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/*
* 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.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMTextHeaderCodec;
import htsjdk.samtools.SamInputResource;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.AsciiWriter;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.SamRecordIntervalIteratorFactory;
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;
import java.io.IOException;
import java.io.PrintStream;
import java.util.List;
/**
* Very simple command that just reads a SAM or BAM file and writes out the header
* and each records to standard out. When an (optional) intervals file is specified,
* only records overlapping those intervals will be output.
*
* @author [email protected]
*/
@CommandLineProgramProperties(
usage = "Prints a SAM or BAM file to the screen.",
usageShort = "Prints a SAM or BAM file to the screen",
programGroup = SamOrBam.class
)
public class ViewSam extends CommandLineProgram {
public static enum AlignmentStatus {Aligned, Unaligned, All}
public static enum PfStatus {PF, NonPF, All}
public final String USAGE = getStandardUsagePreamble() + "Prints a SAM or BAM file to the screen.";
@Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The SAM or BAM file or GA4GH url to view.")
public String INPUT;
@Option(doc = "Print out all reads, just the aligned reads or just the unaligned reads.")
public AlignmentStatus ALIGNMENT_STATUS = AlignmentStatus.All;
@Option(doc = "Print out all reads, just the PF reads or just the non-PF reads.")
public PfStatus PF_STATUS = PfStatus.All;
@Option(doc="Print the SAM header only.", optional = true)
public boolean HEADER_ONLY = false;
@Option(doc="Print the alignment records only.", optional = true)
public boolean RECORDS_ONLY = false;
@Option(doc = "An intervals file used to restrict what records are output.", optional = true)
public File INTERVAL_LIST;
public static void main(final String[] args) {
new ViewSam().instanceMain(args);
}
@Override
protected int doWork() {
return writeSamText(System.out);
}
@Override
protected String[] customCommandLineValidation() {
if (HEADER_ONLY && RECORDS_ONLY) {
return new String[]{"Cannot specify both HEADER_ONLY=true and RECORDS_ONLY=true."};
}
return super.customCommandLineValidation();
}
/**
* This is factored out of doWork only for unit testing.
*/
int writeSamText(PrintStream printStream) {
try {
final CloseableIterator samRecordsIterator;
final SamReader samReader = SamReaderFactory.makeDefault()
.referenceSequence(REFERENCE_SEQUENCE)
.open(SamInputResource.of(INPUT));
// if we are only using the header or we aren't using intervals, then use the reader as the iterator.
// otherwise use the SamRecordIntervalIteratorFactory to make an interval-ed iterator
if (HEADER_ONLY || INTERVAL_LIST == null) {
samRecordsIterator = samReader.iterator();
} else {
IOUtil.assertFileIsReadable(INTERVAL_LIST);
final List intervals = IntervalList.fromFile(INTERVAL_LIST).uniqued().getIntervals();
samRecordsIterator = new SamRecordIntervalIteratorFactory().makeSamRecordIntervalIterator(samReader, intervals, samReader.hasIndex());
}
final AsciiWriter writer = new AsciiWriter(printStream);
final SAMFileHeader header = samReader.getFileHeader();
if (!RECORDS_ONLY) {
if (header.getTextHeader() != null) {
writer.write(header.getTextHeader());
} else {
// Headers that are too large are not retained as text, so need to regenerate text
new SAMTextHeaderCodec().encode(writer, header, true);
}
}
if (!HEADER_ONLY) {
while (samRecordsIterator.hasNext()) {
final SAMRecord rec = samRecordsIterator.next();
if (printStream.checkError()) {
return 1;
}
if (this.ALIGNMENT_STATUS == AlignmentStatus.Aligned && rec.getReadUnmappedFlag()) continue;
if (this.ALIGNMENT_STATUS == AlignmentStatus.Unaligned && !rec.getReadUnmappedFlag()) continue;
if (this.PF_STATUS == PfStatus.PF && rec.getReadFailsVendorQualityCheckFlag()) continue;
if (this.PF_STATUS == PfStatus.NonPF && !rec.getReadFailsVendorQualityCheckFlag()) continue;
writer.write(rec.getSAMString());
}
}
writer.flush();
if (printStream.checkError()) {
return 1;
}
CloserUtil.close(writer);
CloserUtil.close(samRecordsIterator);
return 0;
} catch (IOException e) {
throw new PicardException("Exception writing SAM text", e);
}
}
}
