liftovervcf without sorting the variants

src/main/java/picard/vcf/LiftoverVcf.java

@@ -181,6 +181,9 @@ public class LiftoverVcf extends CommandLineProgram {
  @Argument(doc = "INFO field annotations that should be deleted when swapping reference with variant alleles.", optional = true)
  public Collection<String> TAGS_TO_DROP = new ArrayList<>(LiftoverUtils.DEFAULT_TAGS_TO_DROP);
 
+ @Argument(doc = "Output VCF file will be written on the fly but it won't be sorted and indexed.", optional = true)
+ public boolean DISABLE_SORT = false;
+
  // When a contig used in the chain is not in the reference, exit with this value instead of 0.
  public static int EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE = 1;
 
@@ -250,7 +253,10 @@ public class LiftoverVcf extends CommandLineProgram {
  );
 
  private VariantContextWriter rejects;
+ /** the output VariantContextWriter */
+ private VariantContextWriter accept;
  private final Log log = Log.getInstance(LiftoverVcf.class);
+ /** the Variant sorter, may be null if DISABLE_SORT = null */
  private SortingCollection<VariantContext> sorter;
 
  private long failedLiftover = 0, failedAlleleCheck = 0, totalTrackedAsSwapRefAlt = 0;
@@ -321,11 +327,23 @@ protected int doWork() {
  "The REF and the ALT alleles have been reverse complemented in liftover since the mapping from the " +
  "previous reference to the current one was on the negative strand."));
 
- final VariantContextWriter out = new VariantContextWriterBuilder()
- .setOption(Options.INDEX_ON_THE_FLY)
- .modifyOption(Options.ALLOW_MISSING_FIELDS_IN_HEADER, ALLOW_MISSING_FIELDS_IN_HEADER)
- .setOutputFile(OUTPUT).setReferenceDictionary(walker.getSequenceDictionary()).build();
- out.writeHeader(outHeader);
+ final VariantContextWriterBuilder variantContextWriterBuilder = new VariantContextWriterBuilder()
+ .modifyOption(Options.ALLOW_MISSING_FIELDS_IN_HEADER, ALLOW_MISSING_FIELDS_IN_HEADER)
+ .setOutputFile(OUTPUT)
+ .setReferenceDictionary(walker.getSequenceDictionary())
+ ;
+
+ if (DISABLE_SORT) {
+ this.accept = variantContextWriterBuilder
+ .unsetOption(Options.INDEX_ON_THE_FLY)
+ .build();
+ } else {
+ this.accept = variantContextWriterBuilder
+ .setOption(Options.INDEX_ON_THE_FLY)
+ .build();
+ }
+
+ this.accept.writeHeader(outHeader);
 
  rejects = new VariantContextWriterBuilder().setOutputFile(REJECT)
  .unsetOption(Options.INDEX_ON_THE_FLY)
@@ -346,13 +364,21 @@ protected int doWork() {
  // collection.
  ////////////////////////////////////////////////////////////////////////
  long total = 0;
- log.info("Lifting variants over and sorting (not yet writing the output file.)");
-
- sorter = SortingCollection.newInstance(VariantContext.class,
- new VCFRecordCodec(outHeader, ALLOW_MISSING_FIELDS_IN_HEADER || VALIDATION_STRINGENCY != ValidationStringency.STRICT),
- outHeader.getVCFRecordComparator(),
- MAX_RECORDS_IN_RAM,
- TMP_DIR);
+
+ if (DISABLE_SORT) {
+ log.info("Lifting variants over and writing the output file. Variants will not be sorted");
+
+ sorter = null;
+ }
+ else {
+ log.info("Lifting variants over and sorting (not yet writing the output file.)");
+
+ sorter = SortingCollection.newInstance(VariantContext.class,
+ new VCFRecordCodec(outHeader, ALLOW_MISSING_FIELDS_IN_HEADER || VALIDATION_STRINGENCY != ValidationStringency.STRICT),
+ outHeader.getVCFRecordComparator(),
+ MAX_RECORDS_IN_RAM,
+ TMP_DIR);
+ }
 
  ProgressLogger progress = new ProgressLogger(log, 1000000, "read");
 
@@ -441,21 +467,26 @@ protected int doWork() {
  rejects.close();
  in.close();
 
- ////////////////////////////////////////////////////////////////////////
- // Write the sorted outputs to the final output file
- ////////////////////////////////////////////////////////////////////////
- sorter.doneAdding();
- progress = new ProgressLogger(log, 1000000, "written");
- log.info("Writing out sorted records to final VCF.");
-
- for (final VariantContext ctx : sorter) {
- out.add(ctx);
- progress.record(ctx.getContig(), ctx.getStart());
+
+ if (sorter != null) { 
+ ////////////////////////////////////////////////////////////////////////
+ // Write the sorted outputs to the final output file
+ ////////////////////////////////////////////////////////////////////////
+ sorter.doneAdding();
+ progress = new ProgressLogger(log, 1000000, "written");
+ log.info("Writing out sorted records to final VCF.");
+
+ for (final VariantContext ctx : sorter) {
+ this.accept.add(ctx);
+ progress.record(ctx.getContig(), ctx.getStart());
+ }
+
+
+ sorter.cleanup();
  }
- out.close();
-
- sorter.cleanup();
 
+ this.accept.close();
+
  return 0;
  }
 
@@ -477,7 +508,11 @@ private void trackLiftedVariantContig(Map<String, Long> map, String contig) {
  private void addAndTrack(final VariantContext toAdd, final VariantContext source) {
  trackLiftedVariantContig(liftedBySourceContig, source.getContig());
  trackLiftedVariantContig(liftedByDestContig, toAdd.getContig());
- sorter.add(toAdd);
+ if (sorter != null) { //we're sorting the variants
+ sorter.add(toAdd);
+ } else {
+ this.accept.add(toAdd);
+ }
  }
 
  /**

src/test/java/picard/util/LiftoverVcfTest.java

@@ -248,6 +248,44 @@ public void testWriteOriginalPosition(final boolean shouldWriteOriginalPosition)
  }
  }
 
+ @DataProvider(name = "dataTestSort")
+ public Object[][] dataTestVcfSorted() {
+ return new Object[][]{
+ {false},
+ {true}
+ };
+ }
+
+ @Test(dataProvider = "dataTestSort")
+ public void testVcfSorted(final boolean disableSort) {
+ final File liftOutputFile = new File(OUTPUT_DATA_PATH, "lift-delete-me.vcf");
+ final File rejectOutputFile = new File(OUTPUT_DATA_PATH, "reject-delete-me.vcf");
+ final File input = new File(TEST_DATA_PATH, "testLiftoverBiallelicIndels.vcf");
+
+ liftOutputFile.deleteOnExit();
+ rejectOutputFile.deleteOnExit();
+
+ final String[] args = new String[]{
+ "INPUT=" + input.getAbsolutePath(),
+ "OUTPUT=" + liftOutputFile.getAbsolutePath(),
+ "REJECT=" + rejectOutputFile.getAbsolutePath(),
+ "CHAIN=" + CHAIN_FILE,
+ "REFERENCE_SEQUENCE=" + REFERENCE_FILE,
+ "CREATE_INDEX=" + (!disableSort),
+ "DISABLE_SORT=" + disableSort
+ };
+
+ Assert.assertEquals(runPicardCommandLine(args), 0);
+
+ //try to open with / without index
+ try (final VCFFileReader liftReader = new VCFFileReader(liftOutputFile, !disableSort)) {
+ // nothing
+ }
+ }
+
+
+
+
  @DataProvider
  Iterator<Object[]> testWriteVcfData() {