see_chrom_read_input.c

This file contains functions for reading DNA sequences out of a .fa format file.

The core of the logic is see_chrom_read_go(), which
reads a .fa file, skips over comments, and passes
each nucleotide one at a time to see_chrom_gen_model.

(Conceptually, this is lower-level code, but callbacks are often slower than
normal calls because they are harder to inline/optimize,
and this is a performance-critical loop. So I'll just have read_input.c 
be at a higher level than see_chrom_gen_model and feed it data).

For simplicity, this tool treats lower-case bases
the same as upper-case, and skips over variable bases like n.
For maximum performance, input files must be in .fa format with
only one > comment at the start of the file.
See documentation for more information.

Currently using data from USCS, see the page
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/