/*
* 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,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.tools.walkers.qc;
import htsjdk.samtools.reference.IndexedFastaSequenceFile;
import htsjdk.samtools.reference.ReferenceSequence;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.walkers.RefWalker;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.exceptions.GATKException;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import java.io.PrintStream;
/**
* Quality control for the reference fasta
*
*
* <h3>Input</h3>
* <p>
* One reference file only. And optionally -L intervals
* </p>
*
* <h3>Output</h3>
* <p>
* If ok, nothing, else will throw an exception at the site where there's been a problem
* </p>
*
* <h3>Examples</h3>
* <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T QCRef
* </pre>
*
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class QCRef extends RefWalker<Integer, Integer> {
@Output
public PrintStream out;
String contigName = "";
int contigStart, contigEnd;
IndexedFastaSequenceFile uncachedRef;
byte[] uncachedBases;
@Override
public void initialize() {
super.initialize(); //To change body of overridden methods use File | Settings | File Templates.
uncachedRef = getToolkit().getReferenceDataSource().getReference();
}
private final void throwError(ReferenceContext ref, String message) {
throw new GATKException(String.format("Site %s failed: %s", ref.getLocus(), message));
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
final String locusContigName = ref.getLocus().getContig();
if ( ! locusContigName.equals(contigName) ) {
contigName = locusContigName;
ReferenceSequence refSeq = uncachedRef.getSequence(contigName);
contigStart = 1;
contigEnd = contigStart + refSeq.length() - 1;
uncachedBases = uncachedRef.getSubsequenceAt(contigName, contigStart, contigEnd).getBases();
logger.info(String.format("Loading contig %s (%d-%d)", contigName, contigStart, contigEnd));
}
final byte refBase = ref.getBase();
if (! ( BaseUtils.isRegularBase(refBase) || isExtendFastaBase(refBase) ) )
throwError(ref, String.format("Refbase isn't a regular base (%d %c)", refBase, (char)refBase));
// check bases are equal
final int pos = (int)context.getPosition() - contigStart;
if ( pos > contigEnd )
throwError(ref, String.format("off contig (len=%d)", contigEnd));
final byte uncachedBase = uncachedBases[pos];
if ( uncachedBase != refBase )
throwError(ref, String.format("Provided refBase (%d %c) not equal to uncached one (%d %c)",
refBase, (char)refBase, uncachedBase, (char)uncachedBase));
return 1;
}
private static final boolean isExtendFastaBase(final byte b) {
switch ( b ) {
case 'U':
case 'R':
case 'Y':
case 'K':
case 'M':
case 'S':
case 'W':
case 'B':
case 'D':
case 'H':
case 'V':
case 'N':
case 'X':
case '-':
return true;
default:
return false;
}
}
public Integer reduceInit() {
return 0;
}
public Integer reduce(Integer one, Integer sum) {
return one + sum;
}
}