public static void assignOptions(ExtendOptionParser parser) {
parser.addHeader("Result Reader Options", 1);
parser
.accepts("optresin", "Input result file")
.withRequiredArg()
.ofType(String.class)
.defaultsTo("");
parser
.accepts("optresinformat", ResultFormat.getFormatHelp())
.withOptionalArg()
.ofType(Integer.class)
.defaultsTo(-1);
}
public static void assignOptions(ExtendOptionParser parser, int level) {
parser.addHeader("Result Clustering Options", level);
parser
.accepts(
"clustermode",
"The clustering mode. 0: No clustering. 1: Standard indel cluster. 2: Standard indel-inv cluster. 3. Standard cluster transloc")
.withRequiredArg()
.ofType(Integer.TYPE)
.defaultsTo(0);
parser
.accepts(
"closeref",
"The max distance (reference) between two results to be considered at same cluster.")
.withOptionalArg()
.ofType(Long.class)
.defaultsTo((long) 250000);
parser
.accepts(
"closefrag",
"The max distance (fragment) between two results to be considered at same cluster.")
.withOptionalArg()
.ofType(Long.class)
.defaultsTo((long) 250000);
parser
.accepts("minmatch", "Min match to be consider as a valid partial map.")
.withOptionalArg()
.ofType(Integer.class)
.defaultsTo(3);
parser
.accepts("maxtrim", "Maximum trim of a partial map. ")
.withOptionalArg()
.ofType(Integer.class)
.defaultsTo(5);
parser
.accepts("trimear", "Error acceptable range.")
.withOptionalArg()
.ofType(Double.class)
.defaultsTo(0.1);
parser
.accepts("match", "Score for one label match")
.withOptionalArg()
.ofType(Integer.class)
.defaultsTo(5);
parser
.accepts("fpp", "False Positive Penalty")
.withOptionalArg()
.ofType(Integer.class)
.defaultsTo(2);
parser
.accepts("fnp", "False Negative Penalty")
.withOptionalArg()
.ofType(Integer.class)
.defaultsTo(2);
parser
.accepts("indelp", "Indel Penalty")
.withOptionalArg()
.ofType(Integer.class)
.defaultsTo(10);
parser
.accepts("invp", "Inversion Penalty")
.withOptionalArg()
.ofType(Integer.class)
.defaultsTo(30);
parser
.accepts("transp", "Translocation Penalty")
.withOptionalArg()
.ofType(Integer.class)
.defaultsTo(50);
parser
.accepts("clusterlocalpenalty", "Local Penalty after clustering")
.withOptionalArg()
.ofType(Boolean.class)
.defaultsTo(false);
parser
.accepts("minclusterscore", "Min cluster score.")
.withOptionalArg()
.ofType(Integer.class)
.defaultsTo(30);
parser
.accepts("minconf", "Minimum confidence")
.withOptionalArg()
.ofType(Double.class)
.defaultsTo(0.4);
parser
.accepts("minclusterfragratio", "Min clustered fragment ratio")
.withOptionalArg()
.ofType(Double.class)
.defaultsTo(-1.0);
parser
.accepts("minclustersigratio", "Min clustered mapped signal ratio")
.withOptionalArg()
.ofType(Double.class)
.defaultsTo(-1.0);
parser
.accepts("overlapcluster", "Allow overlapping clusters at results.")
.withOptionalArg()
.ofType(Boolean.class)
.defaultsTo(true);
parser
.accepts("maxclusteritem", "Maximum items output. -1: no limit")
.withOptionalArg()
.ofType(Integer.class)
.defaultsTo(1);
}