Index (Hadoop-BAM 7.9.1 API)

A B C D E F G H I K L M N O P Q R S T U V W X Y

A

AnySAMInputFormat - Class in org.seqdoop.hadoop_bam: An InputFormat for SAM, BAM, and CRAM files.
AnySAMInputFormat() - Constructor for class org.seqdoop.hadoop_bam.AnySAMInputFormat: Creates a new input format, which will use the Configuration from the first public method called.
AnySAMInputFormat(Configuration) - Constructor for class org.seqdoop.hadoop_bam.AnySAMInputFormat: Creates a new input format, reading AnySAMInputFormat.TRUST_EXTS_PROPERTY from the given Configuration.
AnySAMInputFormat(Map<Path, SAMFormat>) - Constructor for class org.seqdoop.hadoop_bam.AnySAMInputFormat: Creates a new input format, trusting the given Map to define the file-to-format associations.
AnySAMOutputFormat<K> - Class in org.seqdoop.hadoop_bam: An abstract OutputFormat for SAM and BAM files.
AnySAMOutputFormat(Configuration) - Constructor for class org.seqdoop.hadoop_bam.AnySAMOutputFormat: Creates a new output format, reading AnySAMOutputFormat.OUTPUT_SAM_FORMAT_PROPERTY from the given Configuration.
AnySAMOutputFormat(SAMFormat) - Constructor for class org.seqdoop.hadoop_bam.AnySAMOutputFormat: Creates a new output format for the given SAM format.
asPath(URI) - Static method in class org.seqdoop.hadoop_bam.util.NIOFileUtil: Convert the given path URI to a Path object.
asPath(String) - Static method in class org.seqdoop.hadoop_bam.util.NIOFileUtil: Convert the given path string to a Path object.

B

BAM_MAGIC - Static variable in class org.seqdoop.hadoop_bam.util.SAMOutputPreparer
BAMInputFormat - Class in org.seqdoop.hadoop_bam: An InputFormat for BAM files.
BAMInputFormat() - Constructor for class org.seqdoop.hadoop_bam.BAMInputFormat
BAMOutputFormat<K> - Class in org.seqdoop.hadoop_bam: Currently this only locks down the value type of the OutputFormat: contains no functionality.
BAMOutputFormat() - Constructor for class org.seqdoop.hadoop_bam.BAMOutputFormat
BAMRecordReader - Class in org.seqdoop.hadoop_bam: The key is the bitwise OR of the reference sequence ID in the upper 32 bits and the 0-based leftmost coordinate in the lower.
BAMRecordReader() - Constructor for class org.seqdoop.hadoop_bam.BAMRecordReader
BAMRecordWriter<K> - Class in org.seqdoop.hadoop_bam: A base RecordWriter for BAM records.
BAMRecordWriter(Path, Path, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.BAMRecordWriter: A SAMFileHeader is read from the input Path.
BAMRecordWriter(Path, SAMFileHeader, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.BAMRecordWriter
BAMRecordWriter(OutputStream, SAMFileHeader, boolean) - Constructor for class org.seqdoop.hadoop_bam.BAMRecordWriter
BAMSplitGuesser - Class in org.seqdoop.hadoop_bam: A class for heuristically finding BAM record positions inside an area of a BAM file.
BAMSplitGuesser(SeekableStream, Configuration) - Constructor for class org.seqdoop.hadoop_bam.BAMSplitGuesser: The stream must point to a valid BAM file, because the header is read from it.
BAMSplitGuesser(SeekableStream, InputStream, Configuration) - Constructor for class org.seqdoop.hadoop_bam.BAMSplitGuesser
