//alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
void GetSeqsCommand::readAlign(){
try {
- string outputFileName = getRootName(alignfile) + "pick" + getExtension(alignfile);;
+ string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
ofstream out;
openOutputFile(outputFileName, out);