/*
* 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 htsjdk.samtools.example;
import htsjdk.samtools.DefaultSAMRecordFactory;
import htsjdk.samtools.SAMFileWriter;
import htsjdk.samtools.SAMFileWriterFactory;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SamInputResource;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.ValidationStringency;
import htsjdk.samtools.seekablestream.SeekableStream;
import java.io.File;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
public class ExampleSamUsage {
public static SeekableStream myIndexSeekableStream() {
throw new UnsupportedOperationException();
}
/** Example usages of {@link htsjdk.samtools.SamReaderFactory} */
public void openSamExamples() throws MalformedURLException {
/**
* Simplest case
*/
final SamReader reader = SamReaderFactory.makeDefault().open(new File("/my.bam"));
/**
* With different reader options
*/
final SamReader readerFromConfiguredFactory =
SamReaderFactory.make()
.enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX)
.validationStringency(ValidationStringency.SILENT)
.samRecordFactory(DefaultSAMRecordFactory.getInstance())
.open(new File("/my.bam"));
/**
* With a more complicated source
*/
final SamReader complicatedReader =
SamReaderFactory.makeDefault()
.open(
SamInputResource.of(new URL("http://broadinstitute.org/my.bam")).index(myIndexSeekableStream())
);
/**
* Broken down
*/
final SamReaderFactory factory =
SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS).validationStringency(ValidationStringency.LENIENT);
final SamInputResource resource = SamInputResource.of(new File("/my.bam")).index(new URL("http://broadinstitute.org/my.bam.bai"));
final SamReader myReader = factory.open(resource);
for (final SAMRecord samRecord : myReader) {
System.err.print(samRecord);
}
}
/**
* Read a SAM or BAM file, convert each read name to upper case, and write a new
* SAM or BAM file.
*/
public void convertReadNamesToUpperCase(final File inputSamOrBamFile, final File outputSamOrBamFile) throws IOException {
final SamReader reader = SamReaderFactory.makeDefault().open(inputSamOrBamFile);
// makeSAMorBAMWriter() writes a file in SAM text or BAM binary format depending
// on the file extension, which must be either .sam or .bam.
// Since the SAMRecords will be written in the same order as they appear in the input file,
// and the output file is specified as having the same sort order (as specified in
// SAMFileHeader.getSortOrder(), presorted == true. This is much more efficient than
// presorted == false, if coordinate or queryname sorting is specified, because the SAMRecords
// can be written to the output file directly rather than being written to a temporary file
// and sorted after all records have been sent to outputSam.
final SAMFileWriter outputSam = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(),
true, outputSamOrBamFile);
for (final SAMRecord samRecord : reader) {
// Convert read name to upper case.
samRecord.setReadName(samRecord.getReadName().toUpperCase());
outputSam.addAlignment(samRecord);
}
outputSam.close();
reader.close();
}
}