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_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);
return 4 + block_len;
}
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);
}
}
}
bam_header_t *bam_header_read(bamFile fp)
{
bam_header_t *header;
char buf[4];
int32_t i, name_len;
// read "BAM1"
if (bam_read(fp, buf, 4) != 4) return 0;
if (strncmp(buf, "BAM\001", 4)) {
fprintf(stderr, "[bam_header_read] wrong header\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;
}
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; }
}
}
bam_header_t *bam_header_read(bamFile fp)
{
bam_header_t *header;
char buf[4];
int magic_len;
int32_t i = 1, 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]);
}
bam_init_header_hash(header);
return header;
}
