diff --git a/src/main/java/org/broadinstitute/hellbender/tools/PrintFileDiagnostics.java b/src/main/java/org/broadinstitute/hellbender/tools/PrintFileDiagnostics.java new file mode 100644 index 00000000000..76a0410c777 --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/tools/PrintFileDiagnostics.java @@ -0,0 +1,79 @@ +package org.broadinstitute.hellbender.tools; + +import org.broadinstitute.barclay.argparser.*; +import org.broadinstitute.hellbender.cmdline.CommandLineProgram; +import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; +import org.broadinstitute.hellbender.engine.GATKPath; +import org.broadinstitute.hellbender.tools.filediagnostics.HTSAnalyzer; +import org.broadinstitute.hellbender.tools.filediagnostics.HTSAnalyzerFactory; +import picard.cmdline.programgroups.OtherProgramGroup; + +import java.io.File; + +/** + * A diagnostic tool that prints meta information about a GATK input file. + * + * Works on files ending in .cram, .crai, and .bai. + * + * Sample Usage: + * + * gatk PrintFileDiagnostics \ + * -I input.cram \ + * -count-limit 10 + */ +@ExperimentalFeature +@WorkflowProperties +@CommandLineProgramProperties( + summary = "Print diagnostic information about a genomics file to stdout", + oneLineSummary = "Print diagnostic information about a genomics file to stdout", + programGroup = OtherProgramGroup.class +) +public class PrintFileDiagnostics extends CommandLineProgram { + + @Argument(fullName = StandardArgumentDefinitions.INPUT_LONG_NAME, + shortName = StandardArgumentDefinitions.INPUT_SHORT_NAME, + doc = "Input path for diagnostics", + optional = false, + common = true) + @WorkflowInput + public GATKPath inputPath; + + @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, + shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, + doc = "Outut file for diagnostics (must be a local file)", + optional = false, + common = true) + @WorkflowInput + public File outputFile; + + @Argument(shortName="count-limit", + fullName="count-limit", + doc="Limit on how much output to emit (.cram only)") + private long countLimit = 1000; + + private HTSAnalyzer htsAnalyzer; + + @Override + protected void onStartup() { + super.onStartup(); + htsAnalyzer = HTSAnalyzerFactory.getFileAnalyzer(inputPath, outputFile, countLimit); + } + + @Override + protected Object doWork() { + htsAnalyzer.analyze(); + return 0; + } + + @Override + protected void onShutdown() { + if ( htsAnalyzer != null ) { + try { + htsAnalyzer.close(); + } catch (Exception e) { + throw new RuntimeException(e); + } + } + } + +} diff --git a/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/BAIAnalyzer.java b/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/BAIAnalyzer.java new file mode 100644 index 00000000000..1de153092ae --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/BAIAnalyzer.java @@ -0,0 +1,31 @@ +package org.broadinstitute.hellbender.tools.filediagnostics; + +import htsjdk.samtools.BAMIndexer; +import org.broadinstitute.hellbender.engine.GATKPath; + +import java.io.File; +import java.io.IOException; + +/** + * Analyzer for BAI files. + */ +public class BAIAnalyzer extends HTSAnalyzer { + + public BAIAnalyzer(final GATKPath inputPath, final File outputFile) { + super(inputPath, outputFile); + } + + /** + * Run the analyzer for the file. + */ + protected void doAnalysis() { + System.out.println(String.format("\nOutput written to %s\n", outputFile)); + BAMIndexer.createAndWriteIndex(inputPath.toPath().toFile(), outputFile, true); + } + + @Override + public void close() throws IOException { + } + +} + diff --git a/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/CRAIAnalyzer.java b/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/CRAIAnalyzer.java new file mode 100644 index 00000000000..dcbe8109938 --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/CRAIAnalyzer.java @@ -0,0 +1,59 @@ +package org.broadinstitute.hellbender.tools.filediagnostics; + +import htsjdk.samtools.CRAMCRAIIndexer; +import htsjdk.samtools.cram.CRAIIndex; +import htsjdk.samtools.util.RuntimeIOException; +import org.broadinstitute.hellbender.engine.GATKPath; + +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStream; + +/** + * Analyzer for CRAM (.crai) index files. + */ +public class CRAIAnalyzer extends HTSAnalyzer { + + final FileOutputStream fos; + + public CRAIAnalyzer(final GATKPath inputPath, final File outputFile) { + super(inputPath, outputFile); + try { + fos = new FileOutputStream(outputFile); + } catch (final IOException e) { + throw new RuntimeIOException(e); + } + } + + protected void emitln(final String s) { + try { + fos.write(s.getBytes()); + fos.write('\n'); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + /** + * Run the analyzer for the file. + */ + protected void doAnalysis() { + try (final InputStream is = inputPath.getInputStream()) { + final CRAIIndex craiIndex = CRAMCRAIIndexer.readIndex(is); + emitln("\nSeqId AlignmentStart AlignmentSpan ContainerOffset SliceOffset SliceSize\n"); + craiIndex.getCRAIEntries().stream().forEach(e -> emitln(e.toString())); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + @Override + public void close() throws IOException { + if (fos != null) { + fos.close(); + } + } + +} + diff --git a/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/CRAMAnalyzer.java b/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/CRAMAnalyzer.java new file mode 100644 index 00000000000..76933277e99 --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/CRAMAnalyzer.java @@ -0,0 +1,308 @@ +package org.broadinstitute.hellbender.tools.filediagnostics; + +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.cram.build.CramIO; +import htsjdk.samtools.cram.encoding.CRAMEncoding; +import htsjdk.samtools.cram.encoding.EncodingFactory; +import htsjdk.samtools.cram.io.ITF8; +import htsjdk.samtools.cram.structure.*; +import htsjdk.samtools.seekablestream.SeekablePathStream; +import htsjdk.samtools.util.RuntimeIOException; +import org.broadinstitute.hellbender.engine.GATKPath; + +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStream; +import java.nio.ByteBuffer; +import java.nio.ByteOrder; +import java.util.Base64; +import java.util.HashMap; +import java.util.LinkedHashMap; +import java.util.Map; + +/** + * Analyzer for CRAM files. Displays metadata for each CRAM container, + * slice, and block. + * + * Note: the analyzer does not require a reference for the since it only + * enumerates metadata and doesn't attempt to dereference the reads. + */ +public class CRAMAnalyzer extends HTSAnalyzer { + + final Map externalDataSeriesDataSizes = new LinkedHashMap<>(); + final Map externalTagDataSizes = new LinkedHashMap<>(); + long coreBlocksDataSize = 0L; + long recordCount = 0; + final long countLimit; + final FileOutputStream fos; + + public CRAMAnalyzer(final GATKPath inputPathName, final File outputFile, final long countLimit) { + super(inputPathName, outputFile); + this.countLimit = countLimit; + try { + fos = new FileOutputStream(outputFile); + } catch (final IOException e) { + throw new RuntimeIOException(e); + } + } + + @Override + public void close() throws IOException { + if (fos != null) { + fos.close(); + } + } + + protected