substantial changes to the allelic filter script

- XS filter did not work as expected
- in the case of paired-end sequencing: if one read matches the
criteria, then the pair is kept
- added coordinate sorting as an option
- duplicates are ignored, so are unmapped reads
- added mapping quality as an additional option (might be less
complicated than removal of multiply aligned reads for paired-end data)
- non-indexed BAM files are accepted now (avoid use of infile.fetch()
that relies on the index)