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 static void append_header_text(bam_header_t *header, char* text, int len)
  26 {
  27         int x = header->l_text + 1;
  28         int y = header->l_text + len + 1; // 1 byte null
  29         kroundup32(x);
  30         kroundup32(y);
  31         if (x < y) header->text = (char*)realloc(header->text, y);
  32         strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
  33         header->l_text += len;
  34         header->text[header->l_text] = 0;
  35 }
  36
  37 samfile_t *samopen(const char *fn, const char *mode, const void *aux)
  38 {
  39         samfile_t *fp;
  40         fp = (samfile_t*)calloc(1, sizeof(samfile_t));
  41         if (mode[0] == 'r') { // read
  42                 fp->type |= TYPE_READ;
  43                 if (mode[1] == 'b') { // binary
  44                         fp->type |= TYPE_BAM;
  45                         fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
  46                         if (fp->x.bam == 0) goto open_err_ret;
  47                         fp->header = bam_header_read(fp->x.bam);
  48                 } else { // text
  49                         fp->x.tamr = sam_open(fn);
  50                         if (fp->x.tamr == 0) goto open_err_ret;
  51                         fp->header = sam_header_read(fp->x.tamr);
  52                         if (fp->header->n_targets == 0) { // no @SQ fields
  53                                 if (aux) { // check if aux is present
  54                                         bam_header_t *textheader = fp->header;
  55                                         fp->header = sam_header_read2((const char*)aux);
  56                                         append_header_text(fp->header, textheader->text, textheader->l_text);
  57                                         bam_header_destroy(textheader);
  58                                 }
  59                                 if (fp->header->n_targets == 0)
  60                                         fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
  61                         } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
  62                 }
  63                 sam_header_parse_rg(fp->header);
  64         } else if (mode[0] == 'w') { // write
  65                 fp->header = bam_header_dup((const bam_header_t*)aux);
  66                 if (mode[1] == 'b') { // binary
  67                         char bmode[3];
  68                         bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
  69                         fp->type |= TYPE_BAM;
  70                         fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
  71                         if (fp->x.bam == 0) goto open_err_ret;
  72                         bam_header_write(fp->x.bam, fp->header);
  73                 } else { // text
  74                         // open file
  75                         fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
  76                         if (fp->x.tamr == 0) goto open_err_ret;
  77                         // write header
  78                         if (strstr(mode, "h")) {
  79                                 int i;
  80                                 bam_header_t *alt;
  81                                 // parse the header text
  82                                 alt = bam_header_init();
  83                                 alt->l_text = fp->header->l_text; alt->text = fp->header->text;
  84                                 sam_header_parse(alt);
  85                                 alt->l_text = 0; alt->text = 0;
  86                                 // check if there are @SQ lines in the header
  87                                 fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
  88                                 if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
  89                                         if (alt->n_targets != fp->header->n_targets)
  90                                                 fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
  91                                 } else { // then dump ->target_{name,len}
  92                                         for (i = 0; i < fp->header->n_targets; ++i)
  93                                                 fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
  94                                 }
  95                                 bam_header_destroy(alt);
  96                         }
  97                 }
  98         }
  99         return fp;
 100
 101 open_err_ret:
 102         free(fp);
 103         return 0;
 104 }
 105
 106 void samclose(samfile_t *fp)
 107 {
 108         if (fp == 0) return;
 109         if (fp->header) bam_header_destroy(fp->header);
 110         if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
 111         else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
 112         else fclose(fp->x.tamw);
 113         free(fp);
 114 }
 115
 116 int samread(samfile_t *fp, bam1_t *b)
 117 {
 118         if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
 119         if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
 120         else return sam_read1(fp->x.tamr, fp->header, b);
 121 }
 122
 123 int samwrite(samfile_t *fp, const bam1_t *b)
 124 {
 125         if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
 126         if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
 127         else {
 128                 char *s = bam_format1(fp->header, b);
 129                 int l = strlen(s);
 130                 fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
 131                 free(s);
 132                 return l + 1;
 133         }
 134 }
 135
 136 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
 137 {
 138         bam_plbuf_t *buf;
 139         int ret;
 140         bam1_t *b;
 141         b = bam_init1();
 142         buf = bam_plbuf_init(func, func_data);
 143         bam_plbuf_set_mask(buf, mask);
 144         while ((ret = samread(fp, b)) >= 0)
 145                 bam_plbuf_push(b, buf);
 146         bam_plbuf_push(0, buf);
 147         bam_plbuf_destroy(buf);
 148         bam_destroy1(b);
 149         return 0;
 150 }