void emitln(final String s) { + try { + fos.write(s.getBytes()); + fos.write('\n'); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + /** + * Run the analyzer for the file. + */ + protected void doAnalysis() { + int containerCount = 0; + try (final SeekablePathStream seekableStream = new SeekablePathStream(this.inputPath.toPath())) { + final CramHeader cramHeader = analyzeCRAMHeader(seekableStream); + boolean isEOF = false; + while (!isEOF && containerCount < countLimit) { + long containerOffset = seekableStream.position(); + final Container container = new Container( + cramHeader.getCRAMVersion(), + seekableStream, + containerOffset); + isEOF = analyzeContainer(container, ++containerCount) ; + } + } + catch (IOException e) { + throw new RuntimeIOException(e); + } + + emitln("\nTotal Record Count: " + recordCount); + emitDataDistribution(); + } + + /** + * Display metadata for a CRAM file header. + * + */ + public CramHeader analyzeCRAMHeader(InputStream is) { + final CramHeader cramHeader = CramIO.readCramHeader(is); + emitln("\nCRAM File: " + inputPath); + emitln("CRAM Version: " + cramHeader.getCRAMVersion().toString()); + emitln("CRAM ID Contents: " + String.format("%s", Base64.getEncoder().encodeToString(cramHeader.getId()))); + + final SAMFileHeader samHeader = Container.readSAMFileHeaderContainer(cramHeader.getCRAMVersion(), is, inputPath.getRawInputString()); + emitln("\n" + samHeader.toString()); + final SAMSequenceDictionary dict = samHeader.getSequenceDictionary(); + emitln(dict.toString()); + dict.getSequences().forEach(e -> emitln(e.toString())); + return cramHeader; + } + + /** + * Display metadata for a CRAM file container. + * return true if container is EOF container + */ + public boolean analyzeContainer(Container container, int containerCount) { + final ContainerHeader containerHeader = container.getContainerHeader(); + emitln(String.format( + "\n***Container #:%d %s byteOffset=%d", + containerCount, containerHeader.toString(), container.getContainerByteOffset())); + if (container.isEOF()) { + return true; + } + // contentID to DataSeries (excludes tags ?) + final Map dataSeriesByContentID = analyzeCompressionHeader(container.getCompressionHeader()); + int sliceCount = 0; + for (final Slice slice : container.getSlices()) { + analyzeSlice(slice, ++sliceCount, dataSeriesByContentID); + } + return false; + } + + public Map analyzeCompressionHeader(final CompressionHeader compressionHeader) { + //preservation map, data series encoding map, and tag encoding map + analyzePreservationMap(compressionHeader); + final Map dataSeriesByContentID = analyzeDataSeriesEncodingMap(compressionHeader); + analyzeTagEncodingMap(compressionHeader); + return dataSeriesByContentID; + } + + public void analyzePreservationMap(final CompressionHeader compressionHeader) { + emitln(String.format( + "Requires reference (%b); Preserved read names (%b); APDelta (%b)", + compressionHeader.isReferenceRequired(), + compressionHeader.isPreserveReadNames(), + compressionHeader.isAPDelta())); + } + + public Map analyzeDataSeriesEncodingMap(final CompressionHeader compressionHeader) { + // Since each container can in theory use a different set of ids for the data series in that + // container, we need to reconstruct the mapping for each container, and return it so that as + // we process Slice blocks and track data, we can calculate the data series to which we should + // accrue that block's data + final Map dataSeriesByContentID = new LinkedHashMap<>(); + + emitln("\nData Series Encodings:\n"); + final CompressionHeaderEncodingMap encodingMap = compressionHeader.getEncodingMap(); + for (final DataSeries dataSeries: DataSeries.values()) { + final EncodingDescriptor encodingDescriptor = encodingMap.getEncodingDescriptorForDataSeries(dataSeries); + if (encodingDescriptor == null) { + emitln(String.format("%-50s not present", + String.format("DataSeries (%s/%s)", + dataSeries.getCanonicalName(), + dataSeries.name()))); + } else { + // the encoding map has an encoding descriptor for this data series; determine if its external + // and if so, update the contentID to data series map so we can track how much data is used for + // the blocks for this data series + final Integer externalContentID = contentIDFromExternalDescriptor(dataSeries.getType(), encodingDescriptor); + if (externalContentID != null) { + dataSeriesByContentID.put(externalContentID, dataSeries); + } + emitln(String.format("%-50s %s", + String.format("DataSeries (%s/%s)", + dataSeries.getCanonicalName(), + dataSeries.name()), + encodingDescriptorAsString( + dataSeries.getType(), + encodingDescriptor))); + } + } + return dataSeriesByContentID; + } + + public void analyzeTagEncodingMap(final CompressionHeader compressionHeader) { + emitln("\nTag Encodings:"); + for (final Map.Entry entry : compressionHeader.getTagEncodingMap().entrySet()) { + final Integer contentID = entry.getKey(); // is this content ID ? + final EncodingDescriptor ep = entry.getValue(); + emitln(String.format("%-50s %s", + String.format("Content ID/Tag (%s/%s)", + contentID, + decomposeTagNameAndType(contentID)), + encodingDescriptorAsString(DataSeriesType.BYTE_ARRAY, ep))); + } + } + + /** + * Display metadata for a CRAM container slice. + * + */ + public void analyzeSlice(final Slice slice, final int sliceCount, final Map dataSeriesByContentID) { + emitln(String.format("\n******Slice #: %d %s", + sliceCount, + slice.toString())); + emitln(String.format("%-50s %s", + "Header block ", + slice.getSliceHeaderBlock())); + emitln(String.format("%-50s %s", + "Core block ", + slice.getSliceBlocks().getCoreBlock())); + + if (slice.getEmbeddedReferenceContentID() != Slice.EMBEDDED_REFERENCE_ABSENT_CONTENT_ID) { + emitln(String.format("Embedded reference block ID %d", slice.getEmbeddedReferenceContentID())); + } + + slice.getSliceBlocks().getExternalContentIDs().forEach((id) -> { + final String blockID = dataSeriesByContentID.get(id) == null ? + Integer.toString(id) : // not a fixed data series (i.e., tag block) + dataSeriesByContentID.get(id).getCanonicalName(); + emitln(String.format("%-50s %s", + String.format("External Block (%s):", blockID), + slice.getSliceBlocks().getExternalBlock(id).toString())); + }); + + updateDataDistribution(slice, dataSeriesByContentID); + recordCount += slice.getNumberOfRecords(); + } + + final void updateDataDistribution(final Slice slice, final Map dataSeriesByContentID) { + final SliceBlocks sliceBlocks = slice.getSliceBlocks(); + + coreBlocksDataSize += sliceBlocks.getCoreBlock().getCompressedContentSize(); + final Map tagContentIDs = slice.getCompressionHeader().getTagEncodingMap(); + for (final Integer contentID : sliceBlocks.getExternalContentIDs()) { + //if (tagContentIDs.containsKey(contentID)) { + final DataSeries ds = dataSeriesByContentID.get(contentID); + if (ds == null) { + // accrue to tag data + externalTagDataSizes.merge( + contentID, + Long.valueOf(slice.getSliceBlocks().getExternalBlock(contentID).getCompressedContentSize()), + (oldValue, increment) -> oldValue + increment); + } else { + // accrue to fixed DataSeries ID + externalDataSeriesDataSizes.merge( + ds, + Long.valueOf(sliceBlocks.getExternalBlock(contentID).getCompressedContentSize()), + (oldValue, increment) -> oldValue + increment); + } + } + } + + public void emitDataDistribution() { + emitln("\nCore Block(s) Total: " + String.format("%,d\n", coreBlocksDataSize)); + emitln("External Data Series Totals (external block resolution - all core data encodings accrue to the core block):\n"); + for (final DataSeries ds : externalDataSeriesDataSizes.keySet()) { + emitln(String.format("%s: %,d", ds, externalDataSeriesDataSizes.get(ds))); + } + + emitln("\nTag Series Distribution:\n"); + for (final Map.Entry externalEntry : externalTagDataSizes.entrySet()) { + final Integer contentID = externalEntry.getKey(); + final String tagName = String.format("%d (%s)", contentID, decomposeTagNameAndType(externalEntry.getKey())); + emitln(String.format("%s: %,d", tagName, externalEntry.getValue())); + } + } + + private String encodingDescriptorAsString(final DataSeriesType dsType, final EncodingDescriptor descriptor) { + final String encodingIDString = EncodingID.values()[descriptor.getEncodingID().getId()].toString(); + final CRAMEncoding encoding = EncodingFactory.createCRAMEncoding( + dsType, descriptor.getEncodingID(), descriptor.getEncodingParameters()); + return String.format("%s (%s)", encodingIDString, encoding.toString()); + } + + private Integer contentIDFromExternalDescriptor(final DataSeriesType dsType, final EncodingDescriptor descriptor) { + final CRAMEncoding encoding = EncodingFactory.createCRAMEncoding( + dsType, descriptor.getEncodingID(), descriptor.getEncodingParameters()); + switch (descriptor.getEncodingID()) { + case EXTERNAL: + return ITF8.readUnsignedITF8(encoding.toSerializedEncodingParams()); + + case BYTE_ARRAY_STOP: + final ByteBuffer buf = ByteBuffer.wrap(encoding.toSerializedEncodingParams()); + buf.order(ByteOrder.LITTLE_ENDIAN); + final byte stopByte = buf.get(); // discard it + return ITF8.readUnsignedITF8(buf); + + // Everything else is either not external, or is hybrid (BYTE_ARRAY_LEN), so we can't + // track the data for these at the block level since the data foes either partially or + // fully into the core block + case BYTE_ARRAY_LEN: + case NULL: + case GOLOMB: + case HUFFMAN: + case BETA: + case SUBEXPONENTIAL: + case GOLOMB_RICE: + case GAMMA: + default: + return null; + } + } + + private String decomposeTagNameAndType(final int contentID) { + return ReadTag.intToNameType4Bytes(contentID); + } + +} + diff --git a/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/HTSAnalyzer.java b/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/HTSAnalyzer.java new file mode 100644 index 00000000000..8339dfaccc4 --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/HTSAnalyzer.java @@ -0,0 +1,46 @@ +package org.broadinstitute.hellbender.tools.filediagnostics; + +import htsjdk.samtools.util.Log; +import org.broadinstitute.hellbender.engine.GATKPath; + +import java.io.Closeable; +import java.io.File; +import java.io.IOException; + +/** + * Base class for alignment file analyzers. + */ +public abstract class HTSAnalyzer implements Closeable { + + protected GATKPath inputPath; + protected File outputFile; + + public HTSAnalyzer(final GATKPath filePath, final File outputFile) { + this.inputPath = filePath; + this.outputFile = outputFile; + } + + /** + * Run the analyzer for the file specified by fileName. + */ + public void analyze() { + // set and then reset the global log level + Log.setGlobalLogLevel(Log.LogLevel.ERROR); + doAnalysis(); + emitln(""); + Log.setGlobalLogLevel(Log.LogLevel.DEBUG); + } + + /** + * Emit a string followed by a newline to the output destination. + * + * @param s + */ + protected void emitln(final String s) { + System.out.println(s); + } + + protected abstract void doAnalysis(); + + public abstract void close() throws IOException; +} diff --git a/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/HTSAnalyzerFactory.java b/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/HTSAnalyzerFactory.java new file mode 100644 index 00000000000..d58438a7b61 --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/tools/filediagnostics/HTSAnalyzerFactory.java @@ -0,0 +1,25 @@ +package org.broadinstitute.hellbender.tools.filediagnostics; + +import htsjdk.samtools.util.FileExtensions; +import org.broadinstitute.hellbender.engine.GATKPath; + +import java.io.File; + +/** + * Class for creating an analyzer based on an alignment file type. + */ +public class HTSAnalyzerFactory { + + public static HTSAnalyzer getFileAnalyzer(final GATKPath inputPath, final File outputFile, final long countLimit) { + System.out.println(inputPath.getRawInputString()); + if (inputPath.isCram()) { + return new CRAMAnalyzer(inputPath, outputFile, countLimit); + } else if (inputPath.hasExtension(FileExtensions.CRAM_INDEX)) { + return new CRAIAnalyzer(inputPath, outputFile); + } else if (inputPath.hasExtension(FileExtensions.BAI_INDEX)) { + return new BAIAnalyzer(inputPath, outputFile); + } else { + throw new RuntimeException("Unsupported diagnostic file type: " + inputPath.getRawInputString()); + } + } +} diff --git a/src/test/java/org/broadinstitute/hellbender/PrintFileDiagnosticsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/PrintFileDiagnosticsIntegrationTest.java new file mode 100644 index 00000000000..e03a36fe5c6 --- /dev/null +++ b/src/test/java/org/broadinstitute/hellbender/PrintFileDiagnosticsIntegrationTest.java @@ -0,0 +1,52 @@ +package org.broadinstitute.hellbender; + +import org.apache.commons.lang3.tuple.Pair; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.IOException; +import java.util.List; + +public class PrintFileDiagnosticsIntegrationTest extends CommandLineProgramTest { + + @DataProvider(name = "fileDiagnosticsTestCases") + public Object[][] getFileDiagnosticsTestCases() { + return new Object[][]{ + { + "src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram", + List.of(Pair.of("count-limit", "10")), + "src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.txt" + }, + { + "src/test/resources/org/broadinstitute/hellbender/metrics/analysis/MeanQualityByCycle/example_pfFail_reads.bam.bai", + null, + "src/test/resources/filediagnostics/example_pfFail_reads.bam.bai.txt" + }, + { + "src/test/resources/org/broadinstitute/hellbender/engine/cram_with_crai_index.cram.crai", + null, + "src/test/resources/filediagnostics/cram_with_crai_index.cram.crai.txt" + }, + }; + } + + @Test(dataProvider = "fileDiagnosticsTestCases") + public void testFileDiagnostics( + final String inputPath, + final List> extraArgs, + final String expectedOutputPath) throws IOException { + final File outFile = createTempFile("testFileDiagnostics", ".txt"); + ArgumentsBuilder argBuilder = new ArgumentsBuilder(); + argBuilder.addInput(inputPath); + argBuilder.addOutput(outFile); + if (extraArgs != null) { + extraArgs.forEach(argPair -> argBuilder.add(argPair.getKey(), argPair.getValue())); + } + runCommandLine(argBuilder.getArgsList()); + + IntegrationTestSpec.assertEqualTextFiles(outFile, new File(expectedOutputPath)); + } +} diff --git a/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.txt b/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.txt new