support non-standard deletion format in VCF

Author: sfchen

src/common.h

@@ -1,7 +1,7 @@
 #ifndef COMMON_H
 #define COMMON_H
 
-#define MUTSCAN_VER "1.13.0"
+#define MUTSCAN_VER "1.13.1"
 
 typedef long int64;
 typedef unsigned long uint64;

src/vcfreader.cpp

@@ -64,7 +64,11 @@ bool VcfReader::readNext()
         var.pos = pos;
         var.id = trim(items[2]);
         var.ref = trim(items[3]);
+        if(var.ref == "-")
+            var.ref = "";
         var.alt = alts[a];
+        if(var.alt == "-")
+            var.alt = "";
         var.qual = trim(items[5]);
         var.filter = trim(items[6]);
         var.info = trim(items[7]);