added support for /dev/stdin and --output-dir to extract-paired-reads
added support for /dev/stdin and --output-dir to extract-paired-reads

Winterflower/khmer,F1000Research/khmer,souravsingh/khmer,Winterflower/khmer,F1000Research/khmer,ged-lab/khmer,souravsingh/khmer,souravsingh/khmer,Winterflower/khmer,ged-lab/khmer,ged-lab/khmer,F1000Research/khmer