file mode 100644 index 00000000000..4a64d41c5b8 --- /dev/null +++ b/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.txt @@ -0,0 +1,1187 @@ + +CRAM File: src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram +CRAM Version: 2.1 +CRAM ID Contents: L1VzZXJzL2FraWV6dW4vSWRlYVA= + +SAMFileHeader{VN=1.5, GO=none, SO=coordinate} +SAMSequenceDictionary:( sequences:2 length:111155415 md5:090fb1cdca0dabd61b568ab56e9f555f) +SAMSequenceRecord(name=20,length=63025520,dict_index=0,assembly=null,alternate_names=[]) +SAMSequenceRecord(name=21,length=48129895,dict_index=1,assembly=null,alternate_names=[]) + +***Container #:1 sequenceId=SINGLE_REFERENCE: 0, start=9999902, span=11055, nRecords=10000, nBlocks=52, nBases=1010000, globalCounter=0 byteOffset=5578 +Requires reference (true); Preserved read names (true); APDelta (true) + +Data Series Encodings: + +DataSeries (BF/BF_BitFlags) EXTERNAL (Content ID: 0) +DataSeries (CF/CF_CompressionBitFlags) EXTERNAL (Content ID: 21) +DataSeries (RI/RI_RefId) EXTERNAL (Content ID: 25) +DataSeries (RL/RL_ReadLength) EXTERNAL (Content ID: 9) +DataSeries (AP/AP_AlignmentPositionOffset) EXTERNAL (Content ID: 1) +DataSeries (RG/RG_ReadGroup) EXTERNAL (Content ID: 10) +DataSeries (RN/RN_ReadName) BYTE_ARRAY_STOP (Content ID: 12 StopByte: 9) +DataSeries (NF/NF_RecordsToNextFragment) EXTERNAL (Content ID: 8) +DataSeries (MF/MF_MateBitFlags) EXTERNAL (Content ID: 19) +DataSeries (NS/NS_NextFragmentReferenceSequenceID) EXTERNAL (Content ID: 20) +DataSeries (NP/NP_NextFragmentAlignmentStart) EXTERNAL (Content ID: 13) +DataSeries (TS/TS_InsertSize) EXTERNAL (Content ID: 14) +DataSeries (TL/TL_TagIdList) EXTERNAL (Content ID: 24) +DataSeries (TC/TC_TagCount) not present +DataSeries (TN/TN_TagNameAndType) not present +DataSeries (MQ/MQ_MappingQualityScore) EXTERNAL (Content ID: 11) +DataSeries (FN/FN_NumberOfReadFeatures) EXTERNAL (Content ID: 15) +DataSeries (FP/FP_FeaturePosition) EXTERNAL (Content ID: 2) +DataSeries (FC/FC_FeatureCode) EXTERNAL (Content ID: 3) +DataSeries (BB/BB_Bases) not present +DataSeries (QQ/QQ_scores) not present +DataSeries (BA/BA_Base) EXTERNAL (Content ID: 6) +DataSeries (QS/QS_QualityScore) EXTERNAL (Content ID: 4) +DataSeries (BS/BS_BaseSubstitutionCode) EXTERNAL (Content ID: 16) +DataSeries (IN/IN_Insertion) BYTE_ARRAY_STOP (Content ID: 17 StopByte: 9) +DataSeries (DL/DL_DeletionLength) EXTERNAL (Content ID: 5) +DataSeries (RS/RS_RefSkip) EXTERNAL (Content ID: 26) +DataSeries (SC/SC_SoftClip) BYTE_ARRAY_STOP (Content ID: 27 StopByte: 9) +DataSeries (PD/PD_padding) EXTERNAL (Content ID: 29) +DataSeries (HC/HC_HardClip) EXTERNAL (Content ID: 28) +DataSeries (TM/TM_TestMark) not present +DataSeries (TV/TV_TestMark) not present + +Tag Encodings: +Content ID/Tag (4279651/AM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 4279651) +Content ID/Tag (4346202/BQ:Z) BYTE_ARRAY_LEN (LenEncoding: Symbols: 102 BitLengths 0 ByteEncoding: Content ID: 4346202) +Content ID/Tag (5063770/MD:Z) BYTE_ARRAY_STOP (Content ID: 5063770 StopByte: 9) +Content ID/Tag (5067107/MQ:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5067107) +Content ID/Tag (5131619/NM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5131619) +Content ID/Tag (5194586/OC:Z) BYTE_ARRAY_STOP (Content ID: 5194586 StopByte: 9) +Content ID/Tag (5197929/OP:i) BYTE_ARRAY_LEN (LenEncoding: Symbols: 4 BitLengths 0 ByteEncoding: Content ID: 5197929) +Content ID/Tag (5198170/OQ:Z) BYTE_ARRAY_LEN (LenEncoding: Symbols: 102 BitLengths 0 ByteEncoding: Content ID: 5198170) +Content ID/Tag (5459299/SM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5459299) +Content ID/Tag (5779523/X0:C) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5779523) +Content ID/Tag (5779555/X0:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5779555) +Content ID/Tag (5779571/X0:s) BYTE_ARRAY_LEN (LenEncoding: Symbols: 2 BitLengths 0 ByteEncoding: Content ID: 5779571) +Content ID/Tag (5779779/X1:C) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 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size=1478 +External Block (4346202): method=RANS, type=EXTERNAL, id=4346202, raw size=858942, compressed size=44520 +External Block (5063770): method=GZIP, type=EXTERNAL, id=5063770, raw size=62190, compressed size=16062 +External Block (5067107): method=RANS, type=EXTERNAL, id=5067107, raw size=9735, compressed size=1397 +External Block (5131619): method=RANS, type=EXTERNAL, id=5131619, raw size=9868, compressed size=1874 +External Block (5194586): method=GZIP, type=EXTERNAL, id=5194586, raw size=681, compressed size=189 +External Block (5197929): method=GZIP, type=EXTERNAL, id=5197929, raw size=168, compressed size=110 +External Block (5198170): method=RANS, type=EXTERNAL, id=5198170, raw size=1020000, compressed size=202723 +External Block (5459299): method=RANS, type=EXTERNAL, id=5459299, raw size=9868, compressed size=1168 +External Block (5779523): method=GZIP, type=EXTERNAL, id=5779523, raw size=1, compressed size=21 +External Block (5779555): method=GZIP, type=EXTERNAL, 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type=EXTERNAL, id=5788737, raw size=9868, compressed size=402 + +***Container #:2 sequenceId=SINGLE_REFERENCE: 0, start=10010859, span=11595, nRecords=10000, nBlocks=52, nBases=1010000, globalCounter=10000 byteOffset=787322 +Requires reference (true); Preserved read names (true); APDelta (true) + +Data Series Encodings: + +DataSeries (BF/BF_BitFlags) EXTERNAL (Content ID: 0) +DataSeries (CF/CF_CompressionBitFlags) EXTERNAL (Content ID: 21) +DataSeries (RI/RI_RefId) EXTERNAL (Content ID: 25) +DataSeries (RL/RL_ReadLength) EXTERNAL (Content ID: 9) +DataSeries (AP/AP_AlignmentPositionOffset) EXTERNAL (Content ID: 1) +DataSeries (RG/RG_ReadGroup) EXTERNAL (Content ID: 10) +DataSeries (RN/RN_ReadName) BYTE_ARRAY_STOP (Content ID: 12 StopByte: 9) +DataSeries (NF/NF_RecordsToNextFragment) EXTERNAL (Content ID: 8) +DataSeries (MF/MF_MateBitFlags) EXTERNAL (Content ID: 19) +DataSeries (NS/NS_NextFragmentReferenceSequenceID) EXTERNAL (Content ID: 20) +DataSeries (NP/NP_NextFragmentAlignmentStart) EXTERNAL (Content ID: 13) +DataSeries (TS/TS_InsertSize) EXTERNAL (Content ID: 14) +DataSeries (TL/TL_TagIdList) EXTERNAL (Content ID: 24) +DataSeries (TC/TC_TagCount) not present +DataSeries (TN/TN_TagNameAndType) not present +DataSeries (MQ/MQ_MappingQualityScore) EXTERNAL (Content ID: 11) +DataSeries (FN/FN_NumberOfReadFeatures) EXTERNAL (Content ID: 15) +DataSeries (FP/FP_FeaturePosition) EXTERNAL (Content ID: 2) +DataSeries (FC/FC_FeatureCode) EXTERNAL (Content ID: 3) +DataSeries (BB/BB_Bases) not present +DataSeries (QQ/QQ_scores) not present +DataSeries (BA/BA_Base) EXTERNAL (Content ID: 6) +DataSeries (QS/QS_QualityScore) EXTERNAL (Content ID: 4) +DataSeries (BS/BS_BaseSubstitutionCode) EXTERNAL (Content ID: 16) +DataSeries (IN/IN_Insertion) BYTE_ARRAY_STOP (Content ID: 17 StopByte: 9) +DataSeries (DL/DL_DeletionLength) EXTERNAL (Content ID: 5) +DataSeries (RS/RS_RefSkip) EXTERNAL (Content ID: 26) +DataSeries (SC/SC_SoftClip) BYTE_ARRAY_STOP (Content ID: 27 StopByte: 9) +DataSeries (PD/PD_padding) EXTERNAL (Content ID: 29) +DataSeries (HC/HC_HardClip) EXTERNAL (Content ID: 28) +DataSeries (TM/TM_TestMark) not present +DataSeries (TV/TV_TestMark) not present + +Tag Encodings: +Content ID/Tag (4279651/AM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 4279651) +Content ID/Tag (4346202/BQ:Z) BYTE_ARRAY_LEN (LenEncoding: Symbols: 102 BitLengths 0 ByteEncoding: Content ID: 4346202) +Content ID/Tag (5063770/MD:Z) BYTE_ARRAY_STOP (Content ID: 5063770 StopByte: 9) +Content ID/Tag (5067107/MQ:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5067107) +Content ID/Tag (5131619/NM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5131619) +Content ID/Tag (5194586/OC:Z) BYTE_ARRAY_STOP (Content ID: 5194586 StopByte: 9) +Content ID/Tag (5197929/OP:i) BYTE_ARRAY_LEN (LenEncoding: Symbols: 4 BitLengths 0 ByteEncoding: Content ID: 5197929) 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raw size=9760, compressed size=1008 +External Block (5131619): method=RANS, type=EXTERNAL, id=5131619, raw size=9880, compressed size=1376 +External Block (5194586): method=GZIP, type=EXTERNAL, id=5194586, raw size=128, compressed size=61 +External Block (5197929): method=GZIP, type=EXTERNAL, id=5197929, raw size=32, compressed size=37 +External Block (5198170): method=RANS, type=EXTERNAL, id=5198170, raw size=1020000, compressed size=207267 +External Block (5459299): method=RANS, type=EXTERNAL, id=5459299, raw size=9880, compressed size=871 +External Block (5779523): method=GZIP, type=EXTERNAL, id=5779523, raw size=10, compressed size=31 +External Block (5779555): method=RANS, type=EXTERNAL, id=5779555, raw size=9652, compressed size=242 +External Block (5779571): method=GZIP, type=EXTERNAL, id=5779571, raw size=16, compressed size=36 +External Block (5779779): method=GZIP, type=EXTERNAL, id=5779779, raw size=14, compressed size=35 +External Block (5779811): method=GZIP, 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APDelta (true) + +Data Series Encodings: + +DataSeries (BF/BF_BitFlags) EXTERNAL (Content ID: 0) +DataSeries (CF/CF_CompressionBitFlags) EXTERNAL (Content ID: 21) +DataSeries (RI/RI_RefId) EXTERNAL (Content ID: 25) +DataSeries (RL/RL_ReadLength) EXTERNAL (Content ID: 9) +DataSeries (AP/AP_AlignmentPositionOffset) EXTERNAL (Content ID: 1) +DataSeries (RG/RG_ReadGroup) EXTERNAL (Content ID: 10) +DataSeries (RN/RN_ReadName) BYTE_ARRAY_STOP (Content ID: 12 StopByte: 9) +DataSeries (NF/NF_RecordsToNextFragment) EXTERNAL (Content ID: 8) +DataSeries (MF/MF_MateBitFlags) EXTERNAL (Content ID: 19) +DataSeries (NS/NS_NextFragmentReferenceSequenceID) EXTERNAL (Content ID: 20) +DataSeries (NP/NP_NextFragmentAlignmentStart) EXTERNAL (Content ID: 13) +DataSeries (TS/TS_InsertSize) EXTERNAL (Content ID: 14) +DataSeries (TL/TL_TagIdList) EXTERNAL (Content ID: 24) +DataSeries (TC/TC_TagCount) not present +DataSeries (TN/TN_TagNameAndType) not present +DataSeries (MQ/MQ_MappingQualityScore) EXTERNAL (Content ID: 11) +DataSeries (FN/FN_NumberOfReadFeatures) EXTERNAL (Content ID: 15) +DataSeries (FP/FP_FeaturePosition) EXTERNAL (Content ID: 2) +DataSeries (FC/FC_FeatureCode) EXTERNAL (Content ID: 3) +DataSeries (BB/BB_Bases) not present +DataSeries (QQ/QQ_scores) not present +DataSeries (BA/BA_Base) EXTERNAL (Content ID: 6) +DataSeries (QS/QS_QualityScore) EXTERNAL (Content ID: 4) +DataSeries (BS/BS_BaseSubstitutionCode) EXTERNAL (Content ID: 16) +DataSeries (IN/IN_Insertion) BYTE_ARRAY_STOP (Content ID: 17 StopByte: 9) +DataSeries (DL/DL_DeletionLength) EXTERNAL (Content ID: 5) +DataSeries (RS/RS_RefSkip) EXTERNAL (Content ID: 26) +DataSeries (SC/SC_SoftClip) BYTE_ARRAY_STOP (Content ID: 27 StopByte: 9) +DataSeries (PD/PD_padding) EXTERNAL (Content ID: 29) +DataSeries (HC/HC_HardClip) EXTERNAL (Content ID: 28) +DataSeries (TM/TM_TestMark) not present +DataSeries (TV/TV_TestMark) not present + +Tag Encodings: +Content ID/Tag (4279651/AM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 4279651) +Content ID/Tag (4346202/BQ:Z) BYTE_ARRAY_LEN (LenEncoding: Symbols: 102 BitLengths 0 ByteEncoding: Content ID: 4346202) +Content ID/Tag (5063770/MD:Z) BYTE_ARRAY_STOP (Content ID: 5063770 StopByte: 9) +Content ID/Tag (5067107/MQ:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5067107) +Content ID/Tag (5131619/NM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5131619) +Content ID/Tag (5194586/OC:Z) BYTE_ARRAY_STOP (Content ID: 5194586 StopByte: 9) +Content ID/Tag (5197929/OP:i) BYTE_ARRAY_LEN (LenEncoding: Symbols: 4 BitLengths 0 ByteEncoding: Content ID: 5197929) +Content ID/Tag (5198170/OQ:Z) BYTE_ARRAY_LEN (LenEncoding: Symbols: 102 BitLengths 0 ByteEncoding: Content ID: 5198170) +Content ID/Tag (5459299/SM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5459299) +Content ID/Tag (5779555/X0:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 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(AP/AP_AlignmentPositionOffset) EXTERNAL (Content ID: 1) +DataSeries (RG/RG_ReadGroup) EXTERNAL (Content ID: 10) +DataSeries (RN/RN_ReadName) BYTE_ARRAY_STOP (Content ID: 12 StopByte: 9) +DataSeries (NF/NF_RecordsToNextFragment) EXTERNAL (Content ID: 8) +DataSeries (MF/MF_MateBitFlags) EXTERNAL (Content ID: 19) +DataSeries (NS/NS_NextFragmentReferenceSequenceID) EXTERNAL (Content ID: 20) +DataSeries (NP/NP_NextFragmentAlignmentStart) EXTERNAL (Content ID: 13) +DataSeries (TS/TS_InsertSize) EXTERNAL (Content ID: 14) +DataSeries (TL/TL_TagIdList) EXTERNAL (Content ID: 24) +DataSeries (TC/TC_TagCount) not present +DataSeries (TN/TN_TagNameAndType) not present +DataSeries (MQ/MQ_MappingQualityScore) EXTERNAL (Content ID: 11) +DataSeries (FN/FN_NumberOfReadFeatures) EXTERNAL (Content ID: 15) +DataSeries (FP/FP_FeaturePosition) EXTERNAL (Content ID: 2) +DataSeries (FC/FC_FeatureCode) EXTERNAL (Content ID: 3) +DataSeries (BB/BB_Bases) not present +DataSeries (QQ/QQ_scores) not present 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BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5067107) +Content ID/Tag (5131619/NM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5131619) +Content ID/Tag (5194586/OC:Z) BYTE_ARRAY_STOP (Content ID: 5194586 StopByte: 9) +Content ID/Tag (5197929/OP:i) BYTE_ARRAY_LEN (LenEncoding: Symbols: 4 BitLengths 0 ByteEncoding: Content ID: 5197929) +Content ID/Tag (5198170/OQ:Z) BYTE_ARRAY_LEN (LenEncoding: Symbols: 102 BitLengths 0 ByteEncoding: Content ID: 5198170) +Content ID/Tag (5459299/SM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5459299) +Content ID/Tag (5779555/X0:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5779555) +Content ID/Tag (5779779/X1:C) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5779779) +Content ID/Tag (5779811/X1:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5779811) +Content ID/Tag (5779827/X1:s) BYTE_ARRAY_LEN (LenEncoding: Symbols: 2 BitLengths 0 ByteEncoding: Content ID: 5779827) +Content ID/Tag (5783898/XA:Z) BYTE_ARRAY_STOP (Content ID: 5783898 StopByte: 9) +Content ID/Tag (5784419/XC:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5784419) +Content ID/Tag (5785443/XG:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5785443) +Content ID/Tag (5786979/XM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5786979) +Content