Integrate alignment MAPQ filter

[milkschen]

For each alignment, optionally write it in a FASTQ file (or a pair of) if the MAPQ of it is below a given cutoff. If this option gets activated, don't write low-MAPQ alignments to the lifted BAM output.

[milkschen]

There's progress with the -S mapq mode.

Single-end reads are easy to deal with. Paired-end reads are trickier because the input is usually not sorted by name. I'm working on a heuristic algorithm to find a balance between efficiency and accuracy. Results from a small dataset look good - will give updates when larger-scale datasets are used.

I'll also provide an option to write to a gz-compressed FASTQ file.