From 46dd0c8c4b2f05d37d201904bdaa24e0aa32a5ed Mon Sep 17 00:00:00 2001
From: mgymrek <mgymrek@mit.edu>
Date: Tue, 29 Jul 2014 13:41:09 -0400
Subject: [PATCH] fixing more problems with allele lengths < 1bp in the VCF

---
 src/Genotyper.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/Genotyper.cpp b/src/Genotyper.cpp
index d696a66..7937ca0 100644
--- a/src/Genotyper.cpp
+++ b/src/Genotyper.cpp
@@ -119,8 +119,9 @@ void Genotyper::GetAlleles(const list<AlignedRead>& aligned_reads,
   for (list<AlignedRead>::const_iterator it = aligned_reads.begin();
        it != aligned_reads.end(); it++) {
     if (it->mate) continue;
+    int refcopy = it->msEnd - it->msStart + 1;
     if (it->diffFromRef != 0 && std::find(alleles->begin(), alleles->end(), it->diffFromRef) == alleles->end() &&
-	it->diffFromRef+it->refCopyNum*it->period > 0) {
+	it->diffFromRef+refcopy >= 1) {
       alleles->push_back(it->diffFromRef);
     }
   }