/*
* Copyright (c) 2007-2013 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.sam.reader;
//~--- non-JDK imports --------------------------------------------------------
//~--- JDK imports ------------------------------------------------------------
import htsjdk.samtools.Cigar;
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.CigarOperator;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.StringUtil;
import org.apache.log4j.Logger;
import org.broad.igv.DirectoryManager;
import org.broad.igv.Globals;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.util.IndexCreatorDialog;
import org.broad.igv.util.FileUtils;
import java.io.File;
import java.io.IOException;
/**
* @author jrobinso
*/
public class SamUtils {
private static Logger log = Logger.getLogger(SamUtils.class);
private static final byte ZERO_BYTE = "0".getBytes()[0];
private static final byte NINE_BYTE = "9".getBytes()[0];
public static FeatureIndex getIndexFor(String samPath) {
String idxPath = samPath + ".sai";
if (FileUtils.resourceExists(idxPath)) {
return new FeatureIndex(idxPath);
} else if (FileUtils.isRemote(idxPath)) {
return null;
} else {
File idxFile = new File(idxPath);
File samFile = new File(samPath);
if (!idxFile.exists()) {
idxFile = getUserIdxFile(samFile);
}
if (idxFile.exists() && idxFile.lastModified() > samFile.lastModified()) {
return new FeatureIndex(idxFile);
} else {
return createIndexFor(samFile);
}
}
}
private static FeatureIndex createIndexFor(File samFile) {
File newIdxFile = new File(samFile.getAbsolutePath() + ".sai");
if (!FileUtils.canWriteTo(newIdxFile)) {
newIdxFile = getUserIdxFile(samFile);
}
if (!Globals.isHeadless()) {
String introText = "An index file for " + samFile.getAbsolutePath() + " could not " +
"be located. An index is required to view SAM files in IGV. " +
"Click \"Go\" to create one now.";
IndexCreatorDialog dialog = IndexCreatorDialog.createShowDialog(IGV.getMainFrame(), samFile, newIdxFile, introText);
return (FeatureIndex) dialog.getIndex();
} else {
AlignmentIndexer indexer = AlignmentIndexer.getInstance(samFile, null, null);
FeatureIndex index = null;
try {
log.info("Creating index " + newIdxFile.getAbsolutePath());
index = indexer.createSamIndex(newIdxFile);
} catch (IOException e) {
e.fillInStackTrace();
}
return index;
}
}
private static File getUserIdxFile(File samFile) {
File idxFile;
File samDir = DirectoryManager.getSamDirectory();
//Need the path information to distinguish like name indices in separate
// directories.
idxFile = new File(samDir, samFile.getName() + "_" + samFile.getParent().hashCode() + ".sai");
return idxFile;
}
public static int getPaddedReferenceLength(String cigarString) {
return decodeCigar(cigarString).getPaddedReferenceLength();
}
/**
* Convert from String CIGAR representation to Cigar class representation. Does not
* do validation beyond the most basic CIGAR string well-formedness, i.e. each operator is
* valid, and preceded by a decimal length.
*
* @param textCigar CIGAR in String form ala SAM text file. "*" means empty CIGAR.
* @throws RuntimeException if textCigar is invalid at the most basic level.
*/
static Cigar decodeCigar(final String textCigar) {
if (SAMRecord.NO_ALIGNMENT_CIGAR.equals(textCigar)) {
return new Cigar();
}
final Cigar ret = new Cigar();
final byte[] cigarBytes = StringUtil.stringToBytes(textCigar);
for (int i = 0; i < cigarBytes.length; ++i) {
if (!isDigit(cigarBytes[i])) {
throw new IllegalArgumentException("Malformed CIGAR string: " + textCigar);
}
int length = (cigarBytes[i] - ZERO_BYTE);
for (++i; isDigit(cigarBytes[i]); ++i) {
length = (length * 10) + cigarBytes[i] - ZERO_BYTE;
}
final CigarOperator operator = CigarOperator.characterToEnum(cigarBytes[i]);
ret.add(new CigarElement(length, operator));
}
return ret;
}
private static boolean isDigit(final byte c) {
return c >= ZERO_BYTE && c <= NINE_BYTE;
}
}