Permalink
Browse files

Fixed Marker_build and added an option -remove_dup to remove duplicat…

…e taxons
  • Loading branch information...
1 parent ee48c87 commit 00a37d509653e35ec521a2aab6295508c7fec94a @gjospin committed May 17, 2012
Showing with 230 additions and 148 deletions.
  1. +2 −1 bin/phylosift
  2. +201 −98 lib/Phylosift/MarkerBuild.pm
  3. +1 −1 lib/Phylosift/Phylosift.pm
  4. +15 −46 lib/Phylosift/Simulations.pm
  5. +9 −2 lib/Phylosift/UpdateDB.pm
  6. +2 −0 tools/readconciler.cpp
View
@@ -112,8 +112,9 @@ GetOptions(
"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.
"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
+ "remove_dup" => \$ps->{"remove_dup"}, #removes duplicate taxons when using build_marker
"h" => \$help, #prints the usage part of the README file
"help" => \$help, #same as -h
"debug" => \$my_debug, #print debugging messages?
Oops, something went wrong.

0 comments on commit 00a37d5

Please sign in to comment.