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         return h;
  23 }
  24
  25 bam_header_t *bam_header_parse(const char *text)
  26 {
  27         bam_header_t *h;
  28         int i;
  29         char *s, *p, *q, *r;
  30
  31         i = strlen(text);
  32         if (i < 3) return 0; // headerless
  33         h = bam_header_init();
  34         h->l_text = i;
  35         h->text = strdup(text);
  36         s = h->text;
  37         while ((s = strstr(s, "@SQ")) != 0) {
  38                 ++h->n_targets;
  39                 s += 3;
  40         }
  41         h->target_len = (uint32_t*)calloc(h->n_targets, 4);
  42         h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
  43         i = 0;
  44         s = h->text;
  45         while ((s = strstr(s, "@SQ")) != 0) {
  46                 s += 3;
  47                 r = s;
  48                 if ((p = strstr(s, "SN:")) != 0) {
  49                         q = p + 3;
  50                         for (p = q; *p && *p != '\t'; ++p);
  51                         h->target_name[i] = (char*)calloc(p - q + 1, 1);
  52                         strncpy(h->target_name[i], q, p - q);
  53                 } else goto header_err_ret;
  54                 if (r < p) r = p;
  55                 if ((p = strstr(s, "LN:")) != 0) h->target_len[i] = strtol(p + 3, 0, 10);
  56                 else goto header_err_ret;
  57                 if (r < p) r = p;
  58                 s = r + 3;
  59                 ++i;
  60         }
  61         if (h->n_targets == 0) {
  62                 bam_header_destroy(h);
  63                 return 0;
  64         } else return h;
  65
  66 header_err_ret:
  67         fprintf(stderr, "[bam_header_parse] missing SN tag in a @SQ line.\n");
  68         bam_header_destroy(h);
  69         return 0;
  70 }
  71
  72 samfile_t *samopen(const char *fn, const char *mode, const void *aux)
  73 {
  74         samfile_t *fp;
  75         fp = (samfile_t*)calloc(1, sizeof(samfile_t));
  76         if (mode[0] == 'r') {
  77                 const char *fn_list = (const char*)aux;
  78                 fp->type |= TYPE_READ;
  79                 if (mode[1] == 'b') { // binary
  80                         fp->type |= TYPE_BAM;
  81                         fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
  82                         fp->header = bam_header_read(fp->x.bam);
  83                 } else {
  84                         fp->x.tamr = sam_open(fn);
  85                         fp->header = sam_header_read2(fn_list);
  86                 }
  87         } else if (mode[0] == 'w') {
  88                 fp->header = bam_header_dup((const bam_header_t*)aux);
  89                 if (mode[1] == 'b') { // binary
  90                         fp->type |= TYPE_BAM;
  91                         fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w");
  92                         bam_header_write(fp->x.bam, fp->header);
  93                 } else {
  94                         int i;
  95                         bam_header_t *alt = 0;
  96                         alt = bam_header_parse(fp->header->text);
  97                         fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
  98                         if (alt) {
  99                                 if (alt->n_targets != fp->header->n_targets)
 100                                         fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
 101                                 bam_header_destroy(alt);
 102                                 fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
 103                         }
 104                         if (strstr(mode, "h")) // print header
 105                                 for (i = 0; i < fp->header->n_targets; ++i)
 106                                         fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
 107                 }
 108         }
 109         return fp;
 110 }
 111
 112 void samclose(samfile_t *fp)
 113 {
 114         if (fp == 0) return;
 115         if (fp->header) bam_header_destroy(fp->header);
 116         if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
 117         else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
 118         else fclose(fp->x.tamw);
 119         free(fp);
 120 }
 121
 122 int samread(samfile_t *fp, bam1_t *b)
 123 {
 124         if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
 125         if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
 126         else return sam_read1(fp->x.tamr, fp->header, b);
 127 }
 128
 129 int samwrite(samfile_t *fp, const bam1_t *b)
 130 {
 131         if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
 132         if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
 133         else {
 134                 char *s = bam_format1(fp->header, b);
 135                 int l = strlen(s);
 136                 fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
 137                 free(s);
 138                 return l + 1;
 139         }
 140 }
 141
 142 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
 143 {
 144         bam_plbuf_t *buf;
 145         int ret;
 146         bam1_t *b;
 147         b = bam_init1();
 148         buf = bam_plbuf_init(func, func_data);
 149         bam_plbuf_set_mask(buf, mask);
 150         while ((ret = samread(fp, b)) >= 0)
 151                 bam_plbuf_push(b, buf);
 152         bam_plbuf_push(0, buf);
 153         bam_plbuf_destroy(buf);
 154         bam_destroy1(b);
 155         return 0;
 156 }