Fix input file nucleotide check

PanTools runs some pre-flight checks to make sure all genome files exist and contain a nucleotide sequence. However, the latter check is run by opening compressed files as if they were uncompressed, leading to complaints about characters other than {A, C, T, G, N} appearing in the input files.

The offending logic happens in this line in check_if_nucleotide_sequence(). Make sure compressed file are handled correctly. Apache Commons Compress might be useful for dealing with a variety of compression formats automatically, although gzip is more or less the standard for compressing FASTA/FASTQ files.