final static private String PRG_NAME = "cladinator";
final static private String PRG_VERSION = "1.05";
- final static private String PRG_DATE = "170919";
+ final static private String PRG_DATE = "170920";
final static private String PRG_DESC = "clades within clades of annotated labels -- analysis of pplacer-type outputs";
final static private String E_MAIL = "phyloxml@gmail.com";
final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
print_help();
System.exit( -1 );
}
- final List<String> allowed_options = new ArrayList<>();
+ final List<String> allowed_options = new ArrayList<String>();
allowed_options.add( SEP_OPTION );
allowed_options.add( QUERY_PATTERN_OPTION );
allowed_options.add( SPECIFICS_CUTOFF_OPTION );
}
extra_processing1_keep = true;
}
-
Pattern special_pattern = null;
boolean special_processing = false;
if ( cla.isOptionSet( SPECIAL_PROCESSING_OPTION ) ) {
System.out.println( " -" + EXTRA_PROCESSING1_KEEP_EXTRA_OPTION
+ " : to keep extra annotations (e.g. \"Q16611|A.1.1\" becomes \"A.1.1.Q16611\")" );
System.out.println( " -" + SPECIAL_PROCESSING_OPTION
- + "=<pattern> : special processing with pattern (e.g. \"(\\d+)([a-z]+)_(.+)\" for \"6q_EF42\" to \"6.q.EF42\")" );
+ + "=<pattern> : special processing with pattern (e.g. \"(\\d+)([a-z]+)_.+\" for changing \"6q_EF42\" to \"6.q\")" );
System.out.println( " -" + VERBOSE_OPTION + " : verbose" );
- System.out.println( " -" + QUIET_OPTION + " : quiet" );
+ System.out.println( " -" + QUIET_OPTION + " : quiet (for when used in a pipeline)" );
System.out.println( " --" + QUERY_PATTERN_OPTION
- + "=<query pattern>: the regular expression for the query (default: \"" + QUERY_PATTERN_DEFAULT
+ + "=<pattern> : the regular expression pattern for the query (default: \"" + QUERY_PATTERN_DEFAULT
+ "\" for pplacer output)" );
System.out.println();
System.out.println( "Examples:" );
System.out.println( " " + PRG_NAME + " -x -xs=& -xk pp_out_trees.sing.tre result.tsv" );
System.out.println( " " + PRG_NAME + " -x -xs=\"|\" pp_out_trees.sing.tre result.tsv" );
System.out.println( " " + PRG_NAME + " -x -xk -m=map.tsv pp_out_trees.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -m=map.tsv -S='(\\d+)([a-z?]*)_.+' pp_out_trees.sing.tre result.tsv" );
System.out.println();
}
}