Updating the BQSR Gatherer to the new file format
This is important for quick turnaround in the analysis cycle of the new covariates. Also added a dummy unit test that doesn't really test anything (disabled), but helps in debugging.
This commit is contained in:
Mauricio Carneiro
parent
1c67a62fc0
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0d4ea30d6d
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/*
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* Copyright (c) 2011 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.bqsr;
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import org.broadinstitute.sting.commandline.Gatherer;
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import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatumOptimized;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.text.XReadLines;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.PrintStream;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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/**
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* User: carneiro
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* Date: 3/29/11
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*/
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public class BQSRGatherer extends Gatherer {
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/////////////////////////////
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// Private Member Variables
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/////////////////////////////
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private static final String EOF_MARKER = "EOF";
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private HashMap<String, RecalDatumOptimized> dataMap = new HashMap<String, RecalDatumOptimized>();
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private void addCSVData (String line) {
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String[] covariates = line.split(",");
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String key = "";
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RecalDatumOptimized values;
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for (int i = 0; i < covariates.length-3; i++)
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key += covariates[i] + ",";
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if (covariates.length < 3)
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throw new ReviewedStingException("Line only has 1 covariate : " + line);
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values = new RecalDatumOptimized(Long.parseLong(covariates[covariates.length - 3]), Long.parseLong(covariates[covariates.length - 2]));
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RecalDatumOptimized currentValues = dataMap.get(key);
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if (currentValues == null)
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dataMap.put(key, values);
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else
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currentValues.increment(values);
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}
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@Override
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public void gather(List<File> inputs, File output) {
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PrintStream o;
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try {
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o = new PrintStream(output);
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} catch ( FileNotFoundException e) {
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throw new UserException("File to be output by CountCovariates Gather function was not found");
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}
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boolean sawEOF = false;
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boolean printedHeader = false;
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// Read input files
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for ( File RECAL_FILE : inputs) {
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try {
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for ( String line : new XReadLines(RECAL_FILE) ) {
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if ( EOF_MARKER.equals(line) ) {
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sawEOF = true; // sanity check
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break;
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}
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else if(line.startsWith("#")) {
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if (!printedHeader)
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o.println(line);
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}
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else // Found a line of data
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addCSVData(line); // Parse the line and add the data to the HashMap
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}
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} catch ( FileNotFoundException e ) {
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throw new UserException.CouldNotReadInputFile(RECAL_FILE, "Can not find input file", e);
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}
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if ( !sawEOF ) {
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final String errorMessage = "No EOF marker was present in the recal covariates table; this could mean that the file is corrupted!";
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throw new UserException.MalformedFile(RECAL_FILE, errorMessage);
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}
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printedHeader = true;
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}
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// Write output file from dataMap
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for(Map.Entry<String, RecalDatumOptimized> entry : dataMap.entrySet())
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o.println(entry.getKey() + entry.getValue().outputToCSV());
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o.println("EOF");
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}
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}
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@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.walkers.recalibration.CountCovariatesGatherer;
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import java.io.PrintStream;
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import java.util.Collections;
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@ -59,7 +58,7 @@ public class RecalibrationArgumentCollection {
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* three items are the data- that is, number of observations for this combination of covariates, number of reference mismatches,
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* and the raw empirical quality score calculated by phred-scaling the mismatch rate.
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*/
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@Gather(CountCovariatesGatherer.class)
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@Gather(BQSRGatherer.class)
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@Output
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protected PrintStream RECAL_FILE;
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@ -0,0 +1,29 @@
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package org.broadinstitute.sting.gatk.walkers.bqsr;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.util.LinkedList;
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import java.util.List;
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/**
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* @author Mauricio Carneiro
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* @since 3/7/12
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*/
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public class BQSRGathererUnitTest {
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RecalibrationArgumentCollection RAC;
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private static File recal1 = new File("public/testdata/exampleCSV.csv");
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private static File recal2 = new File("public/testdata/exampleCSV.2.csv");
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@Test(enabled = false)
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public void testCombineTwoFiles() {
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BQSRGatherer gatherer = new BQSRGatherer();
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List<File> recalFiles = new LinkedList<File> ();
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File output = new File("foo.csv");
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recalFiles.add(recal1);
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recalFiles.add(recal2);
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gatherer.gather(recalFiles, output);
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}
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}
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