misc fixes

atks · Jun 16, 2014 · d949dd5 · d949dd5
1 parent f55ff4c
commit d949dd5
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/genotype2.cpp b/genotype2.cpp
@@ -1029,7 +1029,7 @@ class Igor : Program
     		}
 
             bcf_set_rid(ovcf_rec, bcf_get_rid(ivcf_rec));
-    		bcf_set_pos1(ovcf_rec, bcf_get_pos0(ivcf_rec));
+    		bcf_set_pos1(ovcf_rec, bcf_get_pos1(ivcf_rec));
     		bcf_update_alleles(odw->hdr, ovcf_rec, const_cast<const char**>(bcf_get_allele(ivcf_rec)), bcf_get_n_allele(ivcf_rec));
 
     		if (read_no!=0)

diff --git a/remove_overlap.cpp b/remove_overlap.cpp
@@ -102,7 +102,7 @@ class Igor : Program
         odw = new BCFOrderedWriter(output_vcf_file, 0);
         odw->link_hdr(odr->hdr);
 
-        bcf_hdr_append(odw->hdr, "##FILTER=<ID=TPASS,Description=\"Temporary pass\">");
+        bcf_hdr_append(odw->hdr, "##FILTER=<ID=PASS,Description=\"Passed variant\">");
         bcf_hdr_append(odw->hdr, "##FILTER=<ID=overlap,Description=\"Overlapping variant\">");
 
         odw->write_hdr();
@@ -131,7 +131,7 @@ class Igor : Program
 
         bcf1_t *v = odw->get_bcf1_from_pool();
 
-        int32_t tpass_id = bcf_hdr_id2int(odw->hdr, BCF_DT_ID, "TPASS");
+        int32_t tpass_id = bcf_hdr_id2int(odw->hdr, BCF_DT_ID, "PASS");
         int32_t overlap_id = bcf_hdr_id2int(odw->hdr, BCF_DT_ID, "overlap");
 
         while (odr->read(v))