estimate_abundance: Estimate abundance
In CshlSiepelLab/nascentRNASim:

Estimates abundance for transcript archetypes

Given a set of transcripts constructs query regions and removes transcripts whose query regions go out of bounds

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estimate_abundance(x, err_func, mask = c(0, 0), flank)

construct_query_regions(transcripts, bigwig_plus, bigwig_minus, flank = 5000)

`x`	A vector of counts
`err_func`	error function (currently only identity supported)
`mask`	a two element vector indicating the numbers of bases to skip at the head and tail of the transcripts (respectively)
`flank`	length of flanking regions present in the count vector
`transcripts`	A `GRanges-class` object
`bigwig_plus`	polymerase density signal from the plus strand
`bigwig_minus`	polymerase density signal from the minus strand