max softclip fraction help message

Author: Hossein Asghari

src/Pufferfish.cpp

@@ -251,8 +251,8 @@ int main(int argc, char* argv[]) {
                     (option("--allowSoftclip").set(alignmentOpt.allowSoftclip, true) % "Allow soft-clipping at start and end of alignments"),
                     (option("--maxSoftclipFraction") & value("max softclip fraction general", alignmentOpt.maxSoftclipFractionGeneral)
                     & value("max softclip fraction overhang", alignmentOpt.maxSoftclipFractionOverhang)) % 
-                    "Discard alignments with soft-clip > maxSoftclipFraction * read_length." 
-                    "The general and overhang fractions should be specified differently."
+                    "Discard alignments with soft-clip > maxSoftclipFraction * read_length. " 
+                    "The general and overhang fractions should be specified differently. "
                     "This value must be in the range [0, 1] (default=0.2 0.2)",
                     (option("--computeCIGAR").set(alignmentOpt.computeCIGAR, true) % "Compute CIGAR string during alignment validation"),
                     (option("--endBonus") & value("end bonus", alignmentOpt.endBonus)) % "Specify end bonus value when alignment reaches the end of query",