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#include <ctype.h>
#include "bam.h"
/*!
@abstract Get the color encoding the previous and current base
@param b pointer to an alignment
@param i The i-th position, 0-based
@return color
@discussion Returns 0 no color information is found.
*/
char bam_aux_getCSi(bam1_t *b, int i)
{
uint8_t *c = bam_aux_get(b, "CS");
char *cs = NULL;
// return the base if the tag was not found
if(0 == c) return 0;
cs = bam_aux2Z(c);
// adjust for strandedness and leading adaptor
if(bam1_strand(b)) {
i = strlen(cs) - 1 - i;
// adjust for leading hard clip
uint32_t cigar = bam1_cigar(b)[0];
if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
i -= cigar >> BAM_CIGAR_SHIFT;
}
} else { i++; }
return cs[i];
}
/*!
@abstract Get the color quality of the color encoding the previous and current base
@param b pointer to an alignment
@param i The i-th position, 0-based
@return color quality
@discussion Returns 0 no color information is found.
*/
char bam_aux_getCQi(bam1_t *b, int i)
{
uint8_t *c = bam_aux_get(b, "CQ");
char *cq = NULL;
// return the base if the tag was not found
if(0 == c) return 0;
cq = bam_aux2Z(c);
// adjust for strandedness
if(bam1_strand(b)) {
i = strlen(cq) - 1 - i;
// adjust for leading hard clip
uint32_t cigar = bam1_cigar(b)[0];
if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
i -= (cigar >> BAM_CIGAR_SHIFT);
}
}
return cq[i];
}
char bam_aux_nt2int(char a)
{
switch(toupper(a)) {
case 'A':
return 0;
break;
case 'C':
return 1;
break;
case 'G':
return 2;
break;
case 'T':
return 3;
break;
default:
return 4;
break;
}
}
char bam_aux_ntnt2cs(char a, char b)
{
a = bam_aux_nt2int(a);
b = bam_aux_nt2int(b);
if(4 == a || 4 == b) return '4';
return "0123"[(int)(a ^ b)];
}
/*!
@abstract Get the color error profile at the give position
@param b pointer to an alignment
@return the original color if the color was an error, '-' (dash) otherwise
@discussion Returns 0 no color information is found.
*/
char bam_aux_getCEi(bam1_t *b, int i)
{
int cs_i;
uint8_t *c = bam_aux_get(b, "CS");
char *cs = NULL;
char prev_b, cur_b;
char cur_color, cor_color;
// return the base if the tag was not found
if(0 == c) return 0;
cs = bam_aux2Z(c);
// adjust for strandedness and leading adaptor
if(bam1_strand(b)) { //reverse strand
cs_i = strlen(cs) - 1 - i;
// adjust for leading hard clip
uint32_t cigar = bam1_cigar(b)[0];
if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
cs_i -= cigar >> BAM_CIGAR_SHIFT;
}
// get current color
cur_color = cs[cs_i];
// get previous base. Note: must rc adaptor
prev_b = (cs_i == 1) ? "TGCAN"[(int)bam_aux_nt2int(cs[0])] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
// get current base
cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
}
else {
cs_i=i+1;
// get current color
cur_color = cs[cs_i];
// get previous base
prev_b = (0 == i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i-1)];
// get current base
cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
}
// corrected color
cor_color = bam_aux_ntnt2cs(prev_b, cur_b);
if(cur_color == cor_color) {
return '-';
}
else {
return cur_color;
}
}
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