text: /*  test/test-vcf-sweep.c -- VCF test harness.
  
      Copyright (C) 2013 Genome Research Ltd.
  
      Author: Petr Danecek <pd3@sanger.ac.uk>
  
  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  copies of the Software, and to permit persons to whom the Software is
  furnished to do so, subject to the following conditions:
  
  The above copyright notice and this permission notice shall be included in
  all copies or substantial portions of the Software.
  
  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  DEALINGS IN THE SOFTWARE.  */
  
  #include <config.h>
  
  #include <stdio.h>
  #include <htslib/vcf_sweep.h>
  
  int main(int argc, char **argv)
  {
      if ( argc!=2 )
      {
          fprintf(stderr,"Usage: test-vcf-sweep <file.bcf|file.vcf>\n");
          return 1;
      }
  
      // Init variables. The checksum is just for this test program to output
      // something and verify that all sites are read in both passes - fwd and
      // bwd.
      bcf_sweep_t *sw = bcf_sweep_init(argv[1]);
      bcf_hdr_t *hdr  = bcf_sweep_hdr(sw);
      int chksum = 0;
  
      // First we must sweep forward and read the whole file to build an index.
      // If this is undesirable, we can require the presence of a .gzi index
      // which can be created with `bgzip -r` from the samtools/htslib package
      bcf1_t *rec;
      while ( (rec = bcf_sweep_fwd(sw)) ) chksum += rec->pos+1;
      printf("fwd position chksum: %d\n", chksum);
  
      // Now sweep backward.
      chksum = 0;
      while ( (rec = bcf_sweep_bwd(sw)) ) chksum += rec->pos+1;
      printf("bwd position chksum: %d\n", chksum);
  
      // And forward and backward again, this time summing the PL vectors
      int i,j, mPLs = 0, nPLs;
      int32_t *PLs = NULL;
      chksum = 0;
      while ( (rec = bcf_sweep_fwd(sw)) )
      {
          // get copy of the PL vectors
          nPLs = bcf_get_format_int32(hdr, rec, "PL", &PLs, &mPLs);
          if ( !nPLs ) continue;  // PL not present
  
          // how many values are there per sample
          int nvals = nPLs / bcf_hdr_nsamples(hdr);
  
          int32_t *ptr = PLs;
          for (i=0; i<bcf_hdr_nsamples(hdr); i++)
          {
              for (j=0; j<nvals; j++)
              {
                  // check for shorter vectors (haploid genotypes amongst diploids)
                  if ( ptr[j]==bcf_int32_vector_end ) break;
  
                  // skip missing values
                  if ( ptr[j]==bcf_int32_missing ) continue;
  
                  chksum += ptr[j];
              }
              ptr += nvals;
          }
      }
      printf("fwd PL chksum: %d\n", chksum);
  
      // And the same backwards..
      chksum = 0;
      while ( (rec = bcf_sweep_bwd(sw)) )
      {
          nPLs = bcf_get_format_int32(hdr, rec, "PL", &PLs, &mPLs);
          if ( !nPLs ) continue;
          int nvals = nPLs / bcf_hdr_nsamples(hdr);
          int32_t *ptr = PLs;
          for (i=0; i<bcf_hdr_nsamples(hdr); i++)
          {
              for (j=0; j<nvals; j++)
              {
                  if ( ptr[j]==bcf_int32_vector_end ) break;
                  if ( ptr[j]==bcf_int32_missing ) continue;
                  chksum += ptr[j];
              }
              ptr += nvals;
          }
      }
      printf("bwd PL chksum: %d\n", chksum);
  
      // Clean up
      bcf_sweep_destroy(sw);
      return 0;
  }
  
  
  