changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

changed reading of name file to use buffered reads. note the splitAtWhiteSpace function is sensitive to the gobble function. do not use the two together while reading or the read can get off track. modified trim.seqs group counts to include the redundant sees if a names file is provided.  changed group maps read of a group file to be buffered.  modified appendFiles functions to be buffered.