From f50d16f0062144dd29b7dc92b120b25878c94fae Mon Sep 17 00:00:00 2001
From: Jeremiah Wala <jwala@broadinstitute.org>
Date: Thu, 18 Jun 2015 17:00:36 -0400
Subject: [PATCH] fixed off by one issue

---
 src/GenomicRegion.cpp           | 4 ++--
 src/GenomicRegionCollection.cpp | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/GenomicRegion.cpp b/src/GenomicRegion.cpp
index e44c349dd..2c7bfc307 100644
--- a/src/GenomicRegion.cpp
+++ b/src/GenomicRegion.cpp
@@ -145,9 +145,9 @@ GenomicRegion::GenomicRegion(const std::string& reg, bam_hdr_t* h)
   }
 
   chr = tid;
-  pos1 = beg;
+  pos1 = beg+1;
   pos2 = end;
-  
+
 }
 
 // constructor for SnowTools::GenomicRegion that takes strings. Assumes chr string is in 
diff --git a/src/GenomicRegionCollection.cpp b/src/GenomicRegionCollection.cpp
index 9938e8f95..18b6ee8df 100644
--- a/src/GenomicRegionCollection.cpp
+++ b/src/GenomicRegionCollection.cpp
@@ -408,7 +408,7 @@ GenomicRegionCollection<T>::GenomicRegionCollection(const T& gr)
 template<class T>
 GRC GenomicRegionCollection<T>::intersection(GRC& subject, bool ignore_strand /* false */)
 {
-  std::vector<size_t> sub, que;
+  std::vector<int32_t> sub, que;
   GRC out = this->findOverlaps(subject, que, sub, ignore_strand);
   return out;
 }