added a boundary condition for normalization.

atks · Sep 10, 2014 · 47df3e8 · 47df3e8
1 parent facdd1f
commit 47df3e8
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/normalize.cpp b/normalize.cpp
@@ -171,7 +171,7 @@ class Igor : Program
                 uint32_t pos1 = bcf_get_pos1(v);
 
                 std::vector<std::string> alleles;
-                for (uint32_t i=0; i<bcf_get_n_allele(v); ++i)
+                for (size_t i=0; i<bcf_get_n_allele(v); ++i)
                 {
                     char *s = bcf_get_alt(v, i);
                     while (*s)

diff --git a/variant.cpp b/variant.cpp
@@ -157,7 +157,6 @@ int32_t Variant::classify_variant(const char* chrom, uint32_t pos1, char** allel
                 alt = ALT.s;
             }
 
-
             int32_t mlen = std::min(rl, al);
             int32_t dlen = al-rl;
             int32_t diff = 0;

diff --git a/variant_manip.cpp b/variant_manip.cpp
@@ -494,6 +494,12 @@ void VariantManip::right_trim_or_left_extend(std::vector<std::string>& alleles,
                     to_right_trim = false;
                     //do not break here!!! you need to check for empty alleles that might exist!!!
                 }
+
+                if (pos1==1 && alleles[i].size()==1)
+                {
+                    to_right_trim = false;
+                    break;
+                }
             }
             else
             {
@@ -502,7 +508,7 @@ void VariantManip::right_trim_or_left_extend(std::vector<std::string>& alleles,
                 break;
             }
         }
-
+        
         if (to_right_trim)
         {
             for (size_t i=0; i<alleles.size(); ++i)