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.