Finalized implementation of minOverlap for Velocyto counting.
@@ -144,6 +144,11 @@ void Transcriptome::classifyAlign (Transcript **alignG, uint64 nAlignG, ReadAnno
aG.alignGenes.insert(trGene[tr1]);//genes for each alignment
};
+ if (P.pSolo.featureYes[SoloFeatureTypes::Velocyto]) {
+
+ //6 is the hard code minOverlapMinusOne, to agree with velocyto's MIN_FLANK=5
+ aStatus=alignToTranscript(aG, trS[tr1], trStr[tr1], exSE+2*trExI[tr1], exLenCum+trExI[tr1], trExN[tr1], 6);
+
if (nAlignG>1)
reGe=(uint32)-1; //marks multi-gene align
@@ -162,7 +167,7 @@ void Transcriptome::classifyAlign (Transcript **alignG, uint64 nAlignG, ReadAnno
};
};
};
-
+ };
} while (trEmax[tr1]>=aGend && tr1>0);
};
