updata cpu version

Author: y3tseng

src/twilight-main.cpp

@@ -25,11 +25,13 @@ void parseArguments(int argc, char** argv)
         ("wildcard,w", "Treat unknown or ambiguous bases as wildcards and align them to usual letters.")
         ("verbose,v", "Print out every detail process.")
         ("psgop,p", po::value<std::string>(), "y: Enable, n: Disable position-specific gap open penalty. If not specified, it will be detected automatically.")
+        ("align,a", po::value<std::string>()->default_value("g"), "Alignment types: g - gap penalty at both ends, l - no gap penalty at either end, h - gap penalty at the head, t - gap penalty at the tail.")
         ("match",      po::value<float>()->default_value(18), "Match score.")
         ("mismatch",   po::value<float>()->default_value(-8), "Mismatch penalty for transversions.")
         ("transition", po::value<float>()->default_value(5), "Score for transitions")
         ("gap-open",   po::value<float>()->default_value(-50), "Gap-Open penalty")
         ("gap-extend", po::value<float>()->default_value(-5), "Gap-Extend penalty")
+        ("gap-ends",   po::value<float>(), "Gap penalty at ends, default set to the same as the gap extension penalty.")
         ("xdrop",      po::value<float>()->default_value(600), "X-drop value (scale). The actual X-drop will be multiplied by the gap-extend penalty.")
         ("matrix,x", po::value<std::string>(), "Use a user-defined substitution matrix.")
         ("output-type", po::value<std::string>()->default_value("FASTA"), "FASTA or CIGAR, CIGAR stands for CIGAR-like compressed format.")

src/twilight-main.cu

@@ -39,8 +39,8 @@ void parseArguments(int argc, char** argv)
         ("output-type", po::value<std::string>()->default_value("FASTA"), "FASTA or CIGAR, CIGAR stands for CIGAR-like compressed format.")
         ("merge", po::value<std::string>()->default_value("p"), "t: Transitivity merger, p: Progressive alignment.")
         ("keep-temp,k", "Keep the temporary directory.")
-        ("sum-of-pairs-score,s", "Calculate the sum-of-pairs score after the alignment.")
         ("no-align-gappy", "Do not align gappy columns. This will create a longer MSA (larger file).")
+        ("sum-of-pairs-score,s", "Calculate the sum-of-pairs score after the alignment.")
         ("check", "Check the final alignment. Sequences with no legal alignment will be displayed.")
         ("cpu-only", "Run the program only on CPU.")
         ("help,h", "Print help messages");