char buffer5 [2];
in.read(buffer5, 2);
header.clipQualRight = be_int2(*(unsigned short *)(&buffer5));
-
+
//read clipAdapterLeft
char buffer6 [2];
in.read(buffer6, 2);
try {
int endValue = header.clipQualRight;
- if (header.clipQualRight == 0) { endValue = read.flowIndex.size(); }
+ if (header.clipQualRight == 0) {
+ endValue = read.flowIndex.size();
+ if (m->debug) { m->mothurOut("[DEBUG]: " + header.name + " has clipQualRight=0.\n"); }
+ }
if(endValue > header.clipQualLeft){
int rightIndex = 0;