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Bypass FeatureReader for GenomicsDBImport #7393

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merged 4 commits into from
Oct 27, 2021
Merged

Bypass FeatureReader for GenomicsDBImport #7393

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32f446c
bypass feature reader
mlathara Jul 21, 2021
f87ab74
Merge remote-tracking branch 'upstream/ml_bypass_featurereader' into …
nalinigans Aug 3, 2021
edae3ce
address review comments
mlathara Oct 19, 2021
79c5b82
fix tests
mlathara Oct 26, 2021
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40 changes: 36 additions & 4 deletions src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.Locatable;
import htsjdk.samtools.util.FileExtensions;
import htsjdk.tribble.AbstractFeatureReader;
import htsjdk.tribble.CloseableTribbleIterator;
import htsjdk.tribble.FeatureReader;
Expand Down Expand Up @@ -202,6 +203,7 @@ public final class GenomicsDBImport extends GATKTool {
public static final String VCF_INITIALIZER_THREADS_LONG_NAME = "reader-threads";
public static final String MAX_NUM_INTERVALS_TO_IMPORT_IN_PARALLEL = "max-num-intervals-to-import-in-parallel";
public static final String MERGE_CONTIGS_INTO_NUM_PARTITIONS = "merge-contigs-into-num-partitions";
public static final String BYPASS_FEATURE_READER = "bypass-feature-reader";
public static final int INTERVAL_LIST_SIZE_WARNING_THRESHOLD = 100;
public static final int ARRAY_COLUMN_BOUNDS_START = 0;
public static final int ARRAY_COLUMN_BOUNDS_END = 1;
Expand Down Expand Up @@ -348,6 +350,13 @@ public final class GenomicsDBImport extends GATKTool {
optional = true)
private boolean sharedPosixFSOptimizations = false;

@Argument(fullName = BYPASS_FEATURE_READER,
doc = "Use htslib to read input VCFs instead of GATK's FeatureReader. This will reduce memory usage and potentially speed up " +
"the import. Lower memory requirements may also enable parallelism through " + MAX_NUM_INTERVALS_TO_IMPORT_IN_PARALLEL +
". To enable this option, VCFs must be normalized, block-compressed and indexed.",
optional = true)
private boolean bypassFeatureReader = false;

@Argument(fullName = USE_GCS_HDFS_CONNECTOR,
doc = "Use the GCS HDFS Connector instead of the native GCS SDK client with gs:// URLs.",
optional = true)
Expand Down Expand Up @@ -502,6 +511,15 @@ private static void assertIntervalsCoverEntireContigs(GenomicsDBImporter importe
}
}

private static void assertVariantFileIsCompressedAndIndexed(final Path path) {
if (!path.toString().toLowerCase().endsWith(FileExtensions.COMPRESSED_VCF)) {
throw new UserException("Input variant files must be block compressed vcfs when using " +
BYPASS_FEATURE_READER + ", but " + path.toString() + " does not appear to be");
}
Path indexPath = path.resolveSibling(path.getFileName() + FileExtensions.COMPRESSED_VCF_INDEX);
IOUtils.assertFileIsReadable(indexPath);
}

/**
* sets the values of mergedHeaderLines, mergedHeaderSequenceDictionary, and sampleNameToVcfPath
*/
Expand All @@ -512,6 +530,9 @@ private void initializeHeaderAndSampleMappings() {
final List<VCFHeader> headers = new ArrayList<>(variantPaths.size());
for (final String variantPathString : variantPaths) {
final Path variantPath = IOUtils.getPath(variantPathString);
if (bypassFeatureReader) {
assertVariantFileIsCompressedAndIndexed(variantPath);
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In your testing, did you find that these extra checks for whether the inputs are block-compressed and indexed added significantly to the runtime when dealing with remote files?

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We haven't done a lot of remote testing -- just sanity tests to ensure that they work. In the small remote cases we've tried the native reader is actually slower, but I haven't dug into it to see where the bottleneck is (potentially tweaking buffer sizes, etc). As I mentioned in the PR, that is something we were hoping to explore with Broad.

