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