X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtools_merge.cpp;h=dcea1725b229a4c95200318ebbe0103cc55ec809;hb=155ba46a7dc23b749cc353b194f7ae6336f9f23d;hp=cae61344eb9c8d30b2aa72c620788bf1a06f9270;hpb=20e692c4a06c181ff7216c00d5808966210e47c9;p=bamtools.git

diff --git a/bamtools_merge.cpp b/bamtools_merge.cpp
index cae6134..dcea172 100644
--- a/bamtools_merge.cpp
+++ b/bamtools_merge.cpp
@@ -89,7 +89,7 @@ int MergeTool::Run(int argc, char* argv[]) {
     
     // opens the BAM files without checking for indexes
     BamMultiReader reader;
-    reader.Open(m_settings->InputFiles, false); 
+    reader.Open(m_settings->InputFiles, false, true); 
 
     // retrieve header & reference dictionary info
     std::string mergedHeader = reader.GetHeaderText();
@@ -101,10 +101,10 @@ int MergeTool::Run(int argc, char* argv[]) {
 
     // store alignments to output file
     BamAlignment bAlignment;
-    while (reader.GetNextAlignment(bAlignment)) {
+    while (reader.GetNextAlignmentCore(bAlignment)) {
         writer.SaveAlignment(bAlignment);
     }
-
+    
     // clean & exit
     reader.Close();
     writer.Close();