}
final VCFHeader header = getHeaderFromPath(variantPath);
Utils.validate(header != null, "Null header was found in " + variantPath + ".");
assertGVCFHasOnlyOneSample(variantPathString, header);
Expand Down Expand Up @@ -539,7 +560,7 @@ private void initializeHeaderAndSampleMappings() {
//it's VERY IMPORTANT that this map is Sorted according to String's natural ordering, if it is not
//the resulting database will have incorrect sample names
//see https://github.com/broadinstitute/gatk/issues/3682 for more information
sampleNameToVcfPath = loadSampleNameMapFileInSortedOrder(IOUtils.getPath(sampleNameMapFile));
sampleNameToVcfPath = loadSampleNameMapFileInSortedOrder(IOUtils.getPath(sampleNameMapFile), bypassFeatureReader);
final Path firstHeaderPath = IOUtils.getPath(sampleNameToVcfPath.entrySet().iterator().next().getValue().toString());
final VCFHeader header = getHeaderFromPath(firstHeaderPath);
//getMetaDataInInputOrder() returns an ImmutableSet - LinkedHashSet is mutable and preserves ordering
Expand Down Expand Up @@ -607,6 +628,11 @@ private static void assertGVCFHasOnlyOneSample(final String variantPath, final V
*/
@VisibleForTesting
static LinkedHashMap<String, URI> loadSampleNameMapFile(final Path sampleToFileMapPath) {
return loadSampleNameMapFile(sampleToFileMapPath, false);
}

private static LinkedHashMap<String, URI> loadSampleNameMapFile(final Path sampleToFileMapPath,
final boolean checkVcfIsCompressedAndIndexed) {
try {
final List<String> lines = Files.readAllLines(sampleToFileMapPath);
if (lines.isEmpty()) {
Expand All @@ -631,6 +657,9 @@ static LinkedHashMap<String, URI> loadSampleNameMapFile(final Path sampleToFileM
if (oldPath != null){
throw new UserException.BadInput("Found two mappings for the same sample: " + sample + "\n" + path + "\n" + oldPath );
}
if (checkVcfIsCompressedAndIndexed) {
assertVariantFileIsCompressedAndIndexed(IOUtils.getPath(path));
}
}
catch(final URISyntaxException e) {
throw new UserException("Malformed URI "+e.toString());
Expand All @@ -652,10 +681,12 @@ static LinkedHashMap<String, URI> loadSampleNameMapFile(final Path sampleToFileM
*
* The sample names must be unique.
* @param sampleToFileMapPath path to the mapping file
* @param checkVcfIsCompressedAndIndexed boolean indicating whether to check vcf is compressed and indexed
* @return map of sample name to corresponding file, sorted by sample name
*/
public static SortedMap<String, URI> loadSampleNameMapFileInSortedOrder(final Path sampleToFileMapPath){
return new TreeMap<>(loadSampleNameMapFile(sampleToFileMapPath));
public static SortedMap<String, URI> loadSampleNameMapFileInSortedOrder(final Path sampleToFileMapPath,
final boolean checkVcfIsCompressedAndIndexed){
return new TreeMap<>(loadSampleNameMapFile(sampleToFileMapPath, checkVcfIsCompressedAndIndexed));
}

/**
Expand Down Expand Up @@ -831,7 +862,8 @@ private ImportConfig createImportConfig(final int batchSize) {
importConfigurationBuilder.setConsolidateTiledbArrayAfterLoad(doConsolidation);
importConfigurationBuilder.setEnableSharedPosixfsOptimizations(sharedPosixFSOptimizations);
ImportConfig importConfig = new ImportConfig(importConfigurationBuilder.build(), validateSampleToReaderMap, true,
batchSize, mergedHeaderLines, sampleNameToVcfPath, this::createSampleToReaderMap, doIncrementalImport);
batchSize, mergedHeaderLines, sampleNameToVcfPath, bypassFeatureReader ? null : this::createSampleToReaderMap,
doIncrementalImport);
importConfig.setOutputCallsetmapJsonFile(callsetMapJSONFile);
importConfig.setOutputVidmapJsonFile(vidMapJSONFile);
importConfig.setOutputVcfHeaderFile(vcfHeaderFile);
Expand Down
89 changes: 87 additions & 2 deletions .../java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -203,6 +203,11 @@ public void testGenomicsDBImportFileInputs() throws IOException {
testGenomicsDBImporter(LOCAL_GVCFS, INTERVAL, COMBINED, b38_reference_20_21, true, 1);
}

@Test
public void testGenomicsDBImportFileInputsNativeReader() throws IOException {
testGenomicsDBImporter(LOCAL_GVCFS, INTERVAL, COMBINED, b38_reference_20_21, true, 1, true);
}

