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