Add tag with pre-alignment score to unaligned reads

[jdidion]

I set --pre-align-min-score 200 and had a read fail to align, however the read aligned with minimap2. When I dropped the threshold to 100, the read aligned.

It would be useful to know the pre-alignment scores of reads that are expected to align but fail to do so, so that --pre-align-min-score can be adjusted intelligently.

I don't see any reason why AS couldn't be used.

[nh13]

How about the XS or xs tag, with the latter as per the README:

the sub-optimal alignment score, practically the maximum of any pre-alignment and secondary chain

then one could get the xs tag for all reads

[jdidion]

perfect