sam.c

   1 #include <string.h>
   2 #include "sam.h"
   3
   4 #define TYPE_BAM  1
   5 #define TYPE_READ 2
   6
   7 bam_header_t *bam_header_dup(const bam_header_t *h0)
   8 {
   9         bam_header_t *h;
  10         int i;
  11         h = bam_header_init();
  12         *h = *h0;
  13         h->hash = 0;
  14         h->text = (char*)calloc(h->l_text + 1, 1);
  15         memcpy(h->text, h0->text, h->l_text);
  16         h->target_len = (uint32_t*)calloc(h->n_targets, 4);
  17         h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
  18         for (i = 0; i < h->n_targets; ++i) {
  19                 h->target_len[i] = h0->target_len[i];
  20                 h->target_name[i] = strdup(h0->target_name[i]);
  21         }
  22         if (h0->rg2lib) h->rg2lib = bam_strmap_dup(h0->rg2lib);
  23         return h;
  24 }
  25
  26 samfile_t *samopen(const char *fn, const char *mode, const void *aux)
  27 {
  28         samfile_t *fp;
  29         fp = (samfile_t*)calloc(1, sizeof(samfile_t));
  30         if (mode[0] == 'r') { // read
  31                 fp->type |= TYPE_READ;
  32                 if (mode[1] == 'b') { // binary
  33                         fp->type |= TYPE_BAM;
  34                         fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
  35                         if (fp->x.bam == 0) goto open_err_ret;
  36                         fp->header = bam_header_read(fp->x.bam);
  37                 } else { // text
  38                         fp->x.tamr = sam_open(fn);
  39                         if (fp->x.tamr == 0) goto open_err_ret;
  40                         fp->header = sam_header_read(fp->x.tamr);
  41                         if (fp->header->n_targets == 0) { // no @SQ fields
  42                                 if (aux) { // check if aux is present
  43                                         bam_header_destroy(fp->header);
  44                                         fp->header = sam_header_read2((const char*)aux);
  45                                 }
  46                                 if (fp->header->n_targets == 0)
  47                                         fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
  48                         } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
  49                 }
  50                 sam_header_parse_rg(fp->header);
  51         } else if (mode[0] == 'w') { // write
  52                 fp->header = bam_header_dup((const bam_header_t*)aux);
  53                 if (mode[1] == 'b') { // binary
  54                         char bmode[3];
  55                         bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
  56                         fp->type |= TYPE_BAM;
  57                         fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
  58                         if (fp->x.bam == 0) goto open_err_ret;
  59                         bam_header_write(fp->x.bam, fp->header);
  60                 } else { // text
  61                         // open file
  62                         fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
  63                         if (fp->x.tamr == 0) goto open_err_ret;
  64                         // write header
  65                         if (strstr(mode, "h")) {
  66                                 int i;
  67                                 bam_header_t *alt;
  68                                 // parse the header text
  69                                 alt = bam_header_init();
  70                                 alt->l_text = fp->header->l_text; alt->text = fp->header->text;
  71                                 sam_header_parse(alt);
  72                                 alt->l_text = 0; alt->text = 0;
  73                                 // check if there are @SQ lines in the header
  74                                 fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
  75                                 if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
  76                                         if (alt->n_targets != fp->header->n_targets)
  77                                                 fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
  78                                 } else { // then dump ->target_{name,len}
  79                                         for (i = 0; i < fp->header->n_targets; ++i)
  80                                                 fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
  81                                 }
  82                                 bam_header_destroy(alt);
  83                         }
  84                 }
  85         }
  86         return fp;
  87
  88 open_err_ret:
  89         free(fp);
  90         return 0;
  91 }
  92
  93 void samclose(samfile_t *fp)
  94 {
  95         if (fp == 0) return;
  96         if (fp->header) bam_header_destroy(fp->header);
  97         if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
  98         else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
  99         else fclose(fp->x.tamw);
 100         free(fp);
 101 }
 102
 103 int samread(samfile_t *fp, bam1_t *b)
 104 {
 105         if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
 106         if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
 107         else return sam_read1(fp->x.tamr, fp->header, b);
 108 }
 109
 110 int samwrite(samfile_t *fp, const bam1_t *b)
 111 {
 112         if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
 113         if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
 114         else {
 115                 char *s = bam_format1(fp->header, b);
 116                 int l = strlen(s);
 117                 fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
 118                 free(s);
 119                 return l + 1;
 120         }
 121 }
 122
 123 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
 124 {
 125         bam_plbuf_t *buf;
 126         int ret;
 127         bam1_t *b;
 128         b = bam_init1();
 129         buf = bam_plbuf_init(func, func_data);
 130         bam_plbuf_set_mask(buf, mask);
 131         while ((ret = samread(fp, b)) >= 0)
 132                 bam_plbuf_push(b, buf);
 133         bam_plbuf_push(0, buf);
 134         bam_plbuf_destroy(buf);
 135         bam_destroy1(b);
 136         return 0;
 137 }