ID/Tag (5787491/XO:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5787491) +Content ID/Tag (5788737/XT:A) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5788737) + +******Slice #: 1 slice: sequenceId=SINGLE_REFERENCE: 0, start=10054316, span=11415 globalRecordCounter=50000, nRecords=10000, sliceHeaderOffset=1297, sizeOfBlocks=763062, landmark=0, 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size=39850 +External Block (5063770): method=GZIP, type=EXTERNAL, id=5063770, raw size=52971, compressed size=9340 +External Block (5067107): method=RANS, type=EXTERNAL, id=5067107, raw size=9823, compressed size=527 +External Block (5131619): method=RANS, type=EXTERNAL, id=5131619, raw size=9912, compressed size=1006 +External Block (5194586): method=GZIP, type=EXTERNAL, id=5194586, raw size=19, compressed size=39 +External Block (5197929): method=GZIP, type=EXTERNAL, id=5197929, raw size=8, compressed size=28 +External Block (5198170): method=RANS, type=EXTERNAL, id=5198170, raw size=1020000, compressed size=208578 +External Block (5459299): method=RANS, type=EXTERNAL, id=5459299, raw size=9912, compressed size=505 +External Block (5779555): method=RANS, type=EXTERNAL, id=5779555, raw size=9724, compressed size=78 +External Block (5779779): method=GZIP, type=EXTERNAL, id=5779779, raw size=1, compressed size=21 +External Block (5779811): method=RANS, type=EXTERNAL, id=5779811, raw size=9718, compressed size=102 +External Block (5779827): method=GZIP, type=EXTERNAL, id=5779827, raw size=6, compressed size=26 +External Block (5783898): method=GZIP, type=EXTERNAL, id=5783898, raw size=506, compressed size=223 +External Block (5784419): method=RANS, type=EXTERNAL, id=5784419, raw size=1899, compressed size=1273 +External Block (5785443): method=RANS, type=EXTERNAL, id=5785443, raw size=9912, compressed size=77 +External Block (5786979): method=RANS, type=EXTERNAL, id=5786979, raw size=9912, compressed size=979 +External Block (5787491): method=RANS, type=EXTERNAL, id=5787491, raw size=9912, compressed size=74 +External Block (5788737): method=RANS, type=EXTERNAL, id=5788737, raw size=9912, compressed size=223 + +***Container #:7 sequenceId=SINGLE_REFERENCE: 0, start=10065630, span=11707, nRecords=10000, nBlocks=49, nBases=1010000, globalCounter=60000 byteOffset=4588558 +Requires reference (true); Preserved read names (true); APDelta (true) + +Data Series Encodings: 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(FN/FN_NumberOfReadFeatures) EXTERNAL (Content ID: 15) +DataSeries (FP/FP_FeaturePosition) EXTERNAL (Content ID: 2) +DataSeries (FC/FC_FeatureCode) EXTERNAL (Content ID: 3) +DataSeries (BB/BB_Bases) not present +DataSeries (QQ/QQ_scores) not present +DataSeries (BA/BA_Base) EXTERNAL (Content ID: 6) +DataSeries (QS/QS_QualityScore) EXTERNAL (Content ID: 4) +DataSeries (BS/BS_BaseSubstitutionCode) EXTERNAL (Content ID: 16) +DataSeries (IN/IN_Insertion) BYTE_ARRAY_STOP (Content ID: 17 StopByte: 9) +DataSeries (DL/DL_DeletionLength) EXTERNAL (Content ID: 5) +DataSeries (RS/RS_RefSkip) EXTERNAL (Content ID: 26) +DataSeries (SC/SC_SoftClip) BYTE_ARRAY_STOP (Content ID: 27 StopByte: 9) +DataSeries (PD/PD_padding) EXTERNAL (Content ID: 29) +DataSeries (HC/HC_HardClip) EXTERNAL (Content ID: 28) +DataSeries (TM/TM_TestMark) not present +DataSeries (TV/TV_TestMark) not present + +Tag Encodings: +Content ID/Tag (4279651/AM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 4279651) +Content ID/Tag (4346202/BQ:Z) BYTE_ARRAY_LEN (LenEncoding: Symbols: 102 BitLengths 0 ByteEncoding: Content ID: 4346202) +Content ID/Tag (5063770/MD:Z) BYTE_ARRAY_STOP (Content ID: 5063770 StopByte: 9) +Content ID/Tag (5067107/MQ:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5067107) +Content ID/Tag (5131619/NM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5131619) +Content ID/Tag (5194586/OC:Z) BYTE_ARRAY_STOP (Content ID: 5194586 StopByte: 9) +Content ID/Tag (5197929/OP:i) BYTE_ARRAY_LEN (LenEncoding: Symbols: 4 BitLengths 0 ByteEncoding: Content ID: 5197929) +Content ID/Tag (5198170/OQ:Z) BYTE_ARRAY_LEN (LenEncoding: Symbols: 102 BitLengths 0 ByteEncoding: Content ID: 5198170) +Content ID/Tag (5459299/SM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5459299) +Content ID/Tag (5779555/X0:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5779555) +Content ID/Tag (5779811/X1:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5779811) +Content ID/Tag (5779827/X1:s) BYTE_ARRAY_LEN (LenEncoding: Symbols: 2 BitLengths 0 ByteEncoding: Content ID: 5779827) +Content ID/Tag (5783898/XA:Z) BYTE_ARRAY_STOP (Content ID: 5783898 StopByte: 9) +Content ID/Tag (5784419/XC:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5784419) +Content ID/Tag (5785443/XG:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5785443) +Content ID/Tag (5786979/XM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5786979) +Content ID/Tag (5787491/XO:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5787491) +Content ID/Tag (5788737/XT:A) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5788737) + +******Slice #: 1 slice: sequenceId=SINGLE_REFERENCE: 0, 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raw size=9902, compressed size=768 +External Block (4346202): method=RANS, type=EXTERNAL, id=4346202, raw size=891888, compressed size=46972 +External Block (5063770): method=GZIP, type=EXTERNAL, id=5063770, raw size=56519, compressed size=13522 +External Block (5067107): method=RANS, type=EXTERNAL, id=5067107, raw size=9802, compressed size=599 +External Block (5131619): method=RANS, type=EXTERNAL, id=5131619, raw size=9902, compressed size=1592 +External Block (5194586): method=GZIP, type=EXTERNAL, id=5194586, raw size=104, compressed size=55 +External Block (5197929): method=GZIP, type=EXTERNAL, id=5197929, raw size=56, compressed size=44 +External Block (5198170): method=RANS, type=EXTERNAL, id=5198170, raw size=1020000, compressed size=215179 +External Block (5459299): method=RANS, type=EXTERNAL, id=5459299, raw size=9902, compressed size=623 +External Block (5779555): method=RANS, type=EXTERNAL, id=5779555, raw size=9654, compressed size=99 +External Block (5779811): method=RANS, 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(true) + +Data Series Encodings: + +DataSeries (BF/BF_BitFlags) EXTERNAL (Content ID: 0) +DataSeries (CF/CF_CompressionBitFlags) EXTERNAL (Content ID: 21) +DataSeries (RI/RI_RefId) EXTERNAL (Content ID: 25) +DataSeries (RL/RL_ReadLength) EXTERNAL (Content ID: 9) +DataSeries (AP/AP_AlignmentPositionOffset) EXTERNAL (Content ID: 1) +DataSeries (RG/RG_ReadGroup) EXTERNAL (Content ID: 10) +DataSeries (RN/RN_ReadName) BYTE_ARRAY_STOP (Content ID: 12 StopByte: 9) +DataSeries (NF/NF_RecordsToNextFragment) EXTERNAL (Content ID: 8) +DataSeries (MF/MF_MateBitFlags) EXTERNAL (Content ID: 19) +DataSeries (NS/NS_NextFragmentReferenceSequenceID) EXTERNAL (Content ID: 20) +DataSeries (NP/NP_NextFragmentAlignmentStart) EXTERNAL (Content ID: 13) +DataSeries (TS/TS_InsertSize) EXTERNAL (Content ID: 14) +DataSeries (TL/TL_TagIdList) EXTERNAL (Content ID: 24) +DataSeries (TC/TC_TagCount) not present +DataSeries (TN/TN_TagNameAndType) not