@Test
public void testGenomicsDBImportFileInputs_newMQ() throws IOException {
testGenomicsDBImporter_newMQ(GVCFS_WITH_NEW_MQ, INTERVAL2, COMBINED_WITH_NEW_MQ, b37_reference_20_21, true, Collections.emptyList());
Expand All @@ -213,6 +218,11 @@ public void testGenomicsDBImportFileInputsWithMultipleIntervals() throws IOExcep
testGenomicsDBImporter(LOCAL_GVCFS, MULTIPLE_INTERVALS, COMBINED_MULTI_INTERVAL, b38_reference_20_21, true, 1);
}

@Test
public void testGenomicsDBImportFileInputsWithMultipleIntervalsNativeReader() throws IOException {
testGenomicsDBImporter(LOCAL_GVCFS, MULTIPLE_INTERVALS, COMBINED_MULTI_INTERVAL, b38_reference_20_21, true, 1, true);
}

@Test(timeOut = 1000000)
public void testGenomicsDBImportWith1000IntervalsToBeMerged() throws IOException {
final String workspace = createTempDir("genomicsdb-tests-").getAbsolutePath() + "/workspace";
Expand All @@ -235,6 +245,11 @@ public void testGenomicsDBImportFileInputsAgainstCombineGVCFMergeContigsToSingle
testGenomicsDBAgainstCombineGVCFs(LOCAL_GVCFS, INTERVAL_20_21, b38_reference_20_21, new String[0], 1, 1, false);
}

@Test
public void testGenomicsDBImportFileInputsAgainstCombineGVCFNativeReader() throws IOException {
testGenomicsDBAgainstCombineGVCFs(LOCAL_GVCFS, INTERVAL, b38_reference_20_21, new String[0], 1, 0, true);
}

@Test
public void testGenomicsDBImportMergeContigsManyNonAdjacentContigsToSeveralContigs() throws IOException {
List<SimpleInterval> manyContigs = MANY_CONTIGS_NON_ADJACENT_INTERVALS.stream().map(SimpleInterval::new).collect(Collectors.toList());
Expand All @@ -256,18 +271,35 @@ public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithMultipleInterval
testGenomicsDBAgainstCombineGVCFs(LOCAL_GVCFS, MULTIPLE_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS, b38_reference_20_21, new String[0]);
}

@Test
public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithMultipleIntervalsNativeReader() throws IOException {
testGenomicsDBAgainstCombineGVCFs(LOCAL_GVCFS, MULTIPLE_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS, b38_reference_20_21, new String[0], 1, 0, true);
}

@Test
public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithMultipleIntervalsWithMultipleThreads() throws IOException {
testGenomicsDBAgainstCombineGVCFs(LOCAL_GVCFS, MULTIPLE_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS, b38_reference_20_21,
new String[0], 4);
}

@Test
public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithMultipleIntervalsWithMultipleThreadsNativeReader() throws IOException {
testGenomicsDBAgainstCombineGVCFs(LOCAL_GVCFS, MULTIPLE_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS, b38_reference_20_21,
new String[0], 4, 0, true);
}

@Test
public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithMultipleNonAdjacentIntervals() throws IOException {
testGenomicsDBAgainstCombineGVCFs(LOCAL_GVCFS, MULTIPLE_NON_ADJACENT_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS,
b38_reference_20_21, new String[0]);
}

@Test
public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithMultipleNonAdjacentIntervalsNativeReader() throws IOException {
testGenomicsDBAgainstCombineGVCFs(LOCAL_GVCFS, MULTIPLE_NON_ADJACENT_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS,
b38_reference_20_21, new String[0], 1, 0, true);
}

@Test
public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithMultipleNonAdjacentIntervalsForFilesProducedAfterCombineGVCFs()
throws IOException {
Expand All @@ -276,6 +308,14 @@ public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithMultipleNonAdjac
b38_reference_20_21, new String[0]);
}

@Test
public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithMultipleNonAdjacentIntervalsForFilesProducedAfterCombineGVCFsNativeReader()
throws IOException {
//this test covers the scenario where the input vcfs have spanning deletions
testGenomicsDBAgainstCombineGVCFs(LOCAL_GVCFS_AFTER_COMBINE_GVCFS, MULTIPLE_NON_ADJACENT_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS,
b38_reference_20_21, new String[0], 1, 0, true);
}

