bam.c

/*  bam.c -- BAM format.

    Copyright (C) 2008-2013, 2015, 2019-2020 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"

char *bam_format1(const bam_header_t *header, const bam1_t *b)
{
    kstring_t str;
    str.l = str.m = 0; str.s = NULL;
    if (sam_format1(header, b, &str) < 0) {
        free(str.s);
        str.s = NULL;
        return NULL;
    }
    return str.s;
}

int bam_view1(const bam_header_t *header, const bam1_t *b)
{
    char *s = bam_format1(header, b);
    int ret = -1;
    if (!s) return -1;
    if (puts(s) != EOF) ret = 0;
    free(s);
    return ret;
}

int bam_validate1(const bam_header_t *header, const bam1_t *b)
{
    char *s;

    if (b->core.tid < -1 || b->core.mtid < -1) return 0;
    if (header && (b->core.tid >= sam_hdr_nref(header) || b->core.mtid >= sam_hdr_nref(header))) return 0;

    if (b->data_len < b->core.l_qname) return 0;
    s = memchr(bam1_qname(b), '\0', b->core.l_qname);
    if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0;

    // FIXME: Other fields could also be checked, especially the auxiliary data

    return 1;
}

#ifndef MIN
#define MIN(a,b) ((a)<(b)?(a):(b))
#endif

// FIXME: we should also check the LB tag associated with each alignment
const char *bam_get_library(bam_header_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;
}

int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
{
    int ret;
    bam_iter_t iter;
    bam1_t *b;
    b = bam_init1();
    iter = bam_iter_query(idx, tid, beg, end);
    while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
    bam_iter_destroy(iter);
    bam_destroy1(b);
    return (ret == -1)? 0 : ret;
}

/************
 * 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;
}