bam_color.c

/*  bam_color.c -- color-space support.

    Copyright (C) 2009, 2012 University of California - Los Angeles.

    Author: Nils Homer <nilshomer@gmail.com>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.  */

#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;
    }
}