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; }