Suggestion: statistics overview? E. g. a common statistics overview for ruby-htslib

[rubyFeedback]

Hey there kojix2,

Today I tested ruby-htslib a bit following the examples in the main README e. g.

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

bam.each do |r|
  pp name: r.qname,

And so forth. It shows a lot of information and outputs a LOT. E. g. a 67 MB .bam
file contains so much data.

Would it be possible to add some "central" statistics module into ruby-htslib,
and show in the main README how to use it?

This statistics module should show a summary of the content of the .bam
file such as how many entries it contains and so forth, any information
that is useful, but that can be displayed on the commandline, without
scrolling too much outside. E. g. a full "paper size" at max, not more.
A summary.

The rationale for this proposal would be to get a quick overview from
a .bam file without needing to go through .each - just to understand what
this .bam file is all about. And it would be useful if ruby-htslib could support
this directly as-is, if possible, so people can just use it rather than create
their own custom ad-hoc solution (they can do so anyway but I think it
would be more convenient if ruby-htslib can support this directly).

Anyway it is just a suggestion, please feel free to proceed in any way you
see fit.

[kojix2]

This is an interesting suggestion, but difficult to implement in practice.

This is because the Bam file header does not contain statistics. That means you have to run iterators anyway, and Ruby's iterators are slow. Bam files are often tens to hundreds of gigabytes in size. You do not want to run the Ruby iterator if possible.

I usually access bam files with samtools. Samtools is implemented in C and htslib and is very fast. Samtools can display bam file statistics. For example,

samtools stats a.bam

Ruby-htslib is a binding library and adding the feature to display statistics is beyond the scope.
Perhaps, we can make such tools using htslib.cr. With Crystal language, you can expect good performance. But there is no good statistical library for Crystal language. Honestly, I have thought about creating such a tool many times.

However, the conclusion so far is that it is not easy to create something that outperforms other well-used tools.