present +DataSeries (MQ/MQ_MappingQualityScore) EXTERNAL (Content 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(QS/QS_QualityScore) EXTERNAL (Content ID: 4) +DataSeries (BS/BS_BaseSubstitutionCode) EXTERNAL (Content ID: 16) +DataSeries (IN/IN_Insertion) BYTE_ARRAY_STOP (Content ID: 17 StopByte: 9) +DataSeries (DL/DL_DeletionLength) EXTERNAL (Content ID: 5) +DataSeries (RS/RS_RefSkip) EXTERNAL (Content ID: 26) +DataSeries (SC/SC_SoftClip) BYTE_ARRAY_STOP (Content ID: 27 StopByte: 9) +DataSeries (PD/PD_padding) EXTERNAL (Content ID: 29) +DataSeries (HC/HC_HardClip) EXTERNAL (Content ID: 28) +DataSeries (TM/TM_TestMark) not present +DataSeries (TV/TV_TestMark) not present + +Tag Encodings: +Content ID/Tag (4279651/AM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 4279651) +Content ID/Tag (4346202/BQ:Z) BYTE_ARRAY_LEN (LenEncoding: Symbols: 102 BitLengths 0 ByteEncoding: Content ID: 4346202) +Content ID/Tag (5063770/MD:Z) BYTE_ARRAY_STOP (Content ID: 5063770 StopByte: 9) +Content ID/Tag (5067107/MQ:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 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(NS/NS_NextFragmentReferenceSequenceID) EXTERNAL (Content ID: 20) +DataSeries (NP/NP_NextFragmentAlignmentStart) EXTERNAL (Content ID: 13) +DataSeries (TS/TS_InsertSize) EXTERNAL (Content ID: 14) +DataSeries (TL/TL_TagIdList) EXTERNAL (Content ID: 24) +DataSeries (TC/TC_TagCount) not present +DataSeries (TN/TN_TagNameAndType) not present +DataSeries (MQ/MQ_MappingQualityScore) EXTERNAL (Content ID: 11) +DataSeries (FN/FN_NumberOfReadFeatures) EXTERNAL (Content ID: 15) +DataSeries (FP/FP_FeaturePosition) EXTERNAL (Content ID: 2) +DataSeries (FC/FC_FeatureCode) EXTERNAL (Content ID: 3) +DataSeries (BB/BB_Bases) not present +DataSeries (QQ/QQ_scores) not present +DataSeries (BA/BA_Base) EXTERNAL (Content ID: 6) +DataSeries (QS/QS_QualityScore) EXTERNAL (Content ID: 4) +DataSeries (BS/BS_BaseSubstitutionCode) EXTERNAL (Content ID: 16) +DataSeries (IN/IN_Insertion) BYTE_ARRAY_STOP (Content ID: 17 StopByte: 9) +DataSeries (DL/DL_DeletionLength) EXTERNAL (Content ID: 5) +DataSeries (RS/RS_RefSkip) EXTERNAL (Content ID: 26) +DataSeries (SC/SC_SoftClip) BYTE_ARRAY_STOP (Content ID: 27 StopByte: 9) +DataSeries (PD/PD_padding) EXTERNAL (Content ID: 29) +DataSeries (HC/HC_HardClip) EXTERNAL (Content ID: 28) +DataSeries (TM/TM_TestMark) not present +DataSeries (TV/TV_TestMark) not present + +Tag Encodings: +Content ID/Tag (4279651/AM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 4279651) +Content ID/Tag (4346202/BQ:Z) BYTE_ARRAY_LEN (LenEncoding: Symbols: 102 BitLengths 0 ByteEncoding: Content ID: 4346202) +Content ID/Tag (5063770/MD:Z) BYTE_ARRAY_STOP (Content ID: 5063770 StopByte: 9) +Content ID/Tag (5067107/MQ:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5067107) +Content ID/Tag (5131619/NM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5131619) +Content ID/Tag (5194586/OC:Z) BYTE_ARRAY_STOP (Content ID: 5194586 StopByte: 9) +Content ID/Tag (5197929/OP:i) BYTE_ARRAY_LEN (LenEncoding: Symbols: 4 BitLengths 0 ByteEncoding: Content ID: 5197929) +Content ID/Tag (5198170/OQ:Z) BYTE_ARRAY_LEN (LenEncoding: Symbols: 102 BitLengths 0 ByteEncoding: Content ID: 5198170) +Content ID/Tag (5459299/SM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5459299) +Content ID/Tag (5779523/X0:C) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5779523) +Content ID/Tag (5779555/X0:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5779555) +Content ID/Tag (5779571/X0:s) BYTE_ARRAY_LEN (LenEncoding: Symbols: 2 BitLengths 0 ByteEncoding: Content ID: 5779571) +Content ID/Tag (5779779/X1:C) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5779779) +Content ID/Tag (5779811/X1:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5779811) +Content ID/Tag (5779827/X1:s) BYTE_ARRAY_LEN (LenEncoding: Symbols: 2 BitLengths 0 ByteEncoding: Content ID: 5779827) +Content ID/Tag (5783898/XA:Z) BYTE_ARRAY_STOP (Content ID: 5783898 StopByte: 9) +Content ID/Tag (5784419/XC:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5784419) +Content ID/Tag (5785443/XG:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5785443) +Content ID/Tag (5786979/XM:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5786979) +Content ID/Tag (5787491/XO:c) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5787491) +Content ID/Tag (5788737/XT:A) BYTE_ARRAY_LEN (LenEncoding: Symbols: 1 BitLengths 0 ByteEncoding: Content ID: 5788737) + +******Slice #: 1 slice: sequenceId=SINGLE_REFERENCE: 0, start=10099914, span=11455 globalRecordCounter=90000, nRecords=10000, sliceHeaderOffset=2274, sizeOfBlocks=787838, landmark=0, mapped/unmapped/unplaced: 0/0/0, md5=e9da13dd481201a5ac434cd19f88dd8d +Header block method=RAW, type=MAPPED_SLICE, id=0, raw size=147, compressed size=147 +Core block method=RAW, type=CORE, id=0, raw size=0, compressed size=0 +External Block (BF): method=RANS, type=EXTERNAL, id=0, raw size=15640, compressed size=3675 +External Block (AP): method=RANS, type=EXTERNAL, id=1, raw size=10000, compressed size=2672 +External Block (FP): method=GZIP, type=EXTERNAL, id=2, raw size=6499, compressed size=4855 +External Block (FC): method=GZIP, type=EXTERNAL, id=3, raw size=6499, compressed size=1274 +External Block (QS): method=RANS, type=EXTERNAL, id=4, raw size=1010000, compressed size=360145 +External Block (DL): method=GZIP, type=EXTERNAL, id=5, raw size=261, compressed size=45 +External Block (BA): method=RANS, type=EXTERNAL, id=6, raw size=13229, compressed size=1827 +External Block (7): method=GZIP, type=EXTERNAL, id=7, raw size=0, compressed size=20 +External Block (NF): method=GZIP, type=EXTERNAL, id=8, raw size=130, compressed size=24 +External Block (RL): method=RANS, type=EXTERNAL, id=9, raw size=10000, compressed size=36 +External Block (RG): method=RANS, type=EXTERNAL, id=10, raw size=10000, compressed size=5489 +External Block (MQ): method=GZIP, type=EXTERNAL, id=11, raw size=9870, compressed size=1372 +External Block (RN): method=GZIP, type=EXTERNAL, id=12, raw size=327562, compressed size=64000 +External Block (NP): method=GZIP, type=EXTERNAL, id=13, raw size=38960, compressed size=19765 +External Block (TS): method=RANS, type=EXTERNAL, id=14, raw size=34091, compressed size=14812 +External Block (FN): method=GZIP, type=EXTERNAL, id=15, raw size=9870, compressed size=2647 +External Block (BS): method=GZIP, type=EXTERNAL, id=16, raw size=4064, compressed size=1026 +External Block (IN): method=GZIP, type=EXTERNAL, id=17, raw size=0, compressed size=20 +External Block (18): method=GZIP, type=EXTERNAL, id=18, raw size=0, compressed size=20 +External Block (MF): method=GZIP, type=EXTERNAL, id=19, raw size=9740, compressed size=1679 +External Block (NS): method=RANS, type=EXTERNAL, id=20, raw size=9740, compressed size=31 +External Block (CF): method=RANS, type=EXTERNAL, id=21, raw size=10000, compressed size=175 +External Block (TL): method=GZIP, type=EXTERNAL, id=24, raw size=10000, compressed size=2840 +External Block (RI): method=RANS, type=EXTERNAL, id=25, raw size=0, compressed size=0 +External Block (RS): method=GZIP, type=EXTERNAL, id=26, raw size=0, compressed