X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fsam.c;fp=samtools%2Fsam.c;h=0000000000000000000000000000000000000000;hp=ecdee02dddb98a32d47a59e3154179356acecadf;hb=bd0c3067c187d1f718004fb38acc093af8810a02;hpb=1b740fc70684c92a5e2293013217d5a2fd661d8a diff --git a/samtools/sam.c b/samtools/sam.c deleted file mode 100644 index ecdee02..0000000 --- a/samtools/sam.c +++ /dev/null @@ -1,175 +0,0 @@ -#include -#include -#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; -}