enhance megadepth output to optionally write contig names rather than numerical ids

[nellore]

In many applications, it's useful to grep for variants by locus. It'd be very convenient if megadepth output wrote contig names instead of their corresponding numerical ids from the BAM, perhaps with a command-like option like --write-contigs.

[nellore]

In fact, last night, I was at my laptop, using megadepth on some random BAM. I added the command-line option --write-contigs, and it didn't work. Then my high school English teacher busted into my apartment and said, "You know, I told you to read The Mayor of Contigs," and the taste of castor oil was in my mouth, so I got up to get a glass of water, but the further I walked, the further away the sink was, and I woke up in a cold sweat.

Pretty sure that wouldn't have been a nightmare if --write-contigs were real.