Large update to groupBy.

	1. Assumes stdin when no -i is given.  Credit = Assaf Gordon
	2. New freqasc and freqdesc options.
	3. Better command line parsing.  Credit = Assaf Gordon.

src/genomeCoverageBed/genomeCoverageBed.cpp

@@ -74,7 +74,8 @@ void BedGenomeCoverage::StartNewChrom(const string& newChrom) {
 	_currChromName = newChrom;
 
 	// get the current chrom size and allocate space
-	_currChromSize = _genome->getChromSize(newChrom);
+	_currChromSize = _genome->getChromSize(_currChromName);
+
 	if (_currChromSize >= 0)
 		_currChromCoverage.resize(_currChromSize);
 	else {

src/utils/genomeFile/genomeFile.cpp

@@ -43,7 +43,6 @@ void GenomeFile::loadGenomeFileIntoMap() {
 		
 		// ignore a blank line
 		if (genomeFields.size() > 0) {
-
 			if (genomeFields[0].find("#") == string::npos) {
 
 				// we need at least 2 columns