Automatic determination of file type (fasta or fastq)

[Tillsa]

A common mistake made by users is not giving the --fastq option when aligning fastq reads. Possible solutions to this problem could be:

• automatically determining the file type
• giving a custom error message pointing to the --fastq flag, when the alignment fails

[konrad]

I would prefer the automatic detection, which should not be too hard as only two simple formats are the options. In this is done in this way the "--fastq" needs to be removed.