main.c

   1 #include <string.h>
   2 #include <unistd.h>
   3 #include <stdlib.h>
   4 #include <stdio.h>
   5 #include "bgzf.h"
   6 #include "tabix.h"
   7
   8 #define PACKAGE_VERSION "0.1.2 (r543)"
   9
  10 static int fetch_func(int l, const char *s, void *data)
  11 {
  12         printf("%s\n", s);
  13         return 0;
  14 }
  15
  16 int main(int argc, char *argv[])
  17 {
  18         int c, skip = -1, meta = -1;
  19         ti_conf_t conf = ti_conf_gff;
  20         while ((c = getopt(argc, argv, "p:s:b:e:0S:c:")) >= 0) {
  21                 switch (c) {
  22                 case '0': conf.preset |= TI_FLAG_UCSC; break;
  23                 case 'S': skip = atoi(optarg); break;
  24                 case 'c': meta = optarg[0]; break;
  25                 case 'p':
  26                         if (strcmp(optarg, "gff") == 0) conf = ti_conf_gff;
  27                         else if (strcmp(optarg, "bed") == 0) conf = ti_conf_bed;
  28                         else if (strcmp(optarg, "sam") == 0) conf = ti_conf_sam;
  29                         else if (strcmp(optarg, "vcf") == 0) conf = ti_conf_vcf;
  30                         else if (strcmp(optarg, "psltbl") == 0) conf = ti_conf_psltbl;
  31                         else {
  32                                 fprintf(stderr, "[main] unrecognized preset '%s'\n", optarg);
  33                                 return 1;
  34                         }
  35                         break;
  36                 case 's': conf.sc = atoi(optarg); break;
  37                 case 'b': conf.bc = atoi(optarg); break;
  38                 case 'e': conf.ec = atoi(optarg); break;
  39                 }
  40         }
  41         if (skip >= 0) conf.line_skip = skip;
  42         if (meta >= 0) conf.meta_char = meta;
  43         if (optind == argc) {
  44                 fprintf(stderr, "\n");
  45                 fprintf(stderr, "Program: tabix (TAB-delimited file InderXer)\n");
  46                 fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
  47                 fprintf(stderr, "Usage:   tabix <in.tab.bgz> [region1 [region2 [...]]]\n\n");
  48                 fprintf(stderr, "Options: -p STR     preset: gff, bed, sam, vcf, psltbl [gff]\n");
  49                 fprintf(stderr, "         -s INT     sequence name column [1]\n");
  50                 fprintf(stderr, "         -b INT     start column [4]\n");
  51                 fprintf(stderr, "         -e INT     end column [5]\n");
  52                 fprintf(stderr, "         -S INT     skip first INT lines [0]\n");
  53                 fprintf(stderr, "         -c CHAR    symbol for comment/meta lines [#]\n");
  54                 fprintf(stderr, "         -0         zero-based coordinate\n");
  55                 fprintf(stderr, "\n");
  56                 return 1;
  57         }
  58         if (optind + 1 == argc)
  59                 return ti_index_build(argv[optind], &conf);
  60         { // retrieve
  61                 BGZF *fp;
  62                 fp = bgzf_open(argv[optind], "r");
  63                 if (fp == 0) {
  64                         fprintf(stderr, "[main] fail to open the data file.\n");
  65                         return 1;
  66                 }
  67                 if (strcmp(argv[optind+1], ".") == 0) { // retrieve all
  68                         kstring_t *str = calloc(1, sizeof(kstring_t));
  69                         while (ti_readline(fp, str) >= 0) { // FIXME: check return code for error
  70                                 fputs(str->s, stdout); fputc('\n', stdout);
  71                         }
  72                         free(str->s); free(str);
  73                 } else { // retrieve from specified regions
  74                         ti_index_t *idx;
  75                         int i;
  76                         idx = ti_index_load(argv[optind]);
  77                         if (idx == 0) {
  78                                 bgzf_close(fp);
  79                                 fprintf(stderr, "[main] fail to load the index.\n");
  80                                 return 1;
  81                         }
  82                         for (i = optind + 1; i < argc; ++i) {
  83                                 int tid, beg, end;
  84                                 if (ti_parse_region(idx, argv[i], &tid, &beg, &end) == 0) {
  85                                         fprintf(stderr, "%d,%d\n", beg, end);
  86                                         ti_fetch(fp, idx, tid, beg, end, 0, fetch_func);
  87                                 } else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n");
  88                         }
  89                         ti_index_destroy(idx);
  90                 }
  91                 bgzf_close(fp);
  92         }
  93         return 0;
  94 }