/*
* The MIT License
*
* Copyright (c) 2009 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 picard.sam;
import htsjdk.samtools.BamFileIoUtils;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMFileWriter;
import htsjdk.samtools.SAMFileWriterFactory;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.ValidationStringency;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.ProgressLogger;
import picard.PicardException;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.SamOrBam;
import java.io.File;
/**
* @author alecw@broadinstitute.org
*/
@CommandLineProgramProperties(
usage = "Replace the SAMFileHeader in a SAM file with the given header. " +
"Validation is minimal. It is up to the user to ensure that all the elements referred to in the SAMRecords " +
"are present in the new header. Sort order of the two input files must be the same.",
usageShort = "Replace the SAMFileHeader in a SAM file with the given header",
programGroup = SamOrBam.class
)
public class ReplaceSamHeader extends CommandLineProgram {
@Option(doc="SAM file from which SAMRecords will be read.", shortName = StandardOptionDefinitions.INPUT_SHORT_NAME)
public File INPUT;
@Option(doc="SAM file from which SAMFileHeader will be read.")
public File HEADER;
@Option(doc="SAMFileHeader from HEADER file will be written to this file, followed by SAMRecords from INPUT file",
shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME)
public File OUTPUT;
public static void main(final String[] argv) {
new ReplaceSamHeader().instanceMainWithExit(argv);
}
/**
* Do the work after command line has been parsed.
* RuntimeException may be thrown by this method, and are reported appropriately.
*
* @return program exit status.
*/
@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsReadable(HEADER);
IOUtil.assertFileIsWritable(OUTPUT);
final SAMFileReader headerReader = new SAMFileReader(HEADER);
final SAMFileHeader replacementHeader = headerReader.getFileHeader();
headerReader.close();
final ValidationStringency originalStringency = SAMFileReader.getDefaultValidationStringency();
SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
try {
if (BamFileIoUtils.isBamFile(INPUT)) {
blockCopyReheader(replacementHeader);
} else {
standardReheader(replacementHeader);
}
} finally {
SAMFileReader.setDefaultValidationStringency(originalStringency);
}
return 0;
}
private void standardReheader(final SAMFileHeader replacementHeader) {
final SAMFileReader recordReader = new SAMFileReader(INPUT);
if (replacementHeader.getSortOrder() != recordReader.getFileHeader().getSortOrder()) {
throw new PicardException("Sort orders of INPUT (" + recordReader.getFileHeader().getSortOrder().name() +
") and HEADER (" + replacementHeader.getSortOrder().name() + ") do not agree.");
}
final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(replacementHeader, true, OUTPUT);
final ProgressLogger progress = new ProgressLogger(Log.getInstance(ReplaceSamHeader.class));
for (final SAMRecord rec : recordReader) {
rec.setHeader(replacementHeader);
writer.addAlignment(rec);
progress.record(rec);
}
writer.close();
recordReader.close();
}
private void blockCopyReheader(final SAMFileHeader replacementHeader) {
BamFileIoUtils.reheaderBamFile(replacementHeader, INPUT, OUTPUT, CREATE_MD5_FILE, CREATE_INDEX);
}
}