Modifications in bedweight handling, sorting and fragment size estimation.

BEDWEIGHT files are now extracted in a way (extractBed) that we only keep the 5' end coordinate of each read. Additionally, all reads with identical 5' end get collapsed and their weights get summed up. Reads are sorted by their 5' end.
Fragment size estimation (FragmentLength) no longer sorts and collapses BEDWEIGHT file as this is already done in extractBed.
BinReads component omits now the step where it sorts BEDWEIGHT by 5' end and collapses it.