Improve mGEMS extract

[tmaklin]

Currently running mGEMS extract always names the files with the suffix "_1.fastq.gz", "_2.fastq.gz", "_3.fastq.gz" etc. depending on the number and order of the input files. It would be useful to add an option to change the name (or print to cout) to enable usage with calls like the following:

mGEMS extract --bins input.bin -r reads_1.fastq.gz -o outdir &
mGEMS extract --bins input.bin -r reads_2.fastq.gz -o outdir &
wait

This may be faster than extracting both reads with a single command as compressing the reads sometimes takes more time than actually writing them. Current implementation does not allow the above call to work, because both calls will attempt to write to "input_1.fastq.gz".