size=20 +External Block (SC): method=GZIP, type=EXTERNAL, id=27, raw size=64204, compressed size=17182 +External Block (HC): method=GZIP, type=EXTERNAL, id=28, raw size=0, compressed size=20 +External Block (PD): method=GZIP, type=EXTERNAL, id=29, raw size=0, compressed size=20 +External Block (4279651): method=RANS, type=EXTERNAL, id=4279651, raw size=9870, compressed size=922 +External Block (4346202): method=RANS, type=EXTERNAL, id=4346202, raw size=876180, compressed size=43827 +External Block (5063770): method=GZIP, type=EXTERNAL, id=5063770, raw size=57022, compressed size=13398 +External Block (5067107): method=RANS, type=EXTERNAL, id=5067107, raw size=9740, compressed size=787 +External Block (5131619): method=RANS, type=EXTERNAL, id=5131619, raw size=9870, compressed size=1657 +External Block (5194586): method=GZIP, type=EXTERNAL, id=5194586, raw size=258, compressed size=111 +External Block (5197929): method=GZIP, type=EXTERNAL, id=5197929, raw size=56, compressed size=59 +External Block (5198170): method=RANS, type=EXTERNAL, id=5198170, raw size=1020000, compressed size=214776 +External Block (5459299): method=RANS, type=EXTERNAL, id=5459299, raw size=9870, compressed size=740 +External Block (5779523): method=GZIP, type=EXTERNAL, id=5779523, raw size=1, compressed size=21 +External Block (5779555): method=RANS, type=EXTERNAL, id=5779555, raw size=9635, compressed size=208 +External Block (5779571): method=GZIP, type=EXTERNAL, id=5779571, raw size=2, compressed size=22 +External Block (5779779): method=GZIP, type=EXTERNAL, id=5779779, raw size=10, compressed size=31 +External Block (5779811): method=RANS, type=EXTERNAL, id=5779811, raw size=9605, compressed size=303 +External Block (5779827): method=GZIP, type=EXTERNAL, id=5779827, raw size=22, compressed size=42 +External Block (5783898): method=GZIP, type=EXTERNAL, id=5783898, raw size=2462, compressed size=912 +External Block (5784419): method=RANS, type=EXTERNAL, id=5784419, raw size=2141, compressed size=1432 +External Block (5785443): method=GZIP, type=EXTERNAL, id=5785443, raw size=9870, compressed size=273 +External Block (5786979): method=RANS, type=EXTERNAL, id=5786979, raw size=9870, compressed size=1536 +External Block (5787491): method=RANS, type=EXTERNAL, id=5787491, raw size=9870, compressed size=218 +External Block (5788737): method=RANS, type=EXTERNAL, id=5788737, raw size=9870, compressed size=322 + +Total Record Count: 100000 + +Core Block(s) Total: 0 + +External Data Series Totals (external block resolution - all core data encodings accrue to the core block): + +BF_BitFlags: 36,752 +AP_AlignmentPositionOffset: 26,437 +FP_FeaturePosition: 43,967 +FC_FeatureCode: 11,303 +QS_QualityScore: 3,576,041 +DL_DeletionLength: 453 +BA_Base: 17,779 +NF_RecordsToNextFragment: 240 +RL_ReadLength: 360 +RG_ReadGroup: 54,781 +MQ_MappingQualityScore: 12,252 +RN_ReadName: 639,466 +NP_NextFragmentAlignmentStart: 196,860 +TS_InsertSize: 147,976 +FN_NumberOfReadFeatures: 24,189 +BS_BaseSubstitutionCode: 9,120 +IN_Insertion: 200 +MF_MateBitFlags: 16,746 +NS_NextFragmentReferenceSequenceID: 344 +CF_CompressionBitFlags: 1,602 +TL_TagIdList: 27,366 +RI_RefId: 0 +RS_RefSkip: 200 +SC_SoftClip: 163,713 +HC_HardClip: 200 +PD_padding: 200 + +Tag Series Distribution: + +7 (:): 200 +18 (:): 200 +4279651 (AM:c): 8,804 +4346202 (BQ:Z): 413,436 +5063770 (MD:Z): 118,072 +5067107 (MQ:c): 7,457 +5131619 (NM:c): 14,378 +5194586 (OC:Z): 1,211 +5197929 (OP:i): 551 +5198170 (OQ:Z): 2,074,873 +5459299 (SM:c): 6,909 +5779523 (X0:C): 119 +5779555 (X0:c): 1,384 +5779571 (X0:s): 160 +5779779 (X1:C): 213 +5779811 (X1:c): 1,934 +5779827 (X1:s): 323 +5783898 (XA:Z): 6,511 +5784419 (XC:c): 13,253 +5785443 (XG:c): 2,020 +5786979 (XM:c): 13,370 +5787491 (XO:c): 1,626 +5788737 (XT:A): 2,935 + diff --git a/src/test/resources/filediagnostics/cram_with_crai_index.cram.crai.txt b/src/test/resources/filediagnostics/cram_with_crai_index.cram.crai.txt new file mode 100644 index 00000000000..72ebe6c5679 --- /dev/null +++ b/src/test/resources/filediagnostics/cram_with_crai_index.cram.crai.txt @@ -0,0 +1,8 @@ + +SeqId AlignmentStart AlignmentSpan ContainerOffset SliceOffset SliceSize + +0 200 976 1069 245 598 +1 500 226 1929 242 534 +2 300 176 2722 240 498 +3 700 76 3477 238 453 + diff --git a/src/test/resources/filediagnostics/example_pfFail_reads.bam.bai.txt b/src/test/resources/filediagnostics/example_pfFail_reads.bam.bai.txt new file mode 100644 index 00000000000..ffb4e1cb1d0 --- /dev/null +++ b/src/test/resources/filediagnostics/example_pfFail_reads.bam.bai.txt @@ -0,0 +1,66 @@ +n_ref=8 +Reference 0 has n_bin= 2 + Ref 0 bin 4681 (bin=4681, level=5, first bin=4681, bin size=16,384 bin range=(0-16,384)) has n_chunk= 1 + Chunk: 0:345-0:567 start: 159 end: 237 + Ref 0 bin 37450 has n_chunk= 2 + Chunk: start: 159 end: 237 + Chunk: start: 1 end: 0 +Reference 0 has n_intv= 1 + Ref 0 ioffset for 0 is 0:345 +Reference 1 has n_bin= 2 + Ref 1 bin 4681 (bin=4681, level=5, first bin=4681, bin size=16,384 bin range=(0-16,384)) has n_chunk= 1 + Chunk: 0:567-0:790 start: 237 end: 316 + Ref 1 bin 37450 has n_chunk= 2 + Chunk: start: 237 end: 316 + Chunk: start: 1 end: 0 +Reference 1 has n_intv= 1 + Ref 1 ioffset for 0 is 0:567 +Reference 2 has n_bin= 2 + Ref 2 bin 4681 (bin=4681, level=5, first bin=4681, bin size=16,384 bin range=(0-16,384)) has n_chunk= 1 + Chunk: 0:790-0:1009 start: 316 end: 3f1 + Ref 2 bin 37450 has n_chunk= 2 + Chunk: start: 316 end: 3f1 + Chunk: start: 1 end: 0 +Reference 2 has n_intv= 1 + Ref 2 ioffset for 0 is 0:790 +Reference 3 has n_bin= 2 + Ref 3 bin 4681 (bin=4681, level=5, first bin=4681, bin size=16,384 bin range=(0-16,384)) has n_chunk= 1 + Chunk: 0:1009-0:1228 start: 3f1 end: 4cc + Ref 3 bin 37450 has n_chunk= 2 + Chunk: start: 3f1 end: 4cc + Chunk: start: 1 end: 0 +Reference 3 has n_intv= 1 + Ref 3 ioffset for 0 is 0:1009 +Reference 4 has n_bin= 2 + Ref 4 bin 4681 (bin=4681, level=5, first bin=4681, bin size=16,384 bin range=(0-16,384)) has n_chunk= 1 + Chunk: 0:1228-0:1445 start: 4cc end: 5a5 + Ref 4 bin 37450 has n_chunk= 2 + Chunk: start: 4cc end: 5a5 + Chunk: start: 1 end: 0 +Reference 4 has n_intv= 1 + Ref 4 ioffset for 0 is 0:1228 +Reference 5 has n_bin= 2 + Ref 5 bin 4681 (bin=4681, level=5, first bin=4681, bin size=16,384 bin range=(0-16,384)) has n_chunk= 1 + Chunk: 0:1445-0:1663 start: 5a5 end: 67f + Ref 5 bin 37450 has n_chunk= 2 + Chunk: start: 5a5 end: 67f + Chunk: start: 1 end: 0 +Reference 5 has n_intv= 1 + Ref 5 ioffset for 0 is 0:1445 +Reference 6 has n_bin= 2 + Ref 6 bin 4681 (bin=4681, level=5, first bin=4681, bin size=16,384 bin range=(0-16,384)) has n_chunk= 1 + Chunk: 0:1663-0:2319 start: 67f end: 90f + Ref 6 bin 37450 has n_chunk= 2 + Chunk: start: 67f end: 90f + Chunk: start: 3 end: 0 +Reference 6 has n_intv= 1 + Ref 6 ioffset for 0 is 0:1663 +Reference 7 has n_bin= 2 + Ref 7 bin 4681 (bin=4681, level=5, first bin=4681, bin size=16,384 bin range=(0-16,384)) has n_chunk= 1 + Chunk: 0:2319-0:2755 start: 90f end: ac3 + Ref 7 bin 37450 has n_chunk= 2 + Chunk: start: 90f end: ac3 + Chunk: start: 2 end: 0 +Reference 7 has n_intv= 1 + Ref 7 ioffset for 0 is 0:2319 +No Coordinate Count=8