main.c

   1 #include <string.h>
   2 #include <unistd.h>
   3 #include <stdlib.h>
   4 #include <stdio.h>
   5 #include <sys/stat.h>
   6 #include "bgzf.h"
   7 #include "tabix.h"
   8
   9 #define PACKAGE_VERSION "0.1.5 (r560)"
  10
  11 static int fetch_func(int l, const char *s, void *data)
  12 {
  13         printf("%s\n", s);
  14         return 0;
  15 }
  16
  17 int main(int argc, char *argv[])
  18 {
  19         int c, skip = -1, meta = -1, list_chrms = 0, force = 0;
  20         ti_conf_t conf = ti_conf_gff;
  21         while ((c = getopt(argc, argv, "p:s:b:e:0S:c:lf")) >= 0) {
  22                 switch (c) {
  23                 case '0': conf.preset |= TI_FLAG_UCSC; break;
  24                 case 'S': skip = atoi(optarg); break;
  25                 case 'c': meta = optarg[0]; break;
  26                 case 'p':
  27                         if (strcmp(optarg, "gff") == 0) conf = ti_conf_gff;
  28                         else if (strcmp(optarg, "bed") == 0) conf = ti_conf_bed;
  29                         else if (strcmp(optarg, "sam") == 0) conf = ti_conf_sam;
  30                         else if (strcmp(optarg, "vcf") == 0) conf = ti_conf_vcf;
  31                         else if (strcmp(optarg, "psltbl") == 0) conf = ti_conf_psltbl;
  32                         else {
  33                                 fprintf(stderr, "[main] unrecognized preset '%s'\n", optarg);
  34                                 return 1;
  35                         }
  36                         break;
  37                 case 's': conf.sc = atoi(optarg); break;
  38                 case 'b': conf.bc = atoi(optarg); break;
  39                 case 'e': conf.ec = atoi(optarg); break;
  40         case 'l': list_chrms = 1; break;
  41                 case 'f': force = 1; break;
  42                 }
  43         }
  44         if (skip >= 0) conf.line_skip = skip;
  45         if (meta >= 0) conf.meta_char = meta;
  46         if (optind == argc) {
  47                 fprintf(stderr, "\n");
  48                 fprintf(stderr, "Program: tabix (TAB-delimited file InderXer)\n");
  49                 fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
  50                 fprintf(stderr, "Usage:   tabix <in.tab.bgz> [region1 [region2 [...]]]\n\n");
  51                 fprintf(stderr, "Options: -p STR     preset: gff, bed, sam, vcf, psltbl [gff]\n");
  52                 fprintf(stderr, "         -s INT     sequence name column [1]\n");
  53                 fprintf(stderr, "         -b INT     start column [4]\n");
  54                 fprintf(stderr, "         -e INT     end column [5]\n");
  55                 fprintf(stderr, "         -S INT     skip first INT lines [0]\n");
  56                 fprintf(stderr, "         -c CHAR    symbol for comment/meta lines [#]\n");
  57                 fprintf(stderr, "         -0         zero-based coordinate\n");
  58                 fprintf(stderr, "         -l         list chromosome names\n");
  59                 fprintf(stderr, "         -f         force to overwrite the index\n");
  60                 fprintf(stderr, "\n");
  61                 return 1;
  62         }
  63     if (list_chrms)
  64         return ti_list_chromosomes(argv[optind]);
  65         if (optind + 1 == argc) {
  66                 if (force == 0) {
  67                         struct stat buf;
  68                         char *fnidx = calloc(strlen(argv[optind]) + 5, 1);
  69                         strcat(strcpy(fnidx, argv[optind]), ".tbi");
  70                         if (stat(fnidx, &buf) == 0) {
  71                                 fprintf(stderr, "[tabix] the index file exists. Please use '-f' to overwrite.\n");
  72                                 free(fnidx);
  73                                 return 1;
  74                         }
  75                         free(fnidx);
  76                 }
  77                 return ti_index_build(argv[optind], &conf);
  78         }
  79         { // retrieve
  80                 BGZF *fp;
  81                 fp = bgzf_open(argv[optind], "r");
  82                 if (fp == 0) {
  83                         fprintf(stderr, "[main] fail to open the data file.\n");
  84                         return 1;
  85                 }
  86                 if (strcmp(argv[optind+1], ".") == 0) { // retrieve all
  87                         kstring_t *str = calloc(1, sizeof(kstring_t));
  88                         while (ti_readline(fp, str) >= 0) { // FIXME: check return code for error
  89                                 fputs(str->s, stdout); fputc('\n', stdout);
  90                         }
  91                         free(str->s); free(str);
  92                 } else { // retrieve from specified regions
  93                         ti_index_t *idx;
  94                         int i;
  95                         idx = ti_index_load(argv[optind]);
  96                         if (idx == 0) {
  97                                 bgzf_close(fp);
  98                                 fprintf(stderr, "[main] fail to load the index.\n");
  99                                 return 1;
 100                         }
 101                         for (i = optind + 1; i < argc; ++i) {
 102                                 int tid, beg, end;
 103                                 if (ti_parse_region(idx, argv[i], &tid, &beg, &end) == 0) {
 104                                         ti_fetch(fp, idx, tid, beg, end, 0, fetch_func);
 105                                 } else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n");
 106                         }
 107                         ti_index_destroy(idx);
 108                 }
 109                 bgzf_close(fp);
 110         }
 111         return 0;
 112 }