Reads parsing will quit when encounter reads shorter than expected

[GoogleCodeExporter]

PerM expect reads in the same length as the first two reads in the fastq or 
fasta input. When PerM encoutner a read shorter than expected, the parser will 
stop and think the file has ended. In the 0.4.0 release, the parser will ignore 
the shorter reads and continue to map the reads afterward. 

Original issue reported on code.google.com by Chen.Yan...@gmail.com on 14 Feb 2012 at 11:22