BAMUtils::BAMUtils(BAMRead& BAM_record, std::string qscores, coord_t slop,
bool IUPAC_Flag, bool Keep_IUPAC, bool Truncate_Soft_Clipped,
int error_table_min_len, int error_table_max_len,
int error_table_step_size, int three_prime_clip,
bool rounding_phred_scores, bool Five_Prime_Justify, std::string &Flow_Order):
bam_record(BAM_record),
q_scores(qscores),
num_slop(slop),
total_three_prime_ignore(three_prime_clip)
{
_init();
flow_order = Flow_Order;
iupac_flag = IUPAC_Flag;
keep_iupac = Keep_IUPAC;
truncate_soft_clipped = Truncate_Soft_Clipped;
//set_genome_length(genome_length);
set_genome_length(bam_record.get_ref_len());
set_slop_bases(slop);
init_error_table(error_table_min_len, error_table_max_len, error_table_step_size);
round_phred_scores = rounding_phred_scores;
five_prime_justify = Five_Prime_Justify;
_crunch_data();
}
int init_krb_err_tbl (NOARGS) {
return(init_error_table(krb_err_txt, 39525376, 200));
}