Summary report option

[Adamtaranto]

Add support for plain text reporting of alignments of interest.

• Option to give a summary output file name
• For each alignment: Read ID, bitflag, contig ID, contig start, contig end, contig OH location (left/right), OH seq
• Add padding to internal (contig side) boundary of soft-clip if the alignment does not end exactly at contig end
• Add option to flip left-end extension (i.e report left OH as RC) to help with spotting approximate alignments by eye.
• Write two lines for alignments that overhang both ends of a small contig.

Aim: Summary file that can be awk'd to list all OHs at one end of a given contig for visual inspection.