calculateIRLs_jointMLE: calculateIRLs_MLE
In adamstruck/RECD: Repeat Exansion & Contraction Detection

For repeats that have read pairs flanking them, the implied expansion and length of that repeat is determined.

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  calculateIRLs_jointMLE(flanking_file, facing_file,
    imd_distribution, upper_limit = 0.95, margin = 37.5,
    output_dir)

`flanking_file`	_flanking read pair file
`facing_file`	_facing reads file
`imd_distribution`	.insert_len_dist file (i.e. the inner mate distance distribution for the sample)
`upper_limit`	the value used in mapATR processLastAlignedBase [default= 0.95]
`margin`	the value used in mapATR processLastAlignedBase [default= 37.5]
`output_dir`	path to output directory