", 0, 2222)

for iv in bw.intervals("chr2", 999, 88888): # iterator.
    ## tuple[start: int, stop: int, value: float32]

# single value
var m = bw.stats("chr2", 999, 9999, stat=Stat.mean) 

# broken into 10 bins. Stat is an enum with mean, coverage, sum, std, etc.
var ameans = newSeq[float32](10)
# if start and stop are not given, defaults to entire chrom
bw.stats("chr2", start=999, stop=9999, ameans, stat=Stat.mean) 

once this simple reading interface is complete, I'll open another issue for writing and header manipulation, likely following this once reading is complete