From ed3c94f612826e680032242f56dcd452ec2db84f Mon Sep 17 00:00:00 2001
From: Sebastian Mackowiak <Drmirdeep@users.noreply.github.com>
Date: Fri, 22 Nov 2019 11:01:18 +0100
Subject: [PATCH] Correct binsize calculation

Binsize calculation is based on the gff input file and thus needs to add 1 for the region size. Since this was missing
an offset error accumulated with the number of bins used and the end of a region was never been used for calculation.
E.g. A region with 60 bins would lack the last 60bp of a region due to the offset error accumulation.
---
 bamliquidator_internal/bamliquidator.cpp | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/bamliquidator_internal/bamliquidator.cpp b/bamliquidator_internal/bamliquidator.cpp
index 86bc69d..8b6c443 100755
--- a/bamliquidator_internal/bamliquidator.cpp
+++ b/bamliquidator_internal/bamliquidator.cpp
@@ -198,11 +198,13 @@ std::vector<double> liquidate(const samfile_t* fp, const bam_index_t* bamidx,
   only deal with coord, so use generic item
   */
   int startArr[spnum], stopArr[spnum];
-  int pieceLength = (stop-start) / spnum;
+	
+   // gff has fully closed intervals thus the length needs +1
+  int pieceLength = (stop-start+1) / spnum;
   for(int i=0; i<spnum; i++)
   {
-    startArr[i] = start + pieceLength*i;
-    stopArr[i] = start + pieceLength*(i+1);
+    startArr[i] = start + pieceLength*i; 
+    stopArr[i] = startArr[i] + pieceLength -1;
   }
 
   std::deque<ReadItem> items = bamQuery_region(fp,bamidx,coord,strand,extendlen);