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phylo
fastcodeml
Commits
90e1b32e
Commit
90e1b32e
authored
Mar 11, 2016
by
omid
Browse files
removing non-useful command line options
parent
9c808087
Changes
1
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CmdLine.cpp
View file @
90e1b32e
...
...
@@ -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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