provide option for a different normalization method about pipeline HOT 2 OPEN

Cool idea -- what were you thinking for a different normalization option?

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@semenko I was thinking a method where all the counts for a given .bam file add up to 1

For bamliquidator with bins, just divide each count by the total of the counts, e.g. if two bins and just one chromosome:

1. chr1, bin 1 count is 3, normalized count is 3/(3+4)
2. chr2, bin 2 count is 4, normalized count is 4/(3+4)

For regions, first divide by bin width to normalize on bin width. Then divide each of the normalized-on-bin-width counts by the total of the normalized-on-bin-width counts. For example, if two regions:

1. chr1, start 100, stop 200, count is 1, normalized by bin width count is 1/(200-100)= 0.01, then final normalized count is 0.01/(0.01+0.003)=0.769230...
2. chr2, start 2000, stop 3000, count is 3, normalized by bin width count is 3/(2000-1000)=0.003, then final normalized count is 0.003/(0.01+0.003)=0.230769...

I should probably add twice the extension length to the region size for this calculation.

Maybe I'll add the command line option -u/--unity_normalization to use this alternative normalization method where things add up to 1, and the default will remain bases per million reads per base?

@bradnerComputation : does this sound like a less arbitrary normalization option? Does adding twice the extension length to the region size make sense?

I don't want to add many normalization options, but I would like to add one more normalization option that isn't skewed by bams with different read lengths.

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