This would prevent horrors like:
$ ../scripts/clonotypeR detect .fastq [bam_header_read] EOF marker is absent. The input is probably truncated. [bsw2_aln] fail to open file '.fastq'. Abort! [samopen] SAM header is present: 169 sequences. [sam_read1] reference 'SN:TRDV5 LN:344 3 19 3 ' is recognized as '*'. [main_samview] truncated file.