baseQualityFormat - Variable in class org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter
BCFRecordReader - Class in org.seqdoop.hadoop_bam: See VCFRecordReader for the meaning of the key.
BCFRecordReader() - Constructor for class org.seqdoop.hadoop_bam.BCFRecordReader
BCFRecordWriter<K> - Class in org.seqdoop.hadoop_bam: A base RecordWriter for compressed BCF.
BCFRecordWriter(Path, Path, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.BCFRecordWriter: A VCF header is read from the input Path, which should refer to a VCF or BCF file.
BCFRecordWriter(Path, VCFHeader, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.BCFRecordWriter
BCFRecordWriter(OutputStream, VCFHeader, boolean) - Constructor for class org.seqdoop.hadoop_bam.BCFRecordWriter
BCFSplitGuesser - Class in org.seqdoop.hadoop_bam: A class for heuristically finding BCF record positions inside an area of a BCF file.
BCFSplitGuesser(SeekableStream) - Constructor for class org.seqdoop.hadoop_bam.BCFSplitGuesser: The stream must point to a valid BCF file, because the header is read from it.
BCFSplitGuesser(SeekableStream, InputStream) - Constructor for class org.seqdoop.hadoop_bam.BCFSplitGuesser
BGZFBlockIndex - Class in org.seqdoop.hadoop_bam.util: An index into BGZF-compressed files, for BGZFSplitFileInputFormat.
BGZFBlockIndex() - Constructor for class org.seqdoop.hadoop_bam.util.BGZFBlockIndex
BGZFBlockIndex(File) - Constructor for class org.seqdoop.hadoop_bam.util.BGZFBlockIndex
BGZFBlockIndex(InputStream) - Constructor for class org.seqdoop.hadoop_bam.util.BGZFBlockIndex
BGZFBlockIndexer - Class in org.seqdoop.hadoop_bam.util: An indexing tool for BGZF-compressed files, making them palatable to BGZFSplitFileInputFormat.
BGZFBlockIndexer(int) - Constructor for class org.seqdoop.hadoop_bam.util.BGZFBlockIndexer
BGZFCodec - Class in org.seqdoop.hadoop_bam.util: A Hadoop CompressionCodec for the BGZF compression format, which reads and writes files with a .bgz suffix.
BGZFCodec() - Constructor for class org.seqdoop.hadoop_bam.util.BGZFCodec
BGZFEnhancedGzipCodec - Class in org.seqdoop.hadoop_bam.util: A Hadoop CompressionCodec for the BGZF compression format, which reads and writes files with a .gz suffix.
BGZFEnhancedGzipCodec() - Constructor for class org.seqdoop.hadoop_bam.util.BGZFEnhancedGzipCodec
BGZFSplitFileInputFormat<K,V> - Class in org.seqdoop.hadoop_bam.util: An InputFormat for BGZF-compressed files.
BGZFSplitFileInputFormat() - Constructor for class org.seqdoop.hadoop_bam.util.BGZFSplitFileInputFormat
BGZFSplitGuesser - Class in org.seqdoop.hadoop_bam.util
BGZFSplitGuesser(InputStream) - Constructor for class org.seqdoop.hadoop_bam.util.BGZFSplitGuesser
BGZFSplitGuesser(FSDataInputStream) - Constructor for class org.seqdoop.hadoop_bam.util.BGZFSplitGuesser
BOUNDED_TRAVERSAL_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.BAMInputFormat: If set to true, only include reads that overlap the given intervals (if specified), and unplaced unmapped reads (if specified).
buffer - Variable in class org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter

