Add flag to keep zero length intervals when converting bed -> interval_list

src/main/java/picard/util/BedToIntervalList.java

@@ -107,9 +107,13 @@ public class BedToIntervalList extends CommandLineProgram {
  @Argument(doc = "If true, entries that are on contig-names that are missing from the provided dictionary will be dropped.")
  public boolean DROP_MISSING_CONTIGS = false;
 
+ @Argument(doc = "If true, write length zero intervals in input bed file to resulting interval list file.")
+ public boolean KEEP_ZERO_LENGTH_INTERVALS = false;
+
  private final Log LOG = Log.getInstance(getClass());
  private int missingIntervals = 0;
  private int missingRegion = 0;
+ private int zeroLengthIntervals = 0;
 
  @Override
  protected int doWork() {
@@ -168,8 +172,18 @@ protected int doWork() {
  }
 
  final boolean isNegativeStrand = bedFeature.getStrand() == Strand.NEGATIVE;
- final Interval interval = new Interval(sequenceName, start, end, isNegativeStrand, name);
- intervalList.add(interval);
+
+ // Use end+1 since bed start gets shifted by 1 using 1-based coordinates
+ if ((start == end+1) && !KEEP_ZERO_LENGTH_INTERVALS) {
+ LOG.info(String.format("Skipping writing zero length interval at %s:%d-%d.", sequenceName, start, end));
+ } else {
+ final Interval interval = new Interval(sequenceName, start, end, isNegativeStrand, name);
+ intervalList.add(interval);
+ }
+
+ if (start == end+1) {
+ zeroLengthIntervals++;
+ }
 
  progressLogger.record(sequenceName, start);
  }
@@ -182,6 +196,19 @@ protected int doWork() {
  LOG.warn(String.format("There were %d missing regions with a total of %d bases", missingIntervals, missingRegion));
  }
  }
+
+ if (!KEEP_ZERO_LENGTH_INTERVALS) {
+ if (zeroLengthIntervals == 0) {
+ LOG.info("No input regions had length zero, so none were skipped.");
+ } else {
+ LOG.info(String.format("Skipped writing a total of %d entries with length zero in the input file.", zeroLengthIntervals));
+ }
+ } else {
+ if (zeroLengthIntervals > 0) {
+ LOG.warn(String.format("Input file had %d entries with length zero. Run with the KEEP_ZERO_LENGTH_INTERVALS flag set to false to remove these.", zeroLengthIntervals));
+ }
+ }
+
  // Sort and write the output
  IntervalList out = intervalList;
  if (SORT) {

src/test/java/picard/util/BedToIntervalListTest.java

@@ -16,7 +16,7 @@ public class BedToIntervalListTest {
 
  private static final String TEST_DATA_DIR = "testdata/picard/util/BedToIntervalListTest";
 
- private void doTest(final String inputBed, final String header) throws IOException, SAMException {
+ private void doTest(final String inputBed, final String header, boolean keepZeroLength) throws IOException, SAMException {
  final File outputFile = File.createTempFile("bed_to_interval_list_test.", ".interval_list");
  outputFile.deleteOnExit();
  final BedToIntervalList program = new BedToIntervalList();
@@ -25,6 +25,7 @@ private void doTest(final String inputBed, final String header) throws IOExcepti
  program.SEQUENCE_DICTIONARY = new File(TEST_DATA_DIR, header);
  program.OUTPUT = outputFile;
  program.UNIQUE = true;
+ program.KEEP_ZERO_LENGTH_INTERVALS = keepZeroLength;
  program.doWork();
 
  // Assert they are equal
@@ -34,25 +35,30 @@ private void doTest(final String inputBed, final String header) throws IOExcepti
 
  @Test(dataProvider = "testBedToIntervalListDataProvider")
  public void testBedToIntervalList(final String inputBed) throws IOException {
- doTest(inputBed, "header.sam");
+ doTest(inputBed, "header.sam", true);
  }
 
  // test a fixed bed file using different dictionaries
  @Test(dataProvider = "testBedToIntervalListSequenceDictionaryDataProvider")
  public void testBedToIntervalListSequenceDictionary(final String dictionary) throws IOException {
- doTest("seq_dict_test.bed", dictionary);
+ doTest("seq_dict_test.bed", dictionary, true);
  }
 
  // test for back dictionaries - we expect these to throw exceptions
  @Test(dataProvider = "testBedToIntervalListSequenceDictionaryBadDataProvider",
  expectedExceptions = {SAMException.class, PicardException.class})
  public void testBedToIntervalListBadSequenceDictionary(final String dictionary) throws IOException {
- doTest("seq_dict_test.bed", dictionary);
+ doTest("seq_dict_test.bed", dictionary, true);
  }
 
  @Test(dataProvider = "testBedToIntervalListOutOfBoundsDataProvider", expectedExceptions = PicardException.class)
  public void testBedToIntervalListOutOfBounds(final String inputBed) throws IOException {
- doTest(inputBed, "header.sam");
+ doTest(inputBed, "header.sam", true);
+ }
+
+ @Test(dataProvider = "testZeroLengthIntervalsSkippedProvider")
+ public void testZeroLengthIntervalsSkipped(final String inputBed) throws IOException {
+ doTest(inputBed, "header.sam", false);
  }
 
  @DataProvider
@@ -103,4 +109,11 @@ public Object[][] testBedToIntervalListOutOfBoundsDataProvider() {
  {"off_by_one_interval.bed"}
  };
  }
+
+ @DataProvider
+ public Object[][] testZeroLengthIntervalsSkippedProvider() {
+ return new Object[][]{
+ {"zero_length_test.bed"}
+ };
+ }
 }

testdata/picard/util/BedToIntervalListTest/zero_length_test.bed

@@ -0,0 +1,4 @@
+chr1 1000 1000
+chr2 1000 2000
+chr3 1000 1000
+chr4 1000 2000

testdata/picard/util/BedToIntervalListTest/zero_length_test.bed.interval_list

@@ -0,0 +1,11 @@
+@HD VN:1.6 SO:coordinate
+@SQ SN:chr1 LN:1000000
+@SQ SN:chr2 LN:1000000
+@SQ SN:chr3 LN:1000000
+@SQ SN:chr4 LN:1000000
+@SQ SN:chr5 LN:1000000
+@SQ SN:chr6 LN:1000000
+@SQ SN:chr7 LN:1000000
+@SQ SN:chr8 LN:1000000
+chr2 1001 2000 + .
+chr4 1001 2000 + .