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root/gclib/gffread/gffread.cpp
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# Line 680 | Line 680
680      exit(1);
681      }
682   debugMode=(args.getOpt("debug")!=NULL);
683 + bool forceExons=(args.getOpt("force-exons")!=NULL);
684   mRNAOnly=(args.getOpt('O')==NULL);
685   //sortByLoc=(args.getOpt('S')!=NULL);
686   addDescr=(args.getOpt('A')!=NULL);
# Line 840 | Line 841
841     gffloader.mergeCloseExons=mergeCloseExons;
842     gffloader.showWarnings=(args.getOpt('E')!=NULL);
843     gffloader.load(g_data, &validateGffRec, doCluster, doCollapseRedundant,
844 <                             matchAllIntrons, fuzzSpan);
844 >                             matchAllIntrons, fuzzSpan, forceExons);
845     if (doCluster)
846       collectLocusData(g_data);
847     if (numfiles==0) break;

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