/*
* Copyright (c) 2007-2012 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.cli_plugin;
import org.broad.igv.Globals;
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.feature.tribble.IGVBEDCodec;
import htsjdk.tribble.readers.LineIterator;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
/**
* Codec for reading and writing data with BEDTools
* User: jacob
* Date: 2012-Aug-02
*/
public final class BEDToolsDecoder extends AsciiDecoder<BasicFeature> implements LineFeatureDecoder<BasicFeature> {
private IGVBEDCodec BEDCodec = new IGVBEDCodec();
private boolean hasSplit = false;
private int numTracks = 0;
private int[] numCols = null;
private boolean multiinter;
/**
* The output of the closest and window
* commands are somewhat different from other commands
*/
private boolean closestOrSim;
public BEDToolsDecoder() {
super.lineFeatureDecoder = this;
}
public void setInputs(List<String> commands, Map<Argument, Object> argumentMap) {
super.setInputs(commands, argumentMap);
for (String cmdTok : commands) {
hasSplit |= cmdTok.contains("-split");
}
multiinter = commands.contains("multiinter");
closestOrSim = commands.contains("window") || commands.contains("closest");
for (Map.Entry<Argument, Object> entry : argumentMap.entrySet()) {
Argument curArg = entry.getKey();
hasSplit |= curArg.getCmdArg().contains("-split");
switch (curArg.getType()) {
case TEXT:
String sVal = (String) entry.getValue();
if (sVal == null) continue;
hasSplit |= (sVal).contains("-split");
break;
case FEATURE_TRACK:
numTracks++;
break;
case MULTI_FEATURE_TRACK:
numTracks += ((List) entry.getValue()).size();
break;
}
}
}
@Override
public BasicFeature decode(String line) {
return this.decode(Globals.singleTabMultiSpacePattern.split(line));
}
@Override
public Object readActualHeader(LineIterator reader) throws IOException {
return null;
}
public BasicFeature decode(String[] tokens) {
BasicFeature feat;
if (hasSplit) {
//When we split, the returned feature still has the exons
//We don't want to plot them all a zillion times
tokens = Arrays.copyOfRange(tokens, 0, Math.min(6, tokens.length));
}
if (closestOrSim) {
String[] closest = Arrays.copyOfRange(tokens, numCols[0], numCols[0] + numCols[1]);
//If not found, bedtools returns -1 for positions
if (closest[1].trim().equalsIgnoreCase("-1")) {
return null;
}
feat = BEDCodec.decode(closest);
} else if (multiinter) {
//We only look at regions common to ALL inputs
//Columns: chr \t start \t \end \t # of files which contained this feature \t comma-separated list files +many more
int numRegions = Integer.parseInt(tokens[3]);
if (numRegions < numTracks) {
return null;
}
String[] intersection = Arrays.copyOf(tokens, 3);
feat = BEDCodec.decode(intersection);
} else {
feat = BEDCodec.decode(tokens);
}
return feat;
}
@Override
public void setAttributes(List<Map<String, Object>> attributes) {
super.setAttributes(attributes);
numCols = new int[attributes.size()];
int ind = 0;
for (Map<String, Object> attributeMap : attributes) {
int curOutCols = (Integer) attributeMap.get(AsciiEncoder.NUM_COLS_ATTR);
numCols[ind++] = curOutCols;
}
}
}