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Fixed Marker_build and added an option -remove_dup to remove duplicat…
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…e taxons
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gjospin committed May 17, 2012
1 parent ee48c87 commit 00a37d5
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Showing 6 changed files with 230 additions and 148 deletions.
3 changes: 2 additions & 1 deletion bin/phylosift
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Expand Up @@ -112,8 +112,9 @@ GetOptions(
"coverage=s" => \$ps->{"coverage"}, #provides a contig/scaffold coverage file "coverage=s" => \$ps->{"coverage"}, #provides a contig/scaffold coverage file
"updated_markers=i" => \$ps->{"updated"}, #Indicates if Phylosift uses the updated versions of the Markers. "updated_markers=i" => \$ps->{"updated"}, #Indicates if Phylosift uses the updated versions of the Markers.
"marker_url=s" => \$ps->{"marker_url"}, # an alternate address to retrieve markers from "marker_url=s" => \$ps->{"marker_url"}, # an alternate address to retrieve markers from
"extended" => \$ps->{"extended"}, #Should the full extended set of markers be used? "extended" => \$ps->{"extended"}, #Should the full extended set of markers be used?
"config=s" => \$ps->{"configuration"}, #custom config file "config=s" => \$ps->{"configuration"}, #custom config file
"remove_dup" => \$ps->{"remove_dup"}, #removes duplicate taxons when using build_marker
"h" => \$help, #prints the usage part of the README file "h" => \$help, #prints the usage part of the README file
"help" => \$help, #same as -h "help" => \$help, #same as -h
"debug" => \$my_debug, #print debugging messages? "debug" => \$my_debug, #print debugging messages?
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