/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.gwas;
import org.broad.igv.tdf.BufferedByteWriter;
import org.broad.igv.tools.sort.Sorter;
import org.broad.igv.tools.sort.SorterFactory;
import org.broad.igv.util.CompressionUtils;
import java.io.*;
import java.util.HashMap;
import java.util.Map;
/**
* Class for experimenting with binary EQTL formats.
* <p/>
* SNP SNP_Chr SNP_Pos Gen_ID Gene_Name Gene_Pos T_Stat P_Val Q_Val
* rs3094317 1 739528 ENSG00000237491.2 RP11-206L10.6 714162 -4.41310870534187 3.457968769964e-05 0.0254439762182497
*
SNP SNP_Chr SNP_Pos Gen_ID Gene_Name Gene_Pos T_Stat Beta P_Val min(p) EmpP nom_thresh
chr2:202672143:I 2 202672143 ENSG00000003393.10 ALS2 202645912 -4.90641599377695 -0.410144871510459 4.16077158322729e-06 4.1199296E-8 9 *
*/
public class EqtlPreprocessor {
static int version = 0;
long indexPositionPosition;
int bytesWritten;
BufferedByteWriter currentChrBuffer;
String currentChr;
private FileOutputStream fos;
private Map<String, IndexEntry> chrPositionMap;
private CompressionUtils compressionUtils;
static class IndexEntry {
IndexEntry(long position, int size) {
this.position = position;
this.size = size;
}
long position;
int size;
}
public static void main(String[] args) throws IOException {
File[] files = (new File(args[0])).listFiles();
for (File file : files) {
if (file.getName().endsWith(".eqtl")) {
File sortedFile = new File(file.getAbsolutePath() + ".sorted.eqtl");
Sorter sorter = SorterFactory.getSorter(file, sortedFile);
sorter.run();
(new EqtlPreprocessor()).process(sortedFile.getAbsolutePath(), file.getAbsolutePath() + ".bin");
}
}
}
public void process(String inputFile, String outputFile) throws IOException {
bytesWritten = 0;
BufferedReader br = null;
fos = null;
currentChr = null;
currentChrBuffer = null;
chrPositionMap = new HashMap<String, IndexEntry>();
compressionUtils = new CompressionUtils();
EQTLCodec codec = new EQTLCodec(null);
try {
fos = new FileOutputStream(outputFile);
writeHeader();
br = new BufferedReader(new FileReader(inputFile));
String nextLine = br.readLine();
while ((nextLine = br.readLine()) != null) {
EQTLFeature feature = codec.decode(nextLine);
String chr = feature.getChr();
if (!chr.equals(currentChr)) {
if (currentChrBuffer != null) {
System.out.println(currentChr);
writeChrBuffer();
}
currentChr = chr;
currentChrBuffer = new BufferedByteWriter();
}
currentChrBuffer.put(feature.encodeBinary());
}
if (currentChrBuffer != null) {
writeChrBuffer();
}
long position = bytesWritten;
int nBytes = writeIndex();
fos.close();
writeIndexPosition(outputFile, position, nBytes);
} finally {
if (br != null) br.close();
}
}
private void writeChrBuffer() throws IOException {
// compress and write
byte[] rawBytes = currentChrBuffer.getBytes();
byte[] compressedBytes = rawBytes; //compressionUtils.compress(rawBytes);
int position = bytesWritten;
int size = compressedBytes.length;
write(compressedBytes);
chrPositionMap.put(currentChr, new IndexEntry(position, size));
}
private int writeIndex() throws IOException {
// compress and write
BufferedByteWriter buff = new BufferedByteWriter();
buff.putInt(chrPositionMap.size());
for (Map.Entry<String, IndexEntry> entry : chrPositionMap.entrySet()) {
IndexEntry ie = entry.getValue();
buff.putNullTerminatedString(entry.getKey());
buff.putLong(ie.position);
buff.putInt(ie.size);
}
byte[] bytes = buff.getBytes();
write(bytes);
return bytes.length;
}
private void writeHeader() throws IOException {
// Magic number -- 4 bytes
byte[] magicNumber = new byte[]{'E', 'Q', 'T', 'L'};
BufferedByteWriter buffer = new BufferedByteWriter();
buffer.put(magicNumber);
buffer.putInt(version);
// Reserve space for the master index pointer and byte count.
// The actual values will be written at the end
indexPositionPosition = buffer.bytesWritten();
buffer.putLong(0l); // File position for start of index
buffer.putInt(0); // Size in bytes of index
final byte[] bytes = buffer.getBytes();
write(bytes);
}
private void writeIndexPosition(String file, long indexPosition, int nbytes) {
try {
RandomAccessFile raf = new RandomAccessFile(file, "rw");
raf.getChannel().position(indexPositionPosition);
// Write as little endian
BufferedByteWriter buffer = new BufferedByteWriter();
buffer.putLong(indexPosition);
buffer.putInt(nbytes);
raf.write(buffer.getBytes());
raf.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
private void write(byte[] bytes) throws IOException {
fos.write(bytes);
bytesWritten += bytes.length;
}
}