@Test
public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithNonDiploidData() throws IOException {
testGenomicsDBImporterWithGenotypes(Arrays.asList(NA12878_HG37, MULTIPLOID_DATA_HG37), INTERVAL_NONDIPLOID,
Expand Down Expand Up @@ -307,6 +347,12 @@ public void testGenomicsDBThreeLargeSamplesWithGenotypes() throws IOException {
testGenomicsDBImporterWithGenotypes(LOCAL_GVCFS, intervals, COMBINED_WITH_GENOTYPES, b38_reference_20_21, true, true, false);
}

@Test
public void testGenomicsDBThreeLargeSamplesWithGenotypesNativeReader() throws IOException {
ArrayList<SimpleInterval> intervals = new ArrayList<SimpleInterval>(Arrays.asList(new SimpleInterval("chr20", 1, 64444167)));
testGenomicsDBImporterWithGenotypes(LOCAL_GVCFS, intervals, COMBINED_WITH_GENOTYPES, b38_reference_20_21, true, true, false, true);
}

@Test
public void testGenomicsDBThreeLargeSamplesSitesOnlyQuery() throws IOException {
ArrayList<SimpleInterval> intervals = new ArrayList<SimpleInterval>(Arrays.asList(
Expand Down Expand Up @@ -504,11 +550,21 @@ public void testGenomicsDBImportFileInputsInBatchesWithMultipleIntervals(final i
testGenomicsDBImporterWithBatchSize(LOCAL_GVCFS, MULTIPLE_INTERVALS, COMBINED_MULTI_INTERVAL, batchSize);
}

@Test(dataProvider = "batchSizes")
public void testGenomicsDBImportFileInputsInBatchesWithMultipleIntervalsNativeReader(final int batchSize) throws IOException {
testGenomicsDBImporterWithBatchSize(LOCAL_GVCFS, MULTIPLE_INTERVALS, COMBINED_MULTI_INTERVAL, batchSize, true);
}

@Test(groups = {"bucket"}, dataProvider = "batchSizes")
public void testGenomicsDBImportGCSInputsInBatches(final int batchSize) throws IOException {
testGenomicsDBImporterWithBatchSize(resolveLargeFilesAsCloudURIs(LOCAL_GVCFS), INTERVAL, COMBINED, batchSize);
}

@Test(groups = {"bucket"}, dataProvider = "batchSizes")
public void testGenomicsDBImportGCSInputsInBatchesNativeReader(final int batchSize) throws IOException {
testGenomicsDBImporterWithBatchSize(resolveLargeFilesAsCloudURIs(LOCAL_GVCFS), INTERVAL, COMBINED, batchSize, true);
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testGenomicsDBImporterWithBatchSize() does not propagate the useNativeReader boolean correctly into writeToGenomicsDB()

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Fixed.

}

@DataProvider
public Object[][] getThreads(){
return new Object[][] {
Expand Down Expand Up @@ -581,7 +637,7 @@ private void testGenomicsDBImporterWithBatchSize(final List<String> vcfInputs, f
final boolean useNativeReader) throws IOException {
final String workspace = createTempDir("genomicsdb-batchsize-tests-").getAbsolutePath() + "/workspace-" + batchSize;

writeToGenomicsDB(vcfInputs, intervals, workspace, batchSize, false, 0, 1, false, false, false, 0, true);
writeToGenomicsDB(vcfInputs, intervals, workspace, batchSize, false, 0, 1, false, false, false, 0, useNativeReader);
checkJSONFilesAreWritten(workspace);
checkGenomicsDBAgainstExpected(workspace, intervals, expectedCombinedVCF, b38_reference_20_21, true, ATTRIBUTES_TO_IGNORE);
}
Expand Down Expand Up @@ -632,6 +688,7 @@ private void writeToGenomicsDB(final List<String> vcfInputs, final List<SimpleIn
if (chrsToPartitions != 0) {
args.add(GenomicsDBImport.MERGE_CONTIGS_INTO_NUM_PARTITIONS, String.valueOf(chrsToPartitions));
}
args.add(GenomicsDBImport.BYPASS_FEATURE_READER, useNativeReader);
if (useBufferSize) {
args.add("genomicsdb-vcf-buffer-size", String.valueOf(bufferSizePerSample));
}
Expand Down Expand Up @@ -1091,10 +1148,18 @@ public void testIncrementalMustHaveExistingWorkspace() {
private void testIncrementalImport(final int stepSize, final List<SimpleInterval> intervals, final String workspace,
final int batchSize, final boolean produceGTField, final boolean useVCFCodec, final String expected,
final int chrsToPartitions, final boolean useNativeReader) throws IOException {
testIncrementalImport(stepSize, intervals, workspace, batchSize, produceGTField, useVCFCodec, expected,
chrsToPartitions, useNativeReader, false);
}

