Commit 90e1b32e authored by omid's avatar omid
Browse files

removing non-useful command line options

parent 9c808087
......@@ -161,22 +161,22 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal) {
"only; 2: normal info; 3: MPI trace; 4: "
"more debug) (default: 1)"},
{OPT_VERBOSE, "--verbose", SO_REQ_SEP, ""},
{OPT_QUIET, "-q", SO_NONE, "No messages except results"},
{OPT_QUIET, "--quiet", SO_NONE, ""},
//{OPT_QUIET, "-q", SO_NONE, "No messages except results"},
//{OPT_QUIET, "--quiet", SO_NONE, ""},
{OPT_EXPORT, "-e", SO_REQ_SEP, "Export forest in GML format (if %03d or "
"@03d is present, one is created for each "
"fg branch)"},
{OPT_EXPORT, "--export", SO_REQ_SEP, ""},
{OPT_TRACE, "-r", SO_NONE, "Trace the maximization run"},
{OPT_TRACE, "--trace", SO_NONE, ""},
{OPT_EXTRA_DEBUG, "-x", SO_REQ_SEP,
"Extra debug parameter (zero disables it)"},
{OPT_EXTRA_DEBUG, "--extra-debug", SO_REQ_SEP, ""},
//{OPT_EXTRA_DEBUG, "-x", SO_REQ_SEP,
//"Extra debug parameter (zero disables it)"},
//{OPT_EXTRA_DEBUG, "--extra-debug", SO_REQ_SEP, ""},
{OPT_OUT_RESULTS, "-ou", SO_REQ_SEP,
"Write results formatted to this file"},
{OPT_OUT_RESULTS, "--output", SO_REQ_SEP, ""},
{OPT_CLEAN_DATA, "-cl", SO_NONE,
"Remove ambiguous or missing sites from the MSA (default: no)"},
"Skip ambiguous or missing sites from the MSA (default: no)"},
{OPT_CLEAN_DATA, "--clean-data", SO_NONE, ""},
// configuration parameters
......@@ -250,17 +250,17 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal) {
{OPT_BRANCH_ALL, "-ba", SO_NONE,
"Do for all branches as foreground branch (including leaves)"},
{OPT_BRANCH_ALL, "--branch-all", SO_NONE, ""},
{OPT_COMP_TIMES, "-c", SO_REQ_SEP, "Export the computed times from H0 if "
"0, H1 if 1, otherwise the one read "
"in the phylo tree"},
{OPT_COMP_TIMES, "--export-comp-times", SO_REQ_SEP, ""},
//{OPT_COMP_TIMES, "-c", SO_REQ_SEP, "Export the computed times from H0 if "
// "0, H1 if 1, otherwise the one read "
// "in the phylo tree"},
//{OPT_COMP_TIMES, "--export-comp-times", SO_REQ_SEP, ""},
{OPT_INIT_PARAM, "-p", SO_REQ_SEP, "Pass initialization parameter in the "
"form (otherwise random): P=value (P: w0, k, p0, p1, w2) "
"-> e.g. -p w0=1.1 -p p0=2.1 ..."},
{OPT_INIT_PARAM, "--init-param", SO_REQ_SEP, ""},
{OPT_INIT_DEFAULT, "-ic", SO_NONE,
"Start from default parameter values and times from tree file"},
{OPT_INIT_DEFAULT, "--init-default", SO_NONE, ""},
//{OPT_INIT_DEFAULT, "-ic", SO_NONE,
//"Start from default parameter values and times from tree file"},
//{OPT_INIT_DEFAULT, "--init-default", SO_NONE, ""},
SO_END_OF_OPTIONS};
......
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