/*
* 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.sam.reader;
import org.broad.igv.Globals;
import org.broad.igv.ui.util.IndexCreatorDialog;
import org.broad.igv.ui.util.UIUtilities;
import htsjdk.tribble.readers.AsciiLineReader;
import javax.swing.*;
import java.io.*;
/**
* @author jrobinso
*/
public abstract class AlignmentIndexer {
static int DEFAULT_TILEWIDTH = 16000;
static int MILLISECONDS_IN_MINUTE = 60 * 1000;
/**
* Optional progress bar.
* TODO -- this should be done through event/listeners
*/
IndexCreatorDialog.IndexWorker worker;
JProgressBar progressBar;
File samFile;
public static AlignmentIndexer getInstance(File samFile,
JProgressBar progressBar,
IndexCreatorDialog.SamIndexWorker worker) {
String fn = samFile.getName().toLowerCase();
if (fn.endsWith(".aligned") || fn.endsWith(".bedz") || fn.endsWith(".bed") ||
fn.endsWith(".aligned.txt") || fn.endsWith(".bedz.txt") || fn.endsWith(".bed.txt")) {
return new DotAlignedIndexer(samFile, progressBar, worker);
}
return new SamIndexer(samFile, progressBar, worker);
}
AlignmentIndexer(File samFile,
JProgressBar progressBar,
IndexCreatorDialog.SamIndexWorker worker) {
this.samFile = samFile;
this.progressBar = progressBar;
this.worker = worker;
}
public FeatureIndex createSamIndex() throws
IOException,
FileNotFoundException {
File idxFile = new File(samFile.getParent(), samFile.getName() + ".sai");
return createSamIndex(idxFile);
}
public FeatureIndex createSamIndex(File idxFile) throws
IOException {
return createSamIndex(idxFile, DEFAULT_TILEWIDTH);
}
public FeatureIndex createSamIndex(
File idxFile, int tileWidth) throws
IOException {
FileInputStream is = new FileInputStream(samFile);
InputStream bis = new BufferedInputStream(is);
AsciiLineReader reader = new AsciiLineReader(bis);
long fileLength = samFile.length();
long progressIncrement = fileLength / 100;
long lastFilePosition = 0;
String lastChr = null;
int lastAlignmentStart = 0;
FeatureIndex featureIndex = new FeatureIndex(tileWidth);
int recordCount = 0;
long filePosition = 0;
int currentTile = 0;
int longestFeature = 0;
long startTime = System.currentTimeMillis();
int progressCounter = 1; // progress in %
String nextLine = "";
int lineNumber = 0;
while ((nextLine = reader.readLine()) != null) {
lineNumber++;
if (worker != null && worker.isCancelled()) {
return null;
}
//int nBytes = nextLine.length();
nextLine = nextLine.trim();
String[] fields = Globals.tabPattern.split(nextLine, -1);
int nFields = fields.length;
if (!nextLine.startsWith("@") && nFields > 3 && isMapped(fields)) {
String chr = getChromosome(fields);
int alignmentStart = getAlignmentStart(fields);
int tileNumber = alignmentStart / tileWidth;
if (lastChr == null) {
// First record
currentTile = tileNumber;
for (int i = 0; i < currentTile; i++) {
featureIndex.add(chr, lastFilePosition, 0, longestFeature);
}
lastChr = chr;
} else if (!chr.equals(lastChr)) { // New chromosome
featureIndex.add(lastChr, filePosition, recordCount, longestFeature);
filePosition = lastFilePosition;
currentTile = 0;
recordCount = 0;
lastAlignmentStart = 0;
longestFeature = 0;
lastChr = chr;
} else {
longestFeature = Math.max(longestFeature, getAlignmentLength(fields));
if (alignmentStart < 0) {
System.out.println("Warning: negative start position at line: " + lineNumber + " : " + nextLine);
continue;
}
if (alignmentStart < lastAlignmentStart) {
throw new UnsortedFileException(" File must be sorted by start position. " +
"Sort test failed at: " + nextLine);
}
lastAlignmentStart = alignmentStart;
if (tileNumber > currentTile) {
// We have crossed a tile boundary. Record index and counts for previous tile
featureIndex.add(lastChr, filePosition, recordCount, longestFeature);
// If tiles were skipped record zero counts for these.
for (int cnt = 0; cnt < (tileNumber - currentTile - 1); cnt++) {
featureIndex.add(lastChr, filePosition, 0, longestFeature);
}
filePosition = lastFilePosition;
currentTile = tileNumber;
recordCount = 0;
}
recordCount++;
}
}
lastFilePosition = reader.getPosition();
if (lastFilePosition > (progressCounter * progressIncrement)) {
updateProgress(progressCounter, startTime);
progressCounter++;
}
}
// Record last partial tile
featureIndex.add(lastChr, filePosition, recordCount, longestFeature);
is.close();
if (idxFile != null) {
featureIndex.store(idxFile);
}
//Done now
updateProgress(100, startTime);
if (progressBar == null) {
System.out.println("Done indexing " + samFile.getName());
}
return featureIndex;
}
abstract int getAlignmentStart(String[] fields) throws NumberFormatException;
abstract int getAlignmentLength(String[] fields) throws NumberFormatException;
abstract String getChromosome(String[] fields);
abstract boolean isMapped(String[] fields);
private void updateProgress(int progressCounter, long startTime) {
final long timeToComplete = ((100 - progressCounter) *
(System.currentTimeMillis() - startTime)) / progressCounter;
final int p = progressCounter;
if (progressBar != null) {
UIUtilities.invokeOnEventThread(new Runnable() {
public void run() {
progressBar.setValue(p);
if (worker != null) {
worker.setTimeRemaining(timeToComplete);
}
}
});
} else {
System.out.println(
"Progress: " + progressCounter + "%");
}
}
}