Faulty estimates of Read Length

[karl-az]

I have noticed that RNA-seQC at times underestimates the Read Length

This is the section measuring read length:

rnaseqc/src/RNASeQC.cpp

Lines 274 to 277 in c426536

	unsigned int alignmentSize = alignment.PositionEnd() - alignment.Position();
	if (LegacyMode.Get() && alignmentSize > LEGACY_MAX_READ_LENGTH) continue;
	if (!readLength) current_chrom = chromosomeMap(sequences[alignment.ChrID()].Name);
	if (alignmentSize > readLength) readLength = alignment.Length();

The comparison is on alignmentSize, but the assignment is with alignment.Length(). Could this lead to unfortunate errors? Especially if alignment.Length() sometimes is less than alignmentSize

[kachulis]

I believe this is addressed by #78