
//=============================================================================
// Usage:
// -max|median|mean|min|sum|var [-% overlap] MasterFile SubFile
//   where -% overlap is -% 10 (10 percent) by default.
//   Note that -% 0 means any overlap (1 nucleotide or more)
//
//  Expect 2 inputs files: the first should have at least 3 columns
//   chrom start stop whatever
//  while the second should have at least 5 columns (BED format)
//   chrom start stop encode measure whatever
//
// Case-sensitive, lexicographical sorting of chromosomes, followed by
//  numerical coordinate sorting is assumed.
//
// Receive 1 line of output for each input line from MasterFile.
//  calculated	numNucleotides
//
// where calculated is the calculation made upon the values obtained from
// SubFile.  The column 'numNucleotides' is the number of total nucleotides
// from SubFile that overlap (qualified below) that MasterFile region.
//
// The calculated values are the max|median|mean|min|sum|var of respective
// overlapping regions found in SubFile.  Overlapping regions are those that
// qualify to meet the -% requirements.  -% is the minimum percentage of
// nucleotides from a SubFile row that must overlap a region of the MasterFile
// to be included in that rows calculated value.
// If no regions from SubFile qualify to overlap a MasterFile region, the
// output for that row will contain NAN for the 'calculated' column.
//=============================================================================
