mappability threshold for correctReadCounts

[mr-james-ireland]

Hi,

In utils.R at line 150, I'm wondering if a "mappability" parameter should be passed to the correctReadCounts function? Since the correctReadCounts default is 0.9, I find this step crashes for some chroms with low mappability even when I set minMapThresh to a lower value.

Thanks! -James

if (applyCorrection){

correct read counts

    **counts <- correctReadCounts(counts, chrNormalize = chrNormalize)**
    if (!is.null(map)) {
      ## filter bins by mappability
      counts <- filterByMappabilityScore(counts, map=map, mapScoreThres = mapScoreThres)
    }