C

clear() - Method in class org.seqdoop.hadoop_bam.ReferenceFragment
clear() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
close() - Method in class org.seqdoop.hadoop_bam.BAMRecordReader
close(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.BAMRecordWriter
close() - Method in class org.seqdoop.hadoop_bam.BCFRecordReader
close(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.BCFRecordWriter
close() - Method in class org.seqdoop.hadoop_bam.CRAMRecordReader
close(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.CRAMRecordWriter
close() - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader: Close this RecordReader to future operations.
close() - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader: Close this RecordReader to future operations.
close(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter
close() - Method in class org.seqdoop.hadoop_bam.LineReader: Close the underlying stream.
close() - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader: Close this RecordReader to future operations.
close(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.QseqOutputFormat.QseqRecordWriter
close() - Method in class org.seqdoop.hadoop_bam.SAMRecordReader
close(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.SAMRecordWriter
close() - Method in class org.seqdoop.hadoop_bam.util.SeekableArrayStream: Deprecated.
close() - Method in class org.seqdoop.hadoop_bam.util.WrapSeekable
close() - Method in class org.seqdoop.hadoop_bam.VCFRecordReader
close(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.VCFRecordWriter
CONF_BASE_QUALITY_ENCODING - Static variable in class org.seqdoop.hadoop_bam.FastqInputFormat
CONF_BASE_QUALITY_ENCODING - Static variable in class org.seqdoop.hadoop_bam.FastqOutputFormat
CONF_BASE_QUALITY_ENCODING - Static variable in class org.seqdoop.hadoop_bam.QseqInputFormat
CONF_BASE_QUALITY_ENCODING - Static variable in class org.seqdoop.hadoop_bam.QseqOutputFormat
CONF_BASE_QUALITY_ENCODING_DEFAULT - Static variable in class org.seqdoop.hadoop_bam.FastqInputFormat
CONF_BASE_QUALITY_ENCODING_DEFAULT - Static variable in class org.seqdoop.hadoop_bam.FastqOutputFormat
CONF_BASE_QUALITY_ENCODING_DEFAULT - Static variable in class org.seqdoop.hadoop_bam.QseqInputFormat
CONF_BASE_QUALITY_ENCODING_DEFAULT - Static variable in class org.seqdoop.hadoop_bam.QseqOutputFormat
CONF_FILTER_FAILED_QC - Static variable in class org.seqdoop.hadoop_bam.FastqInputFormat
CONF_FILTER_FAILED_QC - Static variable in class org.seqdoop.hadoop_bam.QseqInputFormat
CONF_INPUT_BASE_QUALITY_ENCODING - Static variable in class org.seqdoop.hadoop_bam.FormatConstants
CONF_INPUT_FILTER_FAILED_QC - Static variable in class org.seqdoop.hadoop_bam.FormatConstants
ConfHelper - Class in org.seqdoop.hadoop_bam.util
ConfHelper() - Constructor for class org.seqdoop.hadoop_bam.util.ConfHelper
controlNumber - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
ControlNumber_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment
convertQuality(Text, FormatConstants.BaseQualityEncoding, FormatConstants.BaseQualityEncoding) - Static method in class org.seqdoop.hadoop_bam.SequencedFragment: Convert quality scores in-place.
CRAMInputFormat - Class in org.seqdoop.hadoop_bam
CRAMInputFormat() - Constructor for class org.seqdoop.hadoop_bam.CRAMInputFormat
CRAMOutputFormat<K> - Class in org.seqdoop.hadoop_bam: Currently this only locks down the value type of the OutputFormat: contains no functionality.
CRAMOutputFormat() - Constructor for class org.seqdoop.hadoop_bam.CRAMOutputFormat
CRAMRecordReader - Class in org.seqdoop.hadoop_bam
CRAMRecordReader() - Constructor for class org.seqdoop.hadoop_bam.CRAMRecordReader
CRAMRecordWriter<K> - Class in org.seqdoop.hadoop_bam: A base RecordWriter for CRAM records.
CRAMRecordWriter(Path, Path, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.CRAMRecordWriter: A SAMFileHeader is read from the input Path.
CRAMRecordWriter(Path, SAMFileHeader, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.CRAMRecordWriter
createBAMRecord(SAMFileHeader, int, int, short, short, int, int, int, int, int, int, int, byte[]) - Method in class org.seqdoop.hadoop_bam.LazyBAMRecordFactory
createCompressor() - Method in class org.seqdoop.hadoop_bam.util.BGZFCodec
createInputStream(InputStream, Decompressor, long, long, SplittableCompressionCodec.READ_MODE) - Method in class org.seqdoop.hadoop_bam.util.BGZFCodec
createInputStream(InputStream, Decompressor, long, long, SplittableCompressionCodec.READ_MODE) - Method in class org.seqdoop.hadoop_bam.util.BGZFEnhancedGzipCodec
createKey() - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader: Create an object of the appropriate type to be used as a key.
createKey() - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader: Create an object of the appropriate type to be used as a key.
createKey() - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader: Create an object of the appropriate type to be used as a key.
createOutputStream(OutputStream) - Method in class org.seqdoop.hadoop_bam.util.BGZFCodec
createOutputStream(OutputStream, Compressor) - Method in class org.seqdoop.hadoop_bam.util.BGZFCodec
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.AnySAMInputFormat: Returns a BAMRecordReader or SAMRecordReader as appropriate, initialized with the given parameters.
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.BAMInputFormat: Returns a BAMRecordReader initialized with the parameters.
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.CRAMInputFormat
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.FastaInputFormat
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.FastqInputFormat
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.QseqInputFormat
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.SAMInputFormat: Returns a SAMRecordReader initialized with the parameters.
createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.VCFInputFormat: Returns a BCFRecordReader or VCFRecordReader as appropriate, initialized with the given parameters.
createSAMRecord(SAMFileHeader) - Method in class org.seqdoop.hadoop_bam.LazyBAMRecordFactory
createValue() - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader: Create an object of the appropriate type to be used as a value.
createValue() - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader: Create an object of the appropriate type to be used as a value.
createValue() - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader: Create an object of the appropriate type to be used as a value.
createVariantContextWriter(Configuration, OutputStream) - Method in class org.seqdoop.hadoop_bam.VCFRecordWriter

D

DataInputWrapper - Class in org.seqdoop.hadoop_bam.util
DataInputWrapper(DataInput) - Constructor