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         if (text == 0) return;
  30         kroundup32(x);
  31         kroundup32(y);
  32         if (x < y) header->text = (char*)realloc(header->text, y);
  33         strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
  34         header->l_text += len;
  35         header->text[header->l_text] = 0;
  36 }
  37
  38 samfile_t *samopen(const char *fn, const char *mode, const void *aux)
  39 {
  40         samfile_t *fp;
  41         fp = (samfile_t*)calloc(1, sizeof(samfile_t));
  42         if (mode[0] == 'r') { // read
  43                 fp->type |= TYPE_READ;
  44                 if (mode[1] == 'b') { // binary
  45                         fp->type |= TYPE_BAM;
  46                         fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
  47                         if (fp->x.bam == 0) goto open_err_ret;
  48                         fp->header = bam_header_read(fp->x.bam);
  49                 } else { // text
  50                         fp->x.tamr = sam_open(fn);
  51                         if (fp->x.tamr == 0) goto open_err_ret;
  52                         fp->header = sam_header_read(fp->x.tamr);
  53                         if (fp->header->n_targets == 0) { // no @SQ fields
  54                                 if (aux) { // check if aux is present
  55                                         bam_header_t *textheader = fp->header;
  56                                         fp->header = sam_header_read2((const char*)aux);
  57                                         append_header_text(fp->header, textheader->text, textheader->l_text);
  58                                         bam_header_destroy(textheader);
  59                                 }
  60                                 if (fp->header->n_targets == 0)
  61                                         fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
  62                         } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
  63                 }
  64                 sam_header_parse_rg(fp->header);
  65         } else if (mode[0] == 'w') { // write
  66                 fp->header = bam_header_dup((const bam_header_t*)aux);
  67                 if (mode[1] == 'b') { // binary
  68                         char bmode[3];
  69                         bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
  70                         fp->type |= TYPE_BAM;
  71                         fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
  72                         if (fp->x.bam == 0) goto open_err_ret;
  73                         bam_header_write(fp->x.bam, fp->header);
  74                 } else { // text
  75                         // open file
  76                         fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
  77                         if (fp->x.tamr == 0) goto open_err_ret;
  78                         if (strstr(mode, "X")) fp->type |= BAM_OFSTR<<2;
  79                         else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
  80                         else fp->type |= BAM_OFDEC<<2;
  81                         // write header
  82                         if (strstr(mode, "h")) {
  83                                 int i;
  84                                 bam_header_t *alt;
  85                                 // parse the header text
  86                                 alt = bam_header_init();
  87                                 alt->l_text = fp->header->l_text; alt->text = fp->header->text;
  88                                 sam_header_parse(alt);
  89                                 alt->l_text = 0; alt->text = 0;
  90                                 // check if there are @SQ lines in the header
  91                                 fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
  92                                 if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
  93                                         if (alt->n_targets != fp->header->n_targets)
  94                                                 fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
  95                                 } else { // then dump ->target_{name,len}
  96                                         for (i = 0; i < fp->header->n_targets; ++i)
  97                                                 fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
  98                                 }
  99                                 bam_header_destroy(alt);
 100                         }
 101                 }
 102         }
 103         return fp;
 104
 105 open_err_ret:
 106         free(fp);
 107         return 0;
 108 }
 109
 110 void samclose(samfile_t *fp)
 111 {
 112         if (fp == 0) return;
 113         if (fp->header) bam_header_destroy(fp->header);
 114         if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
 115         else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
 116         else fclose(fp->x.tamw);
 117         free(fp);
 118 }
 119
 120 int samread(samfile_t *fp, bam1_t *b)
 121 {
 122         if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
 123         if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
 124         else return sam_read1(fp->x.tamr, fp->header, b);
 125 }
 126
 127 int samwrite(samfile_t *fp, const bam1_t *b)
 128 {
 129         if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
 130         if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
 131         else {
 132                 char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
 133                 int l = strlen(s);
 134                 fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
 135                 free(s);
 136                 return l + 1;
 137         }
 138 }
 139
 140 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
 141 {
 142         bam_plbuf_t *buf;
 143         int ret;
 144         bam1_t *b;
 145         b = bam_init1();
 146         buf = bam_plbuf_init(func, func_data);
 147         bam_plbuf_set_mask(buf, mask);
 148         while ((ret = samread(fp, b)) >= 0)
 149                 bam_plbuf_push(b, buf);
 150         bam_plbuf_push(0, buf);
 151         bam_plbuf_destroy(buf);
 152         bam_destroy1(b);
 153         return 0;
 154 }