org.campagnelab.dl.somatic.storage.ProtobufPrinter Maven / Gradle / Ivy
package org.campagnelab.dl.somatic.storage;
import com.google.protobuf.TextFormat;
import it.unimi.dsi.fastutil.ints.IntOpenHashSet;
import org.apache.commons.io.FilenameUtils;
import org.campagnelab.dl.varanalysis.protobuf.BaseInformationRecords;
import java.io.File;
import java.io.IOException;
import java.net.FileNameMap;
import java.util.Set;
/**
* Currently holds the main method. Jar takes two arguments
*
* java -jar var-analysis.jar process /recordsPath/to/genotypes.parquet
* creates mutated and randomized parquet file, then prints the latter
*
* java -jar var-analysis.jar print /recordsPath/to/genotypes.parquet
* prints the parquet file as is
*
* Also, this jar should be a resource for Goby to output variations as a parquet file using its AvroVariationOutputFormat
* class.
* Created by rct66 on 5/17/16.
*
* @author rct66
*/
public class ProtobufPrinter {
String path;
boolean focusPrint = false;
private int refIndex;
private int position;
private boolean customPosOnly = false;
static int actualCount = 0;
private boolean makeDebug = false;
private RecordWriter makeDebugWriter;
private int[] customPos = {
45944850
};
private Set posSet = new IntOpenHashSet(customPos);
public static void main(String[] args) throws IOException {
if (args.length<1) {
System.err.println("usage: printer [focus-ref-index focus-position]");
System.exit(1);
}
ProtobufPrinter protobufPrinter = new ProtobufPrinter(args[0]);
if (args.length >= 3) {
// will only print the record(s) matching a specific position:
protobufPrinter.setFocusOnPosition(Integer.parseInt(args[1]), Integer.parseInt(args[2]));
System.out.println("Scanning for ");
}
protobufPrinter.print();
System.out.println("actual count: " + actualCount);
}
private void setFocusOnPosition(int refIndex, int position) {
focusPrint = true;
this.refIndex = refIndex;
this.position = position;
}
public ProtobufPrinter(String path) throws IOException {
this.path = path;
if (makeDebug){
String debugPath = FilenameUtils.getFullPath(path) + FilenameUtils.getBaseName(path) + "_debug.sbi";
makeDebugWriter = new RecordWriter(debugPath);
}
}
private void recordPrinter(BaseInformationRecords.BaseInformation base) throws IOException {
TextFormat.print(base, System.out);
}
public void print() {
try {
RecordReader reader = new RecordReader(path);
for (BaseInformationRecords.BaseInformation base : reader) {
if (!(focusPrint || customPosOnly) ||
(base.getReferenceIndex() == refIndex && base.getPosition() == position) || (posSet.contains(base.getPosition()))) {
if (/*base.getSamples(0).getIsVariant() && */ base.getSamples(0).getCountsCount() > 5){
recordPrinter(base);
}
actualCount++;
if (makeDebug){
makeDebugWriter.writeRecord(base);
}
}
}
if (makeDebug){
makeDebugWriter.close();
}
} catch (IOException e) {
throw new RuntimeException(e);
}
}
}