public static void main(String[] args) {
try {
String inFile =
"/psychipc01/disk2/references/1000Genome/release/20130502_v5a/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz";
String outFile =
"/psychipc01/disk2/references/1000Genome/release/20130502_v5a/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes1.vcf.gz";
BlockCompressedInputStream br = new BlockCompressedInputStream(new File(inFile));
BlockCompressedOutputStream bw = new BlockCompressedOutputStream(new File(outFile));
String line = null;
String[] cells = null;
int[] orgIndices =
new int[] {
0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 33, 34, 35, 36, 37, 38,
39, 40
};
int selectedColNum = orgIndices.length;
int i, pos;
String delimiter = "\t";
while ((line = br.readLine()) != null) {
line = line.trim();
if (line.trim().length() == 0) {
continue;
}
bw.write(line.replaceAll("[|]", "/").getBytes());
bw.write("\n".getBytes());
}
bw.close();
br.close();
} catch (Exception ex) {
ex.printStackTrace();
}
}
@Override
public void run() {
if (myStartSite >= mySiteCount) {
return;
}
BlockCompressedInputStream reader = getReader();
try {
reader.seek(myIndex.virtualOffset(mySeekIndex));
int numSites = Math.min(myNumLinesPerInterval, mySiteCount - myStartSite);
byte[][] result = new byte[numSites][];
for (int i = 0; i < numSites; i++) {
result[i] = parseLine(reader.readLine(), myTaxaCount, myStartSite + i, myIsOneLetter);
CompletableFuture<byte[]> future = myFutureQueue.remove(myStartSite + i);
if (future != null) {
future.complete(result[i]);
}
}
myGenoCache.put(myProcessBlock, result);
// This get to prevent early eviction from cache
myGenoCache.getIfPresent(myProcessBlock);
myCurrentlyProcessingBlocks.remove(myProcessBlock);
for (int i = 0; i < numSites; i++) {
CompletableFuture<byte[]> future = myFutureQueue.remove(myStartSite + i);
if (future != null) {
future.complete(result[i]);
}
}
myStartSite += myNumLinesPerInterval;
if (myStartSite >= mySiteCount) {
return;
}
for (int b = 1; b < NUM_LOOK_AHEAD_BLOCKS; b++) {
if (myGenoCache.getIfPresent(myProcessBlock + b) != null) {
return;
}
if (!myCurrentlyProcessingBlocks.add(myProcessBlock + b)) {
return;
}
numSites = Math.min(myNumLinesPerInterval, mySiteCount - myStartSite);
result = new byte[numSites][];
for (int i = 0; i < numSites; i++) {
result[i] = parseLine(reader.readLine(), myTaxaCount, myStartSite + i, myIsOneLetter);
}
myGenoCache.put(myProcessBlock + b, result);
// This get to prevent early eviction from cache
myGenoCache.getIfPresent(myProcessBlock + b);
myCurrentlyProcessingBlocks.remove(myProcessBlock + b);
for (int i = 0; i < numSites; i++) {
CompletableFuture<byte[]> future = myFutureQueue.remove(myStartSite + i);
if (future != null) {
future.complete(result[i]);
}
}
myStartSite += myNumLinesPerInterval;
if (myStartSite >= mySiteCount) {
return;
}
}
} catch (Exception e) {
myLogger.error(e.getMessage(), e);
} finally {
myReaders.add(reader);
}
}
