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;
}
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;
}
void _check_is_bam(const char *filename)
{
int magic_len;
char buf[4];
bamFile bfile = bam_open(filename, "r");
if (bfile == 0)
Rf_error("failed to open SAM/BAM file\n file: '%s'", filename);
magic_len = bam_read(bfile, buf, 4);
bam_close(bfile);
if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0)
Rf_error("'filename' is not a BAM file\n file: %s", filename);
}
SEXP bamfile_isincomplete(SEXP ext)
{
int ans = FALSE;
BAM_FILE bfile;
if (NULL != BAMFILE(ext)) {
_checkext(ext, BAMFILE_TAG, "isIncomplete");
bfile = BAMFILE(ext);
if (NULL != bfile && NULL != bfile->file) {
/* heuristic: can we read a record? bam_seek does not
* support SEEK_END */
off_t offset = bam_tell(bfile->file->x.bam);
char buf;
ans = bam_read(bfile->file->x.bam, &buf, 1) > 0;
bam_seek(bfile->file->x.bam, offset, SEEK_SET);
}
}
return ScalarLogical(ans);
}
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;
}
