+++ /dev/null
-#include <string.h>
-#include <unistd.h>
-#include "faidx.h"
-#include "sam.h"
-
-#define TYPE_BAM 1
-#define TYPE_READ 2
-
-bam_header_t *bam_header_dup(const bam_header_t *h0)
-{
- bam_header_t *h;
- int i;
- h = bam_header_init();
- *h = *h0;
- h->hash = h->dict = h->rg2lib = 0;
- h->text = (char*)calloc(h->l_text + 1, 1);
- memcpy(h->text, h0->text, h->l_text);
- h->target_len = (uint32_t*)calloc(h->n_targets, 4);
- h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
- for (i = 0; i < h->n_targets; ++i) {
- h->target_len[i] = h0->target_len[i];
- h->target_name[i] = strdup(h0->target_name[i]);
- }
- return h;
-}
-static void append_header_text(bam_header_t *header, char* text, int len)
-{
- int x = header->l_text + 1;
- int y = header->l_text + len + 1; // 1 byte null
- if (text == 0) return;
- kroundup32(x);
- kroundup32(y);
- if (x < y) header->text = (char*)realloc(header->text, y);
- strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
- header->l_text += len;
- header->text[header->l_text] = 0;
-}
-
-samfile_t *samopen(const char *fn, const char *mode, const void *aux)
-{
- samfile_t *fp;
- fp = (samfile_t*)calloc(1, sizeof(samfile_t));
- if (mode[0] == 'r') { // read
- fp->type |= TYPE_READ;
- if (mode[1] == 'b') { // binary
- fp->type |= TYPE_BAM;
- fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
- if (fp->x.bam == 0) goto open_err_ret;
- fp->header = bam_header_read(fp->x.bam);
- } else { // text
- fp->x.tamr = sam_open(fn);
- if (fp->x.tamr == 0) goto open_err_ret;
- fp->header = sam_header_read(fp->x.tamr);
- if (fp->header->n_targets == 0) { // no @SQ fields
- if (aux) { // check if aux is present
- bam_header_t *textheader = fp->header;
- fp->header = sam_header_read2((const char*)aux);
- if (fp->header == 0) goto open_err_ret;
- append_header_text(fp->header, textheader->text, textheader->l_text);
- bam_header_destroy(textheader);
- }
- if (fp->header->n_targets == 0)
- fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
- } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
- }
- } else if (mode[0] == 'w') { // write
- fp->header = bam_header_dup((const bam_header_t*)aux);
- if (mode[1] == 'b') { // binary
- char bmode[3];
- bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
- fp->type |= TYPE_BAM;
- fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
- if (fp->x.bam == 0) goto open_err_ret;
- bam_header_write(fp->x.bam, fp->header);
- } else { // text
- // open file
- fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
- if (fp->x.tamr == 0) goto open_err_ret;
- if (strstr(mode, "X")) fp->type |= BAM_OFSTR<<2;
- else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
- else fp->type |= BAM_OFDEC<<2;
- // write header
- if (strstr(mode, "h")) {
- int i;
- bam_header_t *alt;
- // parse the header text
- alt = bam_header_init();
- alt->l_text = fp->header->l_text; alt->text = fp->header->text;
- sam_header_parse(alt);
- alt->l_text = 0; alt->text = 0;
- // check if there are @SQ lines in the header
- fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
- if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
- if (alt->n_targets != fp->header->n_targets)
- fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
- } else { // then dump ->target_{name,len}
- for (i = 0; i < fp->header->n_targets; ++i)
- fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
- }
- bam_header_destroy(alt);
- }
- }
- }
- return fp;
-
-open_err_ret:
- free(fp);
- return 0;
-}
-
-void samclose(samfile_t *fp)
-{
- if (fp == 0) return;
- if (fp->header) bam_header_destroy(fp->header);
- if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
- else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
- else fclose(fp->x.tamw);
- free(fp);
-}
-
-int samread(samfile_t *fp, bam1_t *b)
-{
- if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
- if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
- else return sam_read1(fp->x.tamr, fp->header, b);
-}
-
-int samwrite(samfile_t *fp, const bam1_t *b)
-{
- if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
- if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
- else {
- char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
- int l = strlen(s);
- fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
- free(s);
- return l + 1;
- }
-}
-
-int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
-{
- bam_plbuf_t *buf;
- int ret;
- bam1_t *b;
- b = bam_init1();
- buf = bam_plbuf_init(func, func_data);
- bam_plbuf_set_mask(buf, mask);
- while ((ret = samread(fp, b)) >= 0)
- bam_plbuf_push(b, buf);
- bam_plbuf_push(0, buf);
- bam_plbuf_destroy(buf);
- bam_destroy1(b);
- return 0;
-}
-
-char *samfaipath(const char *fn_ref)
-{
- char *fn_list = 0;
- if (fn_ref == 0) return 0;
- fn_list = calloc(strlen(fn_ref) + 5, 1);
- strcat(strcpy(fn_list, fn_ref), ".fai");
- if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
- if (access(fn_ref, R_OK) == -1) {
- fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
- } else {
- fprintf(stderr, "[samfaipath] build FASTA index...\n");
- if (fai_build(fn_ref) == -1) {
- fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
- free(fn_list); fn_list = 0;
- }
- }
- }
- return fn_list;
-}
projects / pysam.git / blobdiff