bam.c

/*  bam.c -- miscellaneous BAM functions.

    Copyright (C) 2008-2013, 2015, 2019-2020, 2022 Genome Research Ltd.
    Portions copyright (C) 2009-2012 Broad Institute.

    Author: Heng Li <lh3@sanger.ac.uk>

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 <config.h>

#include <stdio.h>
#include <ctype.h>
#include <errno.h>
#include "bam.h"
#include "htslib/kstring.h"

// FIXME: we should also check the LB tag associated with each alignment
const char *bam_get_library(sam_hdr_t *h, const bam1_t *b)
{
    const char *rg;
    kstring_t lib = { 0, 0, NULL };
    rg = (char *)bam_aux_get(b, "RG");

    if (!rg)
        return NULL;
    else
        rg++;

    if (sam_hdr_find_tag_id(h, "RG", "ID", rg, "LB", &lib)  < 0)
        return NULL;

    static char LB_text[1024];
    int len = lib.l < sizeof(LB_text) - 1 ? lib.l : sizeof(LB_text) - 1;

    memcpy(LB_text, lib.s, len);
    LB_text[len] = 0;

    free(lib.s);

    return LB_text;
}

/************
 * Remove B *
 ************/

#define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((~(i)&1)<<2) )

int bam_remove_B(bam1_t *b)
{
    int i, j, end_j, k, l, no_qual;
    uint32_t *cigar, *new_cigar;
    uint8_t *seq, *qual, *p;
    // test if removal is necessary
    if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing
    cigar = bam_get_cigar(b);
    for (k = 0; k < b->core.n_cigar; ++k)
        if (bam_cigar_op(cigar[k]) == BAM_CBACK) break;
    if (k == b->core.n_cigar) return 0; // no 'B'
    if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed
    // allocate memory for the new CIGAR
    if (b->l_data + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory
        b->m_data = b->l_data + b->core.n_cigar * 4;
        kroundup32(b->m_data);
        b->data = (uint8_t*)realloc(b->data, b->m_data);
        cigar = bam_get_cigar(b); // after realloc, cigar may be changed
    }
    new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data
    // the core loop
    seq = bam_get_seq(b); qual = bam_get_qual(b);
    no_qual = (qual[0] == 0xff); // test whether base quality is available
    i = j = 0; end_j = -1;
    for (k = l = 0; k < b->core.n_cigar; ++k) {
        int op  = bam_cigar_op(cigar[k]);
        int len = bam_cigar_oplen(cigar[k]);
        if (op == BAM_CBACK) { // the backward operation
            int t, u;
            if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR
            if (len > j) goto rmB_err; // an excessively long backward
            for (t = l - 1, u = 0; t >= 0; --t) { // look back
                int op1  = bam_cigar_op(new_cigar[t]);
                int len1 = bam_cigar_oplen(new_cigar[t]);
                if (bam_cigar_type(op1)&1) { // consume the query
                    if (u + len1 >= len) { // stop
                        new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT;
                        break;
                    } else u += len1;
                }
            }
            if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation
            l = t + 1;
            end_j = j; j -= len;
        } else { // other CIGAR operations
            new_cigar[l++] = cigar[k];
            if (bam_cigar_type(op)&1) { // consume the query
                if (i != j) { // no need to copy if i == j
                    int u, c, c0;
                    for (u = 0; u < len; ++u) { // construct the consensus
                        c = bam_seqi(seq, i+u);
                        if (j + u < end_j) { // in an overlap
                            c0 = bam_seqi(seq, j+u);
                            if (c != c0) { // a mismatch; choose the better base
                                if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better
                                    bam1_seq_seti(seq, j+u, c);
                                    qual[j+u] = qual[i+u] - qual[j+u];
                                } else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality
                            } else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u];
                        } else { // not in an overlap; copy over
                            bam1_seq_seti(seq, j+u, c);
                            qual[j+u] = qual[i+u];
                        }
                    }
                }
                i += len, j += len;
            }
        }
    }
    if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified
    // merge adjacent operations if possible
    for (k = 1; k < l; ++k)
        if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1]))
            new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf;
    // kill zero length operations
    for (k = i = 0; k < l; ++k)
        if (new_cigar[k] >> BAM_CIGAR_SHIFT)
            new_cigar[i++] = new_cigar[k];
    l = i;
    // update b
    memcpy(cigar, new_cigar, l * 4); // set CIGAR
    p = b->data + b->core.l_qname + l * 4;
    memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ
    memmove(p, qual, j); p += j; // set QUAL
    memmove(p, bam_get_aux(b), bam_get_l_aux(b)); p += bam_get_l_aux(b); // set optional fields
    b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length
    b->l_data = p - b->data; // update record length
    return 0;

rmB_err:
    b->core.flag |= BAM_FUNMAP;
    return -1;
}

/* Calculate the current read's start based on the stored cigar string. */
hts_pos_t unclipped_start(bam1_t *b) {
    uint32_t *cigar = bam_get_cigar(b);
    int64_t clipped = 0;
    uint32_t i;

    for (i = 0; i < b->core.n_cigar; i++) {
        char c = bam_cigar_opchr(cigar[i]);

        if (c == 'S' || c == 'H') { // clips
            clipped += bam_cigar_oplen(cigar[i]);
        } else {
            break;
        }
    }

    return b->core.pos - clipped + 1;
}

/* Calculate the mate's unclipped start based on position and cigar string from MC tag. */
hts_pos_t unclipped_other_start(hts_pos_t op, char *cigar) {
    char *c = cigar;
    int64_t clipped = 0;

    while (*c && *c != '*') {
        long num = 0;

        if (isdigit((int)*c)) {
            num = strtol(c, &c, 10);
        } else {
            num = 1;
        }

        if (*c == 'S' || *c == 'H') { // clips
            clipped += num;
        } else {
            break;
        }

        c++;
    }

    return op - clipped + 1;
}

/* Calculate the current read's end based on the stored cigar string. */
hts_pos_t unclipped_end(bam1_t *b) {
    uint32_t *cigar = bam_get_cigar(b);
    hts_pos_t end_pos, clipped = 0;
    int32_t i;

    end_pos = bam_endpos(b);

    // now get the clipped end bases (if any)
    // if we get to the beginning of the cigar string
    // without hitting a non-clip then the results are meaningless
    for (i = b->core.n_cigar - 1; i >= 0; i--) {
        char c = bam_cigar_opchr(cigar[i]);

        if (c == 'S' || c == 'H') { // clips
            clipped += bam_cigar_oplen(cigar[i]);
        } else {
            break;
        }
    }

    return end_pos + clipped;
}


/* Calculate the mate's unclipped end based on start position and cigar string from MC tag.*/
hts_pos_t unclipped_other_end(int64_t op, char *cigar) {
    char *c = cigar;
    int64_t refpos = 0;
    int skip = 1;

    while (*c && *c != '*') {
        long num = 0;

        if (isdigit((int)*c)) {
            num = strtol(c, &c, 10);
        } else {
            num = 1;
        }

        switch (*c) {
            case 'M':
            case 'D':
            case 'N':
            case '=':
            case 'X':
                refpos += num;
                skip = 0; // ignore initial clips
            break;

            case 'S':
            case 'H':
                if (!skip) {
                refpos += num;
            }
            break;
        }

        c++;
   }

    return  op + refpos;
}