/*
* 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.sam;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.PreferenceManager;
import org.broad.igv.feature.Strand;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.readers.AsciiLineReader;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
/**
* @author Jim Robinson
* @date 11/29/11
*/
abstract public class BaseAlignmentCounts implements AlignmentCounts {
private static Logger log = Logger.getLogger(BaseAlignmentCounts.class);
public static final char[] nucleotides = {'a', 'c', 'g', 't', 'n'};
private static Map<String, Set<Integer>> knownSnps;
int start;
int end;
protected boolean countDeletedBasesCovered = false;
private BisulfiteCounts bisulfiteCounts;
public BaseAlignmentCounts(int start, int end, AlignmentTrack.BisulfiteContext bisulfiteContext) {
final PreferenceManager prefs = PreferenceManager.getInstance();
String snpsFile = prefs.get(PreferenceManager.KNOWN_SNPS, null);
if (snpsFile != null && knownSnps == null) {
loadKnownSnps(snpsFile);
}
this.start = start;
this.end = end;
countDeletedBasesCovered = prefs.getAsBoolean(PreferenceManager.SAM_COUNT_DELETED_BASES_COVERED);
if (!Globals.isHeadless() && bisulfiteContext != null) {
bisulfiteCounts = new BisulfiteCounts(bisulfiteContext, GenomeManager.getInstance().getCurrentGenome());
}
}
public int getStart() {
return start;
}
public int getEnd() {
return end;
}
public String getChr() {
return null;
}
public BisulfiteCounts getBisulfiteCounts() {
return bisulfiteCounts;
}
/**
* Increment the counts for this alignment. Does not consider softclips.
*
* @param alignment
*/
public void incCounts(Alignment alignment) {
if (bisulfiteCounts != null) {
bisulfiteCounts.incrementCounts(alignment);
}
int alignmentStart = alignment.getAlignmentStart();
int alignmentEnd = alignment.getAlignmentEnd();
AlignmentBlock[] blocks = alignment.getAlignmentBlocks();
if (blocks != null) {
int lastBlockEnd = -1;
int gapIdx = 0;
char[] gapTypes = alignment.getGapTypes();
for (AlignmentBlock b : blocks) {
if (b.getEnd() < start) continue;
if (b.getStart() > end) break;
//Strand strand = alignment.getFirstOfPairStrand();
Strand strand = alignment.getReadStrand();
// Don't count softclips
if (!b.isSoftClipped() && strand != Strand.NONE) {
final boolean isNegativeStrand = strand == Strand.NEGATIVE;
incBlockCounts(b, isNegativeStrand); //alignment.isNegativeStrand());
// Count deletions
if (gapTypes != null
&& (lastBlockEnd >= 0)
&& (gapIdx < gapTypes.length)) {
if (gapTypes[gapIdx] == SAMAlignment.DELETION) {
for (int pos = lastBlockEnd; pos < b.getStart(); pos++) {
incrementDeletion(pos, isNegativeStrand);
}
}
gapIdx++;
}
lastBlockEnd = b.getEnd();
}
}
// Count insertions
final AlignmentBlock[] insertions = alignment.getInsertions();
if (insertions != null) {
for (AlignmentBlock insBlock : insertions) {
if (insBlock.getEnd() < start) continue;
if (insBlock.getStart() > end) break;
incrementInsertion(insBlock);
}
}
} else {
// No alignment blocks => no bases (e.g. .aln or .aligned files). Just do total count.
for (int pos = alignmentStart; pos < alignmentEnd; pos++) {
byte q = 0;
incPositionCount(pos, (byte) 'n', q, alignment.isNegativeStrand());
}
}
}
public String getValueStringAt(int pos) {
if (pos < getStart() || pos >= getEnd()) return null;
StringBuffer buf = new StringBuffer();
int totalCount = getTotalCount(pos);
buf.append("Total count: " + totalCount);
for (char c : nucleotides) {
int negCount = getNegCount(pos, (byte) c);
int posCount = getPosCount(pos, (byte) c);
int count = negCount + posCount;
int percent = (int) Math.round(((float) count) * 100 / totalCount);
char cU = Character.toUpperCase(c);
buf.append("<br>" + cU + " : " + count);
if (count != 0) {
buf.append(" (" + percent + "%, " + posCount + "+, " + negCount + "- )");
}
}
int delCount = getDelCount(pos);
int insCount = getInsCount(pos);
buf.append("<br>---------------");
if (delCount > 0 || insCount > 0) {
buf.append("<br>DEL: " + delCount);
buf.append("<br>INS: " + insCount);
}
return buf.toString();
}
public boolean isMismatch(int pos, byte ref, String chr, float snpThreshold) {
Set<Integer> filteredSnps = knownSnps == null ? null : knownSnps.get(chr);
if (filteredSnps == null || !filteredSnps.contains(pos + 1)) {
float threshold = snpThreshold * getTotalQuality(pos);
if (ref > 0) {
if (ref < 96) ref += 32; // a fast "toLowercase"
for (char c : nucleotides) {
if (c != ref && c != 'n' && getQuality(pos, (byte) c) > threshold) {
return true;
}
}
}
}
return false;
}
/**
* Load the set of known snps from a tab delimited file, format
* chr < tab> location
* The location is "1 base" (first nucleotide is position 1).
*
* @param snpFile
*/
private static synchronized void loadKnownSnps(String snpFile) {
// This method might get called many times concurrently, but we only want to load these once.
if (knownSnps != null) {
return;
}
knownSnps = new HashMap();
AsciiLineReader reader = null;
try {
reader = ParsingUtils.openAsciiReader(new ResourceLocator(snpFile));
String nextLine = "";
while ((nextLine = reader.readLine()) != null) {
String[] tokens = nextLine.split("\t");
String chr = tokens[0];
Set<Integer> snps = knownSnps.get(chr);
if (snps == null) {
snps = new HashSet(10000);
knownSnps.put(chr, snps);
}
snps.add(new Integer(tokens[1]));
}
} catch (Exception e) {
knownSnps = null;
log.error("", e);
MessageUtils.showMessage("Error loading snps file: " + snpFile + " (" + e.toString() + ")");
} finally {
reader.close();
}
}
protected abstract void incPositionCount(int pos, byte n, byte q, boolean negativeStrand);
protected abstract void incrementInsertion(AlignmentBlock insBlock);
protected abstract void incrementDeletion(int pos, boolean negativeStrand);
protected abstract void incBlockCounts(AlignmentBlock b, boolean isNegativeStrand);
}