Fixed a bug related to using the filenames of paired R1 and R2 input files with formats other than .fastq.gz.
Fixed a bug related to using the filenames of paired R1 and R2 input files with formats other than .fastq.gz.

benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline