changes related to parameters & default files - v3.4.1

[calkan]

* Default output file is now (seqFile1)-output.sam(.gz) & default nohit file is (seqFile1)-output.nohit.fastq(.gz)
* No-hit FASTQ output is new also compressed when --outcomp parameter is used.
* mrsFAST now accepts -t as a short form for --threads.

[calkan]

there was a mistake in calling stripPath, which was not safe for seqFile1