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Faulty estimates of Read Length #77

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Faulty estimates of Read Length#77
@karl-az

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@karl-az
karl-az
opened on Feb 16, 2023

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

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