see_chrom_util.c

This file contains helper functions for DNA sequences and user-defined parameters.

Parameters that can be adjusted by the user

    getparam_region_length()
    getparam_nthreads()
    etc.


Constants:
    nucleotide_a = 0,
    nucleotide_t = 1,
    nucleotide_g = 2,
    nucleotide_c = 3
        (chosen arbitrarily)

    c_bits_per_nucleotide
        storing ntides as bits lets us store them efficiently in memory

    c_markov_sequence_len
        length of sequence: given 9 ntides, what is the next ntide?

    c_num_all_possible_sequences
        the total number of possible ntide sequences

    c_markov_sequence_len_for_test
        in tests, use a shorter sequence of 2 ntides

struct sv_app
    Widely available state like the current log file