c_cpp/lib/htslib/test/test-regidx.c

   1 /*  test/test-regidx.c -- Regions index test harness.
   2
   3     Copyright (C) 2014 Genome Research Ltd.
   4
   5     Author: Petr Danecek <pd3@sanger.ac.uk>
   6
   7     Permission is hereby granted, free of charge, to any person obtaining a copy
   8     of this software and associated documentation files (the "Software"), to deal
   9     in the Software without restriction, including without limitation the rights
  10     to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  11     copies of the Software, and to permit persons to whom the Software is
  12     furnished to do so, subject to the following conditions:
  13
  14     The above copyright notice and this permission notice shall be included in
  15     all copies or substantial portions of the Software.
  16
  17     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  18     IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  19     FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  20     AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  21     LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  22     OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  23     THE SOFTWARE.
  24 */
  25
  26 #include <config.h>
  27
  28 #include <stdarg.h>
  29 #include <stdlib.h>
  30 #include <stdio.h>
  31 #include <string.h>
  32 #include <htslib/regidx.h>
  33 #include "hts_internal.h"
  34
  35 void error(const char *format, ...)
  36 {
  37     va_list ap;
  38     va_start(ap, format);
  39     vfprintf(stderr, format, ap);
  40     va_end(ap);
  41     exit(-1);
  42 }
  43
  44 int custom_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr)
  45 {
  46     // Use the standard parser for CHROM,FROM,TO
  47     int i, ret = regidx_parse_tab(line,chr_beg,chr_end,reg,NULL,NULL);
  48     if ( ret!=0 ) return ret;
  49
  50     // Skip the fields that were parsed above
  51     char *ss = (char*) line;
  52     while ( *ss && isspace_c(*ss) ) ss++;
  53     for (i=0; i<3; i++)
  54     {
  55         while ( *ss && !isspace_c(*ss) ) ss++;
  56         if ( !*ss ) return -2;  // wrong number of fields
  57         while ( *ss && isspace_c(*ss) ) ss++;
  58     }
  59     if ( !*ss ) return -2;
  60
  61     // Parse the payload
  62     char *se = ss;
  63     while ( *se && !isspace_c(*se) ) se++;
  64     char **dat = (char**) payload;
  65     *dat = (char*) malloc(se-ss+1);
  66     memcpy(*dat,ss,se-ss+1);
  67     (*dat)[se-ss] = 0;
  68     return 0;
  69 }
  70 void custom_free(void *payload)
  71 {
  72     char **dat = (char**)payload;
  73     free(*dat);
  74 }
  75
  76 int main(int argc, char **argv)
  77 {
  78     // Init index with no file name, we will insert the regions manually
  79     regidx_t *idx = regidx_init(NULL,custom_parse,custom_free,sizeof(char*),NULL);
  80     if ( !idx ) error("init failed\n");
  81
  82     // Insert regions
  83     char *line;
  84     line = "1 10000000 10000000 1:10000000-10000000"; if ( regidx_insert(idx,line)!=0 ) error("insert failed: %s\n", line);
  85     line = "1 20000000 20000001 1:20000000-20000001"; if ( regidx_insert(idx,line)!=0 ) error("insert failed: %s\n", line);
  86     line = "1 20000002 20000002 1:20000002-20000002"; if ( regidx_insert(idx,line)!=0 ) error("insert failed: %s\n", line);
  87     line = "1 30000000 30000000 1:30000000-30000000"; if ( regidx_insert(idx,line)!=0 ) error("insert failed: %s\n", line);
  88
  89     // Finish initialization
  90     regidx_insert(idx,NULL);
  91
  92     // Test
  93     regitr_t itr;
  94     int from, to;
  95
  96     from = to = 10000000;
  97     if ( !regidx_overlap(idx,"1",from-1,to-1,&itr) ) error("query failed: 1:%d-%d\n",from,to);
  98     if ( strcmp("1:10000000-10000000",REGITR_PAYLOAD(itr,char*)) ) error("query failed: 1:%d-%d vs %s\n", from,to,REGITR_PAYLOAD(itr,char*));
  99     if ( !regidx_overlap(idx,"1",from-2,to-1,&itr) ) error("query failed: 1:%d-%d\n",from-1,to);
 100     if ( !regidx_overlap(idx,"1",from-2,to+3,&itr) ) error("query failed: 1:%d-%d\n",from-1,to+2);
 101     if ( regidx_overlap(idx,"1",from-2,to-2,&itr) ) error("query failed: 1:%d-%d\n",from-1,to-1);
 102
 103     from = to = 20000000;
 104     if ( !regidx_overlap(idx,"1",from-1,to-1,&itr) ) error("query failed: 1:%d-%d\n",from,to);
 105
 106     from = to = 20000002;
 107     if ( !regidx_overlap(idx,"1",from-1,to-1,&itr) ) error("query failed: 1:%d-%d\n",from,to);
 108
 109     from = to = 30000000;
 110     if ( !regidx_overlap(idx,"1",from-1,to-1,&itr) ) error("query failed: 1:%d-%d\n",from,to);
 111
 112     // Clean up
 113     regidx_destroy(idx);
 114
 115     return 0;
 116 }
 117
 118