It correctly takes into account that a sequence can be multiple lines. It does not strip whitespace because according to http://maq.sourceforge.net/fastq.shtml whitespace is not a legal character.
Hum, just read your example files. I guess you can have white. In any case, that should pose not pose any real problem. http://dlang.org/phobos/std_string.html#.removechars
would come in handy here.
