c_cpp/lib/htslib/test/test-bcf-sr.c

   1 /*
   2     Copyright (C) 2017 Genome Research Ltd.
   3
   4     Author: Petr Danecek <pd3@sanger.ac.uk>
   5
   6     Permission is hereby granted, free of charge, to any person obtaining a copy
   7     of this software and associated documentation files (the "Software"), to deal
   8     in the Software without restriction, including without limitation the rights
   9     to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  10     copies of the Software, and to permit persons to whom the Software is
  11     furnished to do so, subject to the following conditions:
  12
  13     The above copyright notice and this permission notice shall be included in
  14     all copies or substantial portions of the Software.
  15
  16     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  17     IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  18     FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  19     AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  20     LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  21     OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  22     THE SOFTWARE.
  23 */
  24
  25 /*
  26     Test bcf synced reader allele pairing
  27 */
  28
  29 #include <config.h>
  30
  31 #include <getopt.h>
  32 #include <stdio.h>
  33 #include <stdarg.h>
  34 #include <htslib/synced_bcf_reader.h>
  35
  36 void error(const char *format, ...)
  37 {
  38     va_list ap;
  39     va_start(ap, format);
  40     vfprintf(stderr, format, ap);
  41     va_end(ap);
  42     exit(-1);
  43 }
  44
  45 void usage(void)
  46 {
  47     fprintf(stderr, "Usage: test-bcf-sr [OPTIONS] vcf-list.txt\n");
  48     fprintf(stderr, "Options:\n");
  49     fprintf(stderr, "   -p, --pair <logic[+ref]>     logic: snps,indels,both,snps+ref,indels+ref,both+ref,exact,some,all\n");
  50     fprintf(stderr, "\n");
  51     exit(-1);
  52 }
  53
  54 int main(int argc, char *argv[])
  55 {
  56     static struct option loptions[] =
  57     {
  58         {"help",no_argument,NULL,'h'},
  59         {"pair",required_argument,NULL,'p'},
  60         {NULL,0,NULL,0}
  61     };
  62
  63     int c, pair = 0;
  64     while ((c = getopt_long(argc, argv, "p:h", loptions, NULL)) >= 0)
  65     {
  66         switch (c)
  67         {
  68             case 'p':
  69                 if ( !strcmp(optarg,"snps") )            pair |= BCF_SR_PAIR_SNPS;
  70                 else if ( !strcmp(optarg,"snp+ref") )    pair |= BCF_SR_PAIR_SNPS|BCF_SR_PAIR_SNP_REF;
  71                 else if ( !strcmp(optarg,"snps+ref") )   pair |= BCF_SR_PAIR_SNPS|BCF_SR_PAIR_SNP_REF;
  72                 else if ( !strcmp(optarg,"indels") )     pair |= BCF_SR_PAIR_INDELS;
  73                 else if ( !strcmp(optarg,"indel+ref") )  pair |= BCF_SR_PAIR_INDELS|BCF_SR_PAIR_INDEL_REF;
  74                 else if ( !strcmp(optarg,"indels+ref") ) pair |= BCF_SR_PAIR_INDELS|BCF_SR_PAIR_INDEL_REF;
  75                 else if ( !strcmp(optarg,"both") )       pair |= BCF_SR_PAIR_BOTH;
  76                 else if ( !strcmp(optarg,"both+ref") )   pair |= BCF_SR_PAIR_BOTH_REF;
  77                 else if ( !strcmp(optarg,"any") )        pair |= BCF_SR_PAIR_ANY;
  78                 else if ( !strcmp(optarg,"all") )        pair |= BCF_SR_PAIR_ANY;
  79                 else if ( !strcmp(optarg,"some") )       pair |= BCF_SR_PAIR_SOME;
  80                 else if ( !strcmp(optarg,"exact") )      pair  = BCF_SR_PAIR_EXACT;
  81                 else error("The --pair logic \"%s\" not recognised.\n", optarg);
  82                 break;
  83             default: usage();
  84         }
  85     }
  86     if ( !pair ) pair = BCF_SR_PAIR_EXACT;
  87     if ( optind == argc ) usage();
  88
  89     int i, j, n, nvcf;
  90     char **vcf = hts_readlist(argv[optind], 1, &nvcf);
  91     if ( !vcf ) error("Could not parse %s\n", argv[optind]);
  92
  93     bcf_srs_t *sr = bcf_sr_init();
  94     bcf_sr_set_opt(sr, BCF_SR_PAIR_LOGIC, pair);
  95     bcf_sr_set_opt(sr, BCF_SR_REQUIRE_IDX);
  96     for (i=0; i<nvcf; i++)
  97         if ( !bcf_sr_add_reader(sr,vcf[i]) ) error("Failed to open %s: %s\n", vcf[i],bcf_sr_strerror(sr->errnum));
  98
  99     kstring_t str = {0,0,0};
 100     while ( (n=bcf_sr_next_line(sr)) )
 101     {
 102         for (i=0; i<sr->nreaders; i++)
 103         {
 104             if ( !bcf_sr_has_line(sr,i) ) continue;
 105             bcf1_t *rec = bcf_sr_get_line(sr, i);
 106             printf("%s:%d", bcf_seqname(bcf_sr_get_header(sr,i),rec),rec->pos+1);
 107             break;
 108         }
 109
 110         for (i=0; i<sr->nreaders; i++)
 111         {
 112             printf("\t");
 113
 114             if ( !bcf_sr_has_line(sr,i) )
 115             {
 116                 printf("%s","-");
 117                 continue;
 118             }
 119
 120             str.l = 0;
 121             bcf1_t *rec = bcf_sr_get_line(sr, i);
 122             kputs(rec->n_allele > 1 ? rec->d.allele[1] : ".", &str);
 123             for (j=2; j<rec->n_allele; j++)
 124             {
 125                 kputc(',', &str);
 126                 kputs(rec->d.allele[j], &str);
 127             }
 128             printf("%s",str.s);
 129         }
 130         printf("\n");
 131     }
 132
 133     free(str.s);
 134     bcf_sr_destroy(sr);
 135     for (i=0; i<nvcf; i++)
 136         free(vcf[i]);
 137     free(vcf);
 138
 139     return 0;
 140 }
 141