// constructor
public Sgr2Bar(String[] args) {
try {
// check for args
processArgs(args);
System.out.println("Genome version -> " + genomeVersion);
System.out.println("Strand -> " + strand);
System.out.println("Stair Step? -> " + stairStep);
System.out.println();
// load tagValues
if (stairStep) tagValues.put(BarParser.GRAPH_TYPE_TAG, BarParser.GRAPH_TYPE_STAIRSTEP);
else tagValues.put(BarParser.GRAPH_TYPE_TAG, BarParser.GRAPH_TYPE_BAR);
for (int x = 0; x < sgrFiles.length; x++) {
System.out.println("\tLoading -> " + sgrFiles[x]);
GrGraph[] grs = GrGraph.loadSgrFile(sgrFiles[x]);
// make save directory
String dirName;
dirName = Misc.removeExtension(sgrFiles[x].getCanonicalPath());
File dir = new File(dirName);
dir.mkdir();
// print bar files
System.out.println("\tSaving...");
for (int i = 0; i < grs.length; i++) {
File barFile = new File(dir, grs[i].getChromosome() + ".bar");
barParser.writeBarFile(
barFile,
grs[i].getChromosome(),
genomeVersion,
strand.charAt(0),
grs[i].getBasePositions(),
grs[i].getValues(),
tagValues);
}
}
System.out.println("\nDone!\n");
} catch (IOException e) {
e.printStackTrace();
Misc.printErrAndExit("\nFailed to parse file!");
}
}