/*
* Copyright (c) 2012 The 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,
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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package org.broadinstitute.gatk.tools.walkers.diagnostics;
import htsjdk.samtools.SAMReadGroupRecord;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.report.GATKReport;
import org.broadinstitute.gatk.engine.report.GATKReportTable;
import org.broadinstitute.gatk.engine.walkers.ReadWalker;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import java.io.PrintStream;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
/**
* Outputs the read lengths of all the reads in a file.
*
* <p>
* Generates a table with the read lengths categorized per sample. If the file has no sample information
* (no read groups) it considers all reads to come from the same sample.
* </p>
*
*
* <h3>Input</h3>
* <p>
* A BAM file.
* </p>
*
* <h3>Output</h3>
* <p>
* A human/R readable table of tab separated values with one column per sample and one row per read.
* </p>
*
* <h3>Examples</h3>
* <pre>
* java
* -jar GenomeAnalysisTK.jar
* -T ReadLengthDistribution
* -I example.bam
* -R reference.fasta
* -o example.tbl
* </pre>
*
* @author Kiran Garimela
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class ReadLengthDistribution extends ReadWalker<Integer, Integer> {
@Output
public PrintStream out;
//A map from RG to its column number (its index in an int[] array)
private Map<SAMReadGroupRecord,Integer> readGroupsLocation;
//Each line in the table is a read length and each column it the number of reads of a specific RG with that length. Thus a table is a map between read lengths to array of values (one for each RG).
private Map<Integer,int[]> table;
private List<SAMReadGroupRecord> readGroups;
public void initialize() {
readGroups = getToolkit().getSAMFileHeader().getReadGroups();
readGroupsLocation = new HashMap<>();
table = new TreeMap<>();
int readGroupsNum = 0;
if (!readGroups.isEmpty()){
for (SAMReadGroupRecord rg : readGroups){
readGroupsLocation.put(rg,readGroupsNum);
readGroupsNum++;
}
}
}
@Override
public Integer map(final ReferenceContext referenceContext,final GATKSAMRecord samRecord,final RefMetaDataTracker RefMetaDataTracker) {
final int length = Math.abs(samRecord.getReadLength());
final SAMReadGroupRecord rg = samRecord.getReadGroup();
increment(table,length, rg);
return null;
}
final private void increment(final Map<Integer,int[]> table,final int length,final SAMReadGroupRecord rg){
if(readGroupsLocation.isEmpty()){
if(table.containsKey(length))
table.get(length)[0]++;
else{
final int[] newLength = {1};
table.put(length,newLength);
}
}
else{
final int rgLocation = readGroupsLocation.get(rg);
if(table.containsKey(length))
table.get(length)[rgLocation]++;
else{
table.put(length,new int[readGroupsLocation.size()]);
table.get(length)[rgLocation]++;
}
}
}
@Override
public Integer reduceInit() {
return null;
}
@Override
public Integer reduce(final Integer integer,final Integer integer1) {
return null;
}
public void onTraversalDone(final Integer sum) {
final GATKReport report = createGATKReport();
report.print(out);
}
final private GATKReport createGATKReport(){
final GATKReport report = new GATKReport();
report.addTable("ReadLengthDistribution", "Table of read length distributions", 1 + (readGroupsLocation.isEmpty() ? 1 : readGroupsLocation.size()));
final GATKReportTable tableReport = report.getTable("ReadLengthDistribution");
tableReport.addColumn("readLength");
if (readGroupsLocation.isEmpty()){
tableReport.addColumn("SINGLE_SAMPLE");
int rowIndex = 0;
for (Integer length : table.keySet()){
tableReport.set(rowIndex,0,length);
tableReport.set(rowIndex,1,table.get(length)[0]);
rowIndex++;
}
}
else{
for (SAMReadGroupRecord rg : readGroups)
tableReport.addColumn(rg.getSample());
int rowIndex = 0;
for (Integer length : table.keySet()){
tableReport.set(rowIndex,0,length);
for (int i=0; i < readGroupsLocation.size(); i++)
tableReport.set(rowIndex,i+1,table.get(length)[i]);
rowIndex++;
}
}
return report;
}
}