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                         if (fp->x.bam == 0) goto open_err_ret;
  83                         fp->header = bam_header_read(fp->x.bam);
  84                 } else {
  85                         fp->x.tamr = sam_open(fn);
  86                         if (fp->x.tamr == 0) goto open_err_ret;
  87                         fp->header = sam_header_read2(fn_list);
  88                 }
  89         } else if (mode[0] == 'w') {
  90                 fp->header = bam_header_dup((const bam_header_t*)aux);
  91                 if (mode[1] == 'b') { // binary
  92                         fp->type |= TYPE_BAM;
  93                         fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w");
  94                         if (fp->x.bam == 0) goto open_err_ret;
  95                         bam_header_write(fp->x.bam, fp->header);
  96                 } else {
  97                         int i;
  98                         bam_header_t *alt = 0;
  99                         alt = bam_header_parse(fp->header->text);
 100                         fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
 101                         if (fp->x.tamr == 0) goto open_err_ret;
 102                         if (alt) {
 103                                 if (alt->n_targets != fp->header->n_targets)
 104                                         fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
 105                                 bam_header_destroy(alt);
 106                                 fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
 107                         }
 108                         if (strstr(mode, "h")) // print header
 109                                 for (i = 0; i < fp->header->n_targets; ++i)
 110                                         fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
 111                 }
 112         }
 113         return fp;
 114
 115 open_err_ret:
 116         free(fp);
 117         return 0;
 118 }
 119
 120 void samclose(samfile_t *fp)
 121 {
 122         if (fp == 0) return;
 123         if (fp->header) bam_header_destroy(fp->header);
 124         if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
 125         else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
 126         else fclose(fp->x.tamw);
 127         free(fp);
 128 }
 129
 130 int samread(samfile_t *fp, bam1_t *b)
 131 {
 132         if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
 133         if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
 134         else return sam_read1(fp->x.tamr, fp->header, b);
 135 }
 136
 137 int samwrite(samfile_t *fp, const bam1_t *b)
 138 {
 139         if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
 140         if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
 141         else {
 142                 char *s = bam_format1(fp->header, b);
 143                 int l = strlen(s);
 144                 fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
 145                 free(s);
 146                 return l + 1;
 147         }
 148 }
 149
 150 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
 151 {
 152         bam_plbuf_t *buf;
 153         int ret;
 154         bam1_t *b;
 155         b = bam_init1();
 156         buf = bam_plbuf_init(func, func_data);
 157         bam_plbuf_set_mask(buf, mask);
 158         while ((ret = samread(fp, b)) >= 0)
 159                 bam_plbuf_push(b, buf);
 160         bam_plbuf_push(0, buf);
 161         bam_plbuf_destroy(buf);
 162         bam_destroy1(b);
 163         return 0;
 164 }