private void testIncrementalImport(final int stepSize, final List<SimpleInterval> intervals, final String workspace,
final int batchSize, final boolean produceGTField, final boolean useVCFCodec, final String expected,
final int chrsToPartitions, final boolean useNativeReader, final boolean useNativeReaderInitial)
throws IOException {
for(int i=0; i<LOCAL_GVCFS.size(); i+=stepSize) {
int upper = Math.min(i+stepSize, LOCAL_GVCFS.size());
writeToGenomicsDB(LOCAL_GVCFS.subList(i, upper), intervals, workspace, batchSize, false, 0, 1, false, false, i!=0,
chrsToPartitions, i!=0 && useNativeReader);
chrsToPartitions, (i == 0 && useNativeReaderInitial) || (i > 0 && useNativeReader));
checkJSONFilesAreWritten(workspace);
}
for(SimpleInterval currInterval : intervals) {
Expand All @@ -1120,13 +1185,33 @@ public void testGenomicsDBBasicIncremental() throws IOException {
createAndCheckIntervalListFromExistingWorkspace(workspace, INTERVAL_PICARD_STYLE_EXPECTED);
}

@Test
public void testGenomicsDBBasicIncrementalAllNativeReader() throws IOException {
final String workspace = createTempDir("genomicsdb-incremental-tests").getAbsolutePath() + "/workspace";
testIncrementalImport(2, INTERVAL, workspace, 0, true, true, COMBINED_WITH_GENOTYPES, 0, true, true);
createAndCheckIntervalListFromExistingWorkspace(workspace, INTERVAL_PICARD_STYLE_EXPECTED);
}

@Test
public void testGenomicsDBIncrementalAndBatchSize1WithNonAdjacentIntervals() throws IOException {
final String workspace = createTempDir("genomicsdb-incremental-tests").getAbsolutePath() + "/workspace";
testIncrementalImport(2, MULTIPLE_NON_ADJACENT_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS, workspace, 1, false, true, "", 0, false);
createAndCheckIntervalListFromExistingWorkspace(workspace, MULTIPLE_NON_ADJACENT_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS_PICARD_STYLE_EXPECTED);
}

@Test
public void testGenomicsDBIncrementalAndBatchSize1WithNonAdjacentIntervalsNativeReader() throws IOException {
final String workspace = createTempDir("genomicsdb-incremental-tests").getAbsolutePath() + "/workspace";
testIncrementalImport(2, MULTIPLE_NON_ADJACENT_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS, workspace, 1, false, true, "", 0, true);
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testIncrementalImport() does not use the native reader for the first batch (i == 0) -- why is that?

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Ah - not entirely sure anymore, I think I wanted to check that a given workspace could be imported to using feature reader and htslib. Refactored a bit to make that a bit more clear, and added a test that does all htslib/native incremental import

createAndCheckIntervalListFromExistingWorkspace(workspace, MULTIPLE_NON_ADJACENT_INTERVALS_THAT_WORK_WITH_COMBINE_GVCFS_PICARD_STYLE_EXPECTED);
}

@Test(expectedExceptions = {UserException.class}, expectedExceptionsMessageRegExp=".*must be block compressed.*")
public void testGenomicsDBImportNativeReaderNoCompressedVcf() throws IOException {
testGenomicsDBImporterWithGenotypes(Arrays.asList(NA_12878_PHASED), MULTIPLE_INTERVALS, NA_12878_PHASED, b37_reference_20_21,
false, true, false, true);
}

@Test
public void testGenomicsDBIncrementalAndBatchSize1WithNonAdjacentIntervalsMergeContigsIntoPartitions() throws IOException {
final String workspace = createTempDir("genomicsdb-incremental-tests").getAbsolutePath() + "/workspace";
Expand Down
2 changes: 1 addition & 1 deletion src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportUnitTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@ public void testLoadSampleNameMapFileInSortedOrder(final String sampleMapText){
catch(URISyntaxException e) {
throw new RuntimeException("Malformed URI "+e.toString());
}
final Map<String, URI> actual = GenomicsDBImport.loadSampleNameMapFileInSortedOrder(sampleFile.toPath());
final Map<String, URI> actual = GenomicsDBImport.loadSampleNameMapFileInSortedOrder(sampleFile.toPath(), false);
Assert.assertEquals(actual, expected);
Assert.assertEquals(actual.keySet().iterator().next(), "Sample1");
}
Expand Down