Update cis_splice_effects_identifier.cc

Author: kcotto

src/cis-splice-effects/cis_splice_effects_identifier.cc

@@ -59,6 +59,7 @@ void CisSpliceEffectsIdentifier::usage(ostream& out) {
     out << "\t\t" << "-E\tAnnotate variants in exonic space within a transcript(not to be used with -e)." << endl;
     out << "\t\t" << "-S\tDon't skip single exon transcripts." << endl;
     out << "\t\t" << "-b STR\tThe file containing the barcodes of interest for single cell data." << endl;
+    out << "\t\t" << "-C\tTells cis-splice-effects identify that you want intron-motif method to take priority when assigning strand. i.e. decide strandedness based on the fasta rather than what is encoded in the alignment file.
     out << endl;
 }