a0e8e6b7cdb37cf071a36fc0eeb3d78a879fb9a0,src/main/java/japsa/tools/bio/hts/VNTRLongReadsCmd.java,VNTRLongReadsCmd,VNTRLongReadsCmd,#,76
Before Change
"Name of the output file, - for stdout");
addString("xafFile", null, "Name of the regions file in xaf",
true);
addInt("flanking", 30, "Size of the flanking regions");
addInt("qual", 0, "Minimum quality");
addInt("iteration", 1, "Number of iteration");
addInt("nploidy",2,
After Change
addString("xafFile", null, "Name of the regions file in xaf",
true);
CommandLine.Option flankingOpt =
addInt("flanking", 30, "Size of the flanking regions");
CommandLine.Option minQualOpt =
addInt("qual", 0, "Minimum quality");
addInt("iteration", 1, "Number of iteration");
addInt("nploidy",2,
"The ploidy of the genome 1 = happloid, 2 = diploid. Currenly only support up to 2-ploidy");
addString("prefix", "",
"Prefix of temporary files, if not specified, will be automatically generated");
///////////////Adding galaxy support/////////////
flankingOpt.setGalaxySetting(new GalaxySetting("integer", null,false));
minQualOpt.setGalaxySetting(new GalaxySetting("integer", null,false));
xafFileOpt.setGalaxySetting(new GalaxySetting("data", "tabular",false));