/*
* 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.SAMFileReader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMTextHeaderCodec;
import htsjdk.samtools.util.AsciiWriter;
import htsjdk.samtools.util.IOUtil;
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;
/**
* Very simple command that just reads a SAM or BAM file and writes out the header
* and each records to standard out.
*
* @author tfennell@broad.mit.edu
*/
@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 }
@Option(shortName=StandardOptionDefinitions.INPUT_SHORT_NAME, doc="The SAM or BAM file to view.")
public File 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;
public static void main(final String[] args) {
new ViewSam().instanceMain(args);
}
@Override
protected int doWork() {
return writeSamText(System.out);
}
/**
* This is factored out of doWork only for unit testing.
*/
int writeSamText(PrintStream printStream) {
try {
IOUtil.assertFileIsReadable(INPUT);
final SAMFileReader in = new SAMFileReader(INPUT);
final AsciiWriter writer = new AsciiWriter(printStream);
final SAMFileHeader header = in.getFileHeader();
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);
}
for (final SAMRecord rec : in) {
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;
}
return 0;
} catch (IOException e) {
throw new PicardException("Exception writing SAM text", e);
}
}
}