+++ /dev/null
-#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;
-char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
-
-/**************************
- * CIGAR related routines *
- **************************/
-
-uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
-{
- uint32_t k, end;
- end = c->pos;
- for (k = 0; k < c->n_cigar; ++k) {
- int op = cigar[k] & BAM_CIGAR_MASK;
- if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
- end += cigar[k] >> BAM_CIGAR_SHIFT;
- }
- return end;
-}
-
-int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
-{
- uint32_t k;
- int32_t l = 0;
- for (k = 0; k < c->n_cigar; ++k) {
- int op = cigar[k] & BAM_CIGAR_MASK;
- if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP)
- l += cigar[k] >> BAM_CIGAR_SHIFT;
- }
- return l;
-}
-
-/********************
- * BAM I/O routines *
- ********************/
-
-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;
- 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, 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.\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, name_len, 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; }
- }
-}
-
-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;
-}
-
-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 { kputs(header->target_name[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 {
- for (i = 0; i < c->n_cigar; ++i) {
- kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
- kputc("MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
- }
- }
- kputc('\t', &str);
- if (c->mtid < 0) kputsn("*\t", 2, &str);
- else if (c->mtid == c->tid) kputsn("=\t", 2, &str);
- else { kputs(header->target_name[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_table[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, 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; }
- }
- 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);
-}
-
-// 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));
-}
projects / pysam.git / blobdiff