bam.c

#include <stdio.h>
#include <ctype.h>
#include <errno.h>
#include <assert.h>
#include "bam.h"
#include "bam_endian.h"
#include "kstring.h"
#include "sam_header.h"

int bam_is_be = 0;
int bam_verbose = 2;
int bam_no_B = 0;
char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
char bam_nt16_rev_table2[16] = {'=','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N'};

/**************************
 * CIGAR related routines *
 **************************/

uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
{
    int k;
    int end;

    end = c->pos;

    for (k=0; k < c->n_cigar; ++k)
    {
        int op;
        int len;
        op  = bam_cigar_op(cigar[k]);
        len = bam_cigar_oplen(cigar[k]);
        if (op == BAM_CBACK)
        {
            // move backward
            int l;
            int u;
            int v;
            if (k == c->n_cigar-1)
                break; // skip trailing 'B'
            for (l=k-1, u=v=0; l >= 0; --l)
            {
                int op1;
                int len1;
                op1  = bam_cigar_op(cigar[l]);
                len1 = bam_cigar_oplen(cigar[l]);
                if (bam_cigar_type(op1) & 1)
                {
                    // consume query
                    if (u + len1 >= len)
                    {
                        // stop
                        if (bam_cigar_type(op1)&2)
                            v += len-u;
                        break;
                    }
                    else
                        u += len1;
                }
                if (bam_cigar_type(op1) & 2)
                    v += len1;
            }
            end = l < 0 ? c->pos : end-v;
        }
        else if (bam_cigar_type(op) & 2)
            end += bam_cigar_oplen(cigar[k]);
    }

    return end;
}

int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
{
    uint32_t k;
    int32_t l;

    l = 0;

    for (k=0; k < c->n_cigar; ++k)
        if (bam_cigar_type(bam_cigar_op(cigar[k]))&1)
            l += bam_cigar_oplen(cigar[k]);

    return l;
}

/********************
 * BAM I/O routines *
 ********************/

bam_header_t *bam_header_init(void)
{
    bam_is_be = bam_is_big_endian();
    return (bam_header_t*)calloc(1, sizeof(bam_header_t));
}

void bam_header_destroy(bam_header_t *header)
{
    int32_t i;
    extern void bam_destroy_header_hash(bam_header_t *header);

    if (header == 0)
        return;
    if (header->target_name)
    {
        for (i=0; i < header->n_targets; ++i)
            free(header->target_name[i]);
        free(header->target_name);
        free(header->target_len);
    }
    free(header->text);
    if (header->dict)
        sam_header_free(header->dict);
    if (header->rg2lib)
        sam_tbl_destroy(header->rg2lib);
    bam_destroy_header_hash(header);
    free(header);
}

bam_header_t *bam_header_read(bamFile fp)
{
    bam_header_t *header;
    char buf[4];
    int magic_len;
    int32_t i = 1;
    int32_t name_len;

    // check EOF
    i = bgzf_check_EOF(fp);
    if (i < 0)
    {
        // If the file is a pipe, checking the EOF marker will *always* fail
        // with ESPIPE.  Suppress the error message in this case.
        if (errno != ESPIPE)
            perror("[bam_header_read] bgzf_check_EOF");
    }
    else if (i == 0)
        fprintf(stderr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
    // read "BAM1"
    magic_len = bam_read(fp, buf, 4);
    if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0)
    {
        fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
        return 0;
    }
    header = bam_header_init();
    // read plain text and the number of reference sequences
    bam_read(fp, &header->l_text, 4);
    if (bam_is_be)
        bam_swap_endian_4p(&header->l_text);
    header->text = (char*)calloc(header->l_text+1, 1);
    bam_read(fp, header->text, header->l_text);
    bam_read(fp, &header->n_targets, 4);
    if (bam_is_be)
        bam_swap_endian_4p(&header->n_targets);
    // read reference sequence names and lengths
    header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
    header->target_len = (uint32_t*)calloc(header->n_targets, 4);
    for (i=0; i != header->n_targets; ++i)
    {
        bam_read(fp, &name_len, 4);
        if (bam_is_be)
            bam_swap_endian_4p(&name_len);
        header->target_name[i] = (char*)calloc(name_len, 1);
        bam_read(fp, header->target_name[i], name_len);
        bam_read(fp, &header->target_len[i], 4);
        if (bam_is_be)
            bam_swap_endian_4p(&header->target_len[i]);
    }
    return header;
}

int bam_header_write(bamFile fp, const bam_header_t *header)
{
    char buf[4];
    int32_t i;
    int32_t name_len;
    int32_t x;

