Crate rsomics_compute_gc_bias 

GC-bias estimation for a BAM over a 2bit genome — deeptools computeGCBias.

For each genomic position sampled at stepSize, the fragment-length window contributes its G+C count to n_gc (expected, from the genome) and the number of forward reads starting at that position to f_gc (observed). The per-GC ratio r_gc = (f/n) * (sum n / sum f) is the bias estimate (Benjamini & Speed 2012, doi:10.1093/nar/gks001).

Structs

GcBiasOpts

GcBiasTable

One row per GC count 0..=fragment_length.

TwoBit

Functions

compute

write_freq

deeptools writes the table with numpy savetxt defaults: three space-separated columns in %.18e, one row per GC count.