bamlite.c

#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include <stdio.h>
#include <errno.h>
#include "bamlite.h"

/*********************
 * from bam_endian.c *
 *********************/

static inline int bam_is_big_endian()
{
    long one= 1;
    return !(*((char *)(&one)));
}
static inline uint16_t bam_swap_endian_2(uint16_t v)
{
    return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
}
static inline void *bam_swap_endian_2p(void *x)
{
    *(uint16_t*)x = bam_swap_endian_2(*(uint16_t*)x);
    return x;
}
static inline uint32_t bam_swap_endian_4(uint32_t v)
{
    v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
    return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
}
static inline void *bam_swap_endian_4p(void *x)
{
    *(uint32_t*)x = bam_swap_endian_4(*(uint32_t*)x);
    return x;
}
static inline uint64_t bam_swap_endian_8(uint64_t v)
{
    v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
    v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
    return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
}
static inline void *bam_swap_endian_8p(void *x)
{
    *(uint64_t*)x = bam_swap_endian_8(*(uint64_t*)x);
    return x;
}

/**************
 * from bam.c *
 **************/

int bam_is_be;

bam_header_t *bam_header_init()
{
    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;
    if (header == 0) return;
    if (header->target_name) {
        for (i = 0; i < header->n_targets; ++i)
            if (header->target_name[i]) free(header->target_name[i]);
        if (header->target_len) free(header->target_len);
        free(header->target_name);
    }
    if (header->text) free(header->text);
    free(header);
}

bam_header_t *bam_header_read(bamFile fp)
{
    bam_header_t *header;
    char buf[4];
    int magic_len;
    int32_t i = 1, name_len;
    // 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 NULL;
    }
    header = bam_header_init();
    // read plain text and the number of reference sequences
    if (bam_read(fp, &header->l_text, 4) != 4) goto fail; 
    if (bam_is_be) bam_swap_endian_4p(&header->l_text);
    header->text = (char*)calloc(header->l_text + 1, 1);
    if (bam_read(fp, header->text, header->l_text) != header->l_text) goto fail;
    if (bam_read(fp, &header->n_targets, 4) != 4) goto fail;
    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) {
        if (bam_read(fp, &name_len, 4) != 4) goto fail;
        if (bam_is_be) bam_swap_endian_4p(&name_len);
        header->target_name[i] = (char*)calloc(name_len, 1);
        if (bam_read(fp, header->target_name[i], name_len) != name_len) {
            goto fail;
        }
        if (bam_read(fp, &header->target_len[i], 4) != 4) goto fail;
        if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
    }
    return header;
 fail:
    bam_header_destroy(header);
    return NULL;
}

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; }
    }
}

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

    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, sizeof(bam1_core_t)) != sizeof(bam1_core_t)) 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 - sizeof(bam1_core_t);
    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);
    return 4 + block_len;
}

enum bam_sort_order bam_hrecs_sort_order(bam_header_t *header)
{
    char *hdr;
    size_t i, j, len;

    len = header->l_text;
    hdr = header->text;
    
    if (len < 3)
        if (len == 0 || *hdr == '\0')
            return ORDER_UNKNOWN;

    for (i = 0; i < len; i++) {
        if (!strncmp(hdr + i, "@HD", 3)) {
            i += 3;
            if (hdr[i] != '\t')
                return ORDER_UNKNOWN;
            i++;
            while (hdr[i]!='\n') {
                for (j = i; j < len && hdr[j] != '\0' && hdr[j] != '\n' && hdr[j] != '\t'; j++)
                    ;

                if (j - i < 3 || hdr[i + 2] != ':') {
                    return ORDER_UNKNOWN;
                }

                if (!strncmp(hdr + i, "SO", 2)) {
                    i += 3;
                    if (!strncmp(hdr + i, "unsorted", 8))
                        return ORDER_UNSORTED;
                    else if (!strncmp(hdr + i, "queryname", 9))
                        return ORDER_NAME;
                    else if (!strncmp(hdr + i, "coordinate", 10))
                        return ORDER_COORD;
                    else
                        return ORDER_UNKNOWN;
                }

                i = j + 1;
            }
        }
        while(hdr[i]!='\n')
            i++;
    }
    
    return ORDER_UNKNOWN;
}

int get_target_end(bam1_t *b)
{
    int i, s;
    uint8_t c;
    uint32_t n_cigar, *cigar;
    s = b->core.pos;
    cigar = bam1_cigar(b);
    n_cigar = b->core.n_cigar;
    for (i = 0; i < n_cigar; ++i) {
        c = cigar[i] & BAM_CIGAR_MASK;
        if (c == BAM_CMATCH || c == BAM_CDEL)
            s += cigar[i] >> BAM_CIGAR_SHIFT;
    }
    return s;
}

#ifdef USE_VERBOSE_ZLIB_WRAPPERS
// Versions of gzopen, gzread and gzclose that print up error messages

gzFile bamlite_gzopen(const char *fn, const char *mode) {
    gzFile fp;
    if (strcmp(fn, "-") == 0) {
        fp = gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode);
        if (!fp) {
            fprintf(stderr, "Couldn't open %s : %s",
                    (strstr(mode, "r"))? "stdin" : "stdout",
                    strerror(errno));
        }
        return fp;
    }
    if ((fp = gzopen(fn, mode)) == 0) {
        fprintf(stderr, "Couldn't open %s : %s\n", fn,
                errno ? strerror(errno) : "Out of memory");
    }
    return fp;
}

int bamlite_gzread(gzFile file, void *ptr, unsigned int len) {
    int ret = gzread(file, ptr, len);
    
    if (ret < 0) {
        int errnum = 0;
        const char *msg = gzerror(file, &errnum);
        fprintf(stderr, "gzread error: %s\n",
                Z_ERRNO == errnum ? strerror(errno) : msg);
    }
    return ret;
}

int bamlite_gzclose(gzFile file) {
    int ret = gzclose(file);
    if (Z_OK != ret) {
        fprintf(stderr, "gzclose error: %s\n",
                          Z_ERRNO == ret ? strerror(errno) : zError(ret));
    }
    
    return ret;
}
#endif /* USE_VERBOSE_ZLIB_WRAPPERS */