How To Read Bam File Line By Line Using Ruby

Question

[Gangcai]

Dear all,

I am trying to read bam file line by line by using ruby scripts. Although there is ruby gem bio-samtools(http://rubygems.org/gems/bio-samtools), I don't find a way to read the whole bam file line by line(can get the alignments for given genomic regions). Any suggestion will be appreciated.

BTW, I have used IO.open("samtools view sample1.bam").each do {|x| ...}, however it will put the whole bam file into the memory first.

[lh3]

Really? At least in C, the whole idea of popen() is NOT to read the whole file into memory.

Answer 1

[kojix2]

I know it's a 9 year old question, but I think you could make Ruby bindings for htslib or noodles. No one would do such a thing? I'm trying to make ruby-htslib. It's still buggy, though.

require 'htslib'

bam = HTS::Bam.open("foo.bam")

bam.each do |r|
  pp name: r.qname,
     flag: r.flag,
     chrm: r.chrom,
     strt: r.pos + 1,
     mapq: r.mapq,
     cigr: r.cigar.to_s,
     mchr: r.mate_chrom,
     mpos: r.mpos + 1,
     isiz: r.isize,
     seqs: r.seq,
     qual: r.qual.map { |i| (i + 33).chr }.join,
     MC:   r.aux("MC")
end

bam.close