Plugins to use bcf_gt_is_missing instead of the old bcf_int32_missing

dlaehnemann · Sep 16, 2015 · f46aa3e · f46aa3e
1 parent 4dd02c3
commit f46aa3e
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/plugins/dosage.c b/plugins/dosage.c
@@ -140,7 +140,7 @@ int calc_dosage_GT(bcf1_t *rec)
         float dsg = 0;
         for (j=0; j<nret; j++)
         {
-            if ( ptr[j]==bcf_int32_missing || ptr[j]==bcf_int32_vector_end || ptr[j]==bcf_gt_missing ) break;
+            if ( ptr[j]==bcf_int32_vector_end || bcf_gt_is_missing(ptr[j]) ) break;
             if ( bcf_gt_allele(ptr[j]) ) dsg += 1;
         }
         printf("\t%.1f", j>0 ? dsg : -1);

diff --git a/plugins/vcf2sex.c b/plugins/vcf2sex.c
@@ -169,8 +169,10 @@ int process_region_precise(args_t *args, char *seq, regitr_t *itr)
             int32_t *gts = args->gts + ngts*ismpl;
             int igt, ploidy = 0;
             for (igt=0; igt<ngts; igt++)
-                if ( gts[igt]==bcf_gt_missing || gts[igt]==bcf_int32_missing || gts[igt]==bcf_int32_vector_end ) break;
+            {
+                if ( gts[igt]==bcf_int32_vector_end || bcf_gt_is_missing(gts[igt]) ) break;
                 else ploidy++;
+            }
             args->counts[ismpl*(args->max_ploidy+1) + ploidy]++;
             if ( args->verbose )
                 fprintf(stderr,"%s:%d\t%s\tploidy=%d\n", seq,rec->pos+1,args->hdr->samples[ismpl],ploidy);