    // write "BAM1"
    strncpy(buf, "BAM\001", 4);
    bam_write(fp, buf, 4);
    // write plain text and the number of reference sequences
    if (bam_is_be)
    {
        x = bam_swap_endian_4(header->l_text);
        bam_write(fp, &x, 4);
        if (header->l_text)
            bam_write(fp, header->text, header->l_text);
        x = bam_swap_endian_4(header->n_targets);
        bam_write(fp, &x, 4);
    }
    else
    {
        bam_write(fp, &header->l_text, 4);
        if (header->l_text)
            bam_write(fp, header->text, header->l_text);
        bam_write(fp, &header->n_targets, 4);
    }
    // write sequence names and lengths
    for (i=0; i != header->n_targets; ++i)
    {
        char *p = header->target_name[i];
        name_len = strlen(p)+1;
        if (bam_is_be)
        {
            x = bam_swap_endian_4(name_len);
            bam_write(fp, &x, 4);
        }
        else
            bam_write(fp, &name_len, 4);
        bam_write(fp, p, name_len);
        if (bam_is_be)
        {
            x = bam_swap_endian_4(header->target_len[i]);
            bam_write(fp, &x, 4);
        }
        else
            bam_write(fp, &header->target_len[i], 4);
    }
    bgzf_flush(fp);
    return 0;
}

static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
{
    uint8_t *s;
    uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);

    s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
    for (i=0; i < c->n_cigar; ++i)
        bam_swap_endian_4p(&cigar[i]);
    while (s < data + data_len)
    {
        uint8_t type;
        s += 2; // skip key
        type = toupper(*s);
        ++s; // skip type
        if (type == 'C' || type == 'A')
            ++s;
        else if (type == 'S')
        {
            bam_swap_endian_2p(s);
            s += 2;
        }
        else if (type == 'I' || type == 'F')
        {
            bam_swap_endian_4p(s);
            s += 4;
        }
        else if (type == 'D')
        {
            bam_swap_endian_8p(s);
            s += 8;
        }
        else if (type == 'Z' || type == 'H')
        {
            while (*s)
                ++s;
            ++s;
        }
        else if (type == 'B')
        {
            int32_t n, Bsize = bam_aux_type2size(*s);
            memcpy(&n, s + 1, 4);
            if (1 == Bsize)
            {
            }
            else if (2 == Bsize)
            {
                for (i=0; i < n; i += 2)
                    bam_swap_endian_2p(s + 5 + i);
            }
            else if (4 == Bsize)
            {
                for (i=0; i < n; i += 4)
                    bam_swap_endian_4p(s + 5 + i);
            }
            bam_swap_endian_4p(s+1);
        }
    }
}

int bam_read1(bamFile fp, bam1_t *b)
{
    bam1_core_t *c = &b->core;
    int32_t block_len, ret, i;
    uint32_t x[8];

    assert(BAM_CORE_SIZE == 32);
    if ((ret = bam_read(fp, &block_len, 4)) != 4)
    {
        if (ret == 0)
            return -1; // normal end-of-file
        else
            return -2; // truncated
    }
    if (bam_read(fp, x, BAM_CORE_SIZE) != BAM_CORE_SIZE)
        return -3;
    if (bam_is_be)
    {
        bam_swap_endian_4p(&block_len);
        for (i=0; i < 8; ++i)
            bam_swap_endian_4p(x+i);
    }
    c->tid = x[0];
    c->pos = x[1];
    c->bin = x[2]>>16;
    c->qual = x[2]>>8&0xff;
    c->l_qname = x[2]&0xff;
    c->flag = x[3]>>16;
    c->n_cigar = x[3]&0xffff;
    c->l_qseq = x[4];
    c->mtid = x[5];
    c->mpos = x[6];
    c->isize = x[7];
    b->data_len = block_len - BAM_CORE_SIZE;
    if (b->m_data < b->data_len)
    {
        b->m_data = b->data_len;
        kroundup32(b->m_data);
        b->data = (uint8_t*)realloc(b->data, b->m_data);
    }
    if (bam_read(fp, b->data, b->data_len) != b->data_len)
        return -4;
    b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
    if (bam_is_be)
        swap_endian_data(c, b->data_len, b->data);
    if (bam_no_B)
        bam_remove_B(b);
    return 4 + block_len;
}

inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data)
{
    uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y;
    int i;

    assert(BAM_CORE_SIZE == 32);
    x[0] = c->tid;
    x[1] = c->pos;
    x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
    x[3] = (uint32_t)c->flag<<16 | c->n_cigar;
    x[4] = c->l_qseq;
    x[5] = c->mtid;
    x[6] = c->mpos;
    x[7] = c->isize;
    bgzf_flush_try(fp, 4 + block_len);
    if (bam_is_be)
    {
        for (i=0; i < 8; ++i)
            bam_swap_endian_4p(x + i);
        y = block_len;
        bam_write(fp, bam_swap_endian_4p(&y), 4);
        swap_endian_data(c, data_len, data);
    }
    else
        bam_write(fp, &block_len, 4);
    bam_write(fp, x, BAM_CORE_SIZE);
    bam_write(fp, data, data_len);
    if (bam_is_be)
        swap_endian_data(c, data_len, data);
    return 4 + block_len;
}

int bam_write1(bamFile fp, const bam1_t *b)
{
    return bam_write1_core(fp, &b->core, b->data_len, b->data);
}

char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
{
    uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
    int i;
    const bam1_core_t *c = &b->core;
    kstring_t str;
    str.l = str.m = 0;
    str.s = 0;

    kputsn(bam1_qname(b), c->l_qname-1, &str);
    kputc('\t', &str);
    if (of == BAM_OFDEC)
    {
        kputw(c->flag, &str);
        kputc('\t', &str);
    }
    else if (of == BAM_OFHEX)
        ksprintf(&str, "0x%x\t", c->flag);
    else
    {
        // BAM_OFSTR
        for (i=0; i < 16; ++i)
            if ((c->flag & 1<<i) && bam_flag2char_table[i])
                kputc(bam_flag2char_table[i], &str);
        kputc('\t', &str);
    }
    if (c->tid < 0)
        kputsn("*\t", 2, &str);
    else
    {
        if (header)
            kputs(header->target_name[c->tid] , &str);
        else
            kputw(c->tid, &str);
        kputc('\t', &str);
    }
    kputw(c->pos + 1, &str);
    kputc('\t', &str);
    kputw(c->qual, &str);
    kputc('\t', &str);
    if (c->n_cigar == 0)
        kputc('*', &str);
    else
    {
        uint32_t *cigar = bam1_cigar(b);
        for (i=0; i < c->n_cigar; ++i)
        {
            kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
            kputc(bam_cigar_opchr(cigar[i]), &str);
        }
    }
    kputc('\t', &str);
    if (c->mtid < 0)
        kputsn("*\t", 2, &str);
    else if (c->mtid == c->tid)
        kputsn("=\t", 2, &str);
    else
    {
        if (header)
            kputs(header->target_name[c->mtid], &str);
        else
            kputw(c->mtid, &str);
        kputc('\t', &str);
    }
    kputw(c->mpos + 1, &str);
    kputc('\t', &str);
    kputw(c->isize, &str);
    kputc('\t', &str);
    if (c->l_qseq)
    {
        for (i=0; i < c->l_qseq; ++i)
            kputc(bam_nt16_rev_table2[bam1_seqi(s, i)], &str);
        kputc('\t', &str);
        if (t[0] == 0xff)
            kputc('*', &str);
        else
            for (i=0; i < c->l_qseq; ++i)
                kputc(t[i] + 33, &str);
    }
    else
        kputsn("*\t*", 3, &str);
    s = bam1_aux(b);
    while (s < b->data + b->data_len)
    {
        uint8_t type;
        uint8_t key[2];

        key[0] = s[0];
        key[1] = s[1];
        s += 2;
        type = *s;
        ++s;
        kputc('\t', &str);
        kputsn((char*)key, 2, &str);
        kputc(':', &str);
        if (type == 'A')
        {
            kputsn("A:", 2, &str);
            kputc(*s, &str);
            ++s;
        }
        else if (type == 'C')
        {
            kputsn("i:", 2, &str);
            kputw(*s, &str);
            ++s;
        }
        else if (type == 'c')
        {
            kputsn("i:", 2, &str);
            kputw(*(int8_t*)s, &str);
            ++s;
        }
        else if (type == 'S')
        {
            kputsn("i:", 2, &str);
            kputw(*(uint16_t*)s, &str);
            s += 2;
        }
        else if (type == 's')
        {
            kputsn("i:", 2, &str);
            kputw(*(int16_t*)s, &str);
            s += 2;
        }
        else if (type == 'I')
        {
            kputsn("i:", 2, &str);
            kputuw(*(uint32_t*)s, &str);
            s += 4;
        }
        else if (type == 'i')
        {
            kputsn("i:", 2, &str);
            kputw(*(int32_t*)s, &str);
            s += 4;
        }
        else if (type == 'f')
        {
            ksprintf(&str, "f:%g", *(float*)s);
            s += 4;
        }
        else if (type == 'd')
        {
            ksprintf(&str, "d:%lg", *(double*)s);
            s += 8;
        }
        else if ((type == 'Z') || (type == 'H'))
        {
            kputc(type, &str);
            kputc(':', &str);
            while (*s)
                kputc(*s++, &str);
            ++s;
        }
        else if (type == 'B')
        {
            uint8_t sub_type = *(s++);
            int32_t n;
            memcpy(&n, s, 4);
            s += 4; // no point to the start of the array
            kputc(type, &str);
            kputc(':', &str);
            kputc(sub_type, &str); // write the typing
            for (i=0; i < n; ++i)
            {
                kputc(',', &str);
                if (('c' == sub_type) || ('c' == sub_type))
                {
                    kputw(*(int8_t*)s, &str);
                    ++s;
                }
                else if ('C' == sub_type)
                {
                    kputw(*(uint8_t*)s, &str);
                    ++s;
                }
                else if ('s' == sub_type)
                {
                    kputw(*(int16_t*)s, &str);
                    s += 2;
                }
                else if ('S' == sub_type)
                {
                    kputw(*(uint16_t*)s, &str);
                    s += 2;
                }
                else if ('i' == sub_type)
                {
                    kputw(*(int32_t*)s, &str);
                    s += 4;
                }
                else if ('I' == sub_type)
                {
                    kputuw(*(uint32_t*)s, &str);
                    s += 4;
                }
                else if ('f' == sub_type)
                {
                    ksprintf(&str, "%g", *(float*)s);
                    s += 4;
                }
            }
        }
    }

    return str.s;
}

char *bam_format1(const bam_header_t *header, const bam1_t *b)
{
    return bam_format1_core(header, b, BAM_OFDEC);
}

void bam_view1(const bam_header_t *header, const bam1_t *b)
{
    char *s = bam_format1(header, b);
    puts(s);
    free(s);
}

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 >= header->n_targets) || (b->core.mtid >= header->n_targets)))
        return 0;
    if (b->data_len < b->core.l_qname)
        return 0;
    s = (char*)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;
}

// 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 uint8_t *rg;

    if (h->dict == 0)
        h->dict = sam_header_parse2(h->text);
    if (h->rg2lib == 0)
        h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
    rg = bam_aux_get(b, "RG");
    return (rg == 0) ? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg+1));
}

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

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 = bam1_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->data_len + (b->core.n_cigar + 1) * 4 > b->m_data)
    {
        // not enough memory
        b->m_data = b->data_len + b->core.n_cigar * 4;
        kroundup32(b->m_data);
        b->data = (uint8_t*)realloc(b->data, b->m_data);
        cigar = bam1_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 = bam1_seq(b);
    qual = bam1_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 = bam1_seqi(seq, i+u);
                        if (j + u < end_j)
                        {
                            // in an overlap
                            c0 = bam1_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, bam1_aux(b), b->l_aux);
    p += b->l_aux; // set optional fields
    b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length
    b->data_len = p - b->data; // update record length
    return 0;

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