Add ability for rust uniwig to create output files from input .bam files

[donaldcampbelljr]

Some work accomplished with PR #40.

We would like to use this code as a drop in replacement for bamSitesToWig.py from PEPATAC: https://github.com/databio/pepatac/blob/master/tools/bamSitesToWig.py

bamSitesToWig.py creates three files as output:

1. • exact.bw
2. • smoothed.bw
3. • shift.bed

Currently, uniwig can take an input file of either:
bed, narrowPeak, bam

and create an output of:
wig
npy
bedGraph
bw (via an intermediate bedGraph conversion)

Some items to accomplish for this task:

• add bed output support if given a non-bed-like file as input (i.e. bam).
• Original bamSitesToWig adjusts positions based on flags. Noodles does support Flags but on first glance they are named differently and must be reviewed.
• I believe PEPATAC pipeline only needs starts counts? So add ability to only output any counts the user wishes instead of always outputting all three (starts,ends, core).
• Scaling is used in bamSitesToWig.py. Currently, uniwig does not scale counts. Should it?
• Smooth vs Exact, currently uniwig only offers the smooth option, though the user can set smoothing =0. Is this the same output as the exact code? If so, why were two perl scripts used? For original counting algorithms, see:
  https://github.com/databio/pepatac/blob/master/tools/cutsToWig.pl
  https://github.com/databio/pepatac/blob/master/tools/smoothWig.pl

Nice to have:

• if associated .bai does not exist, have uniwig create it (using noodles crate)

[donaldcampbelljr]

Working proof of concept in #40 , however, it uses an intermediate BedGraph file written to disk.

Therefore, we are exploring an alternative method in #47 which streams values directly to bigtools bw writer.

However, some challenges remain, namely:

• when spawning separate threads to handle consumer/producer workflows, I see issues with error handling where an error does not seem to close the producer, causing the consumer to "hang"