Thanks for the response. It is true that I don't know which strand the assembled transcripts belong to. However, if the library prep was strand-specific, then for each assembled transcript all F reads that map to it should map in the same direction, right? If it was unstranded, then the F reads would map equally in both directions. Or am I missing something?
BED file for infer_experiment.py
Isotopes class JavaDoc
Added a null check to MolecularFormulaRange
Removed the nonsense isNotZero() method
Patched a bug in IsotopePatternGenerator
Fixed failing test: testCalculateIsotopesC10000
Added a test for isotope pattern generation for...