public Bed2Bar(String[] args) {
try {
processArgs(args);
// load Window[]
for (int i = 0; i < bedFiles.length; i++) {
bedFile = bedFiles[i];
System.out.println("Parsing " + bedFile.getName());
bedLinesHash = Bed.parseBedFile(bedFile, true, false);
if (bedLinesHash == null || bedLinesHash.size() == 0) {
System.out.println("Problem parsing bed file, skipping!");
continue;
}
barDirectory = IO.makeDirectory(bedFile, "");
File bedOutFile =
new File(Misc.removeExtension(bedFile.toString()) + "_" + threshold + "_Filt.bed");
bedOut = new PrintWriter(new FileWriter(bedOutFile));
makeStairStepBarFiles();
}
bedOut.close();
System.out.println("\nDone!\n");
} catch (IOException e) {
e.printStackTrace();
}
}
/** Make a heatmap blocks from given window indexes, stop not included. */
public void sumHeatMapBlocks(int startIndex, int stopIndex) {
// create arrays of float, one per base to hold sums
// windows are sorted by start and length
int startBase = windows[startIndex].getStart();
int stopBase = findMaxStop(startIndex, stopIndex);
int numBases = 1 + stopBase - startBase;
float[] sums = new float[numBases];
// load max arrays with max scores
// for each window
for (int i = startIndex; i < stopIndex; i++) {
float score = windows[i].getScore();
int baseIndex = windows[i].getStart() - startBase;
int length = windows[i].getStop() - windows[i].getStart() + baseIndex + 1;
for (int j = baseIndex; j < length; j++) sums[j] += score;
}
// build blocks
// open first block
// set zero mark
int previousBase = startBase - 1;
if (previousBase < 0) previousBase = 0;
add(previousBase, 0);
// set block value
float blockValue = sums[0];
add(startBase, blockValue);
// advance each base opening and closing blocks
for (int i = 1; i < numBases; i++) {
float testValue = sums[i];
if (testValue != blockValue) {
// close old
add(i - 1 + startBase, blockValue);
// open new
blockValue = testValue;
add(i + startBase, blockValue);
}
}
// close last block
add(numBases - 2 + startBase, blockValue);
add(numBases - 1 + startBase, 0);
// make merged filtered bed file?
if (bedOut != null) {
boolean[] falseMask = new boolean[sums.length];
Arrays.fill(falseMask, true);
for (int i = 0; i < sums.length; i++) if (sums[i] >= threshold) falseMask[i] = false;
int[][] blocks = ExportIntergenicRegions.fetchFalseBlocks(falseMask, 0, 0);
// print bed file
for (int i = 0; i < blocks.length; i++) {
bedOut.println(
chromosome + "\t" + (startBase + blocks[i][0]) + "\t" + (startBase + blocks[i][1]));
}
}
}