package picard.util;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.ProgressLogger;
import htsjdk.tribble.AbstractFeatureReader;
import htsjdk.tribble.CloseableTribbleIterator;
import htsjdk.tribble.FeatureReader;
import htsjdk.tribble.annotation.Strand;
import htsjdk.tribble.bed.BEDCodec;
import htsjdk.tribble.bed.BEDFeature;
import picard.PicardException;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.Intervals;
import java.io.File;
import java.io.IOException;
/**
* @author nhomer
*/
@CommandLineProgramProperties(
usage = "Converts a BED file to an Picard Interval List.",
usageShort = "Converts a BED file to an Picard Interval List.",
programGroup = Intervals.class
)
public class BedToIntervalList extends CommandLineProgram {
@Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The input BED file")
public File INPUT;
@Option(shortName = StandardOptionDefinitions.SEQUENCE_DICTIONARY_SHORT_NAME, doc = "The sequence dictionary")
public File SEQUENCE_DICTIONARY;
@Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "The output Picard Interval List")
public File OUTPUT;
final Log LOG = Log.getInstance(getClass());
// Stock main method
public static void main(final String[] args) {
new BedToIntervalList().instanceMainWithExit(args);
}
@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);
IOUtil.assertFileIsWritable(OUTPUT);
try {
final SamReader samReader = SamReaderFactory.makeDefault().open(SEQUENCE_DICTIONARY);
final SAMFileHeader header = samReader.getFileHeader();
final IntervalList intervalList = new IntervalList(header);
CloserUtil.close(samReader);
/**
* NB: BED is zero-based, but a BEDCodec by default (since it is returns tribble Features) has an offset of one,
* so it returns 1-based starts. Ugh. Set to zero.
*/
final FeatureReader<BEDFeature> bedReader = AbstractFeatureReader.getFeatureReader(INPUT.getAbsolutePath(), new BEDCodec(BEDCodec.StartOffset.ZERO), false);
final CloseableTribbleIterator<BEDFeature> iterator = bedReader.iterator();
final ProgressLogger progressLogger = new ProgressLogger(LOG, (int) 1e6);
while (iterator.hasNext()) {
final BEDFeature bedFeature = iterator.next();
final String sequenceName = bedFeature.getChr();
/**
* NB: BED is zero-based, so we need to add one here to make it one-based. Please observe we set the start
* offset to zero when creating the BEDCodec.
*/
final int start = bedFeature.getStart() + 1;
/**
* NB: BED is 0-based OPEN (which, for the end is equivalent to 1-based closed).
*/
final int end = bedFeature.getEnd();
// NB: do not use an empty name within an interval
String name = bedFeature.getName();
if (name.isEmpty()) name = null;
final SAMSequenceRecord sequenceRecord = header.getSequenceDictionary().getSequence(sequenceName);
// Do some validation
if (null == sequenceRecord) {
throw new PicardException(String.format("Sequence '%s' was not found in the sequence dictionary", sequenceName));
}
else if (start < 1) {
throw new PicardException(String.format("Start on sequence '%s' was less than one: %d", sequenceName, start));
}
else if (sequenceRecord.getSequenceLength() < start) {
throw new PicardException(String.format("Start on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), start));
}
else if (end < 1) {
throw new PicardException(String.format("End on sequence '%s' was less than one: %d", sequenceName, end));
}
else if (sequenceRecord.getSequenceLength() < end) {
throw new PicardException(String.format("End on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), end));
}
else if (end < start - 1) {
throw new PicardException(String.format("On sequence '%s', end < start-1: %d <= %d", sequenceName, end, start));
}
final Interval interval = new Interval(sequenceName, start, end, bedFeature.getStrand() == Strand.POSITIVE, name);
intervalList.add(interval);
progressLogger.record(sequenceName, start);
}
CloserUtil.close(bedReader);
// Sort and write the output
intervalList.uniqued().write(OUTPUT);
} catch (final IOException e) {
throw new RuntimeException(e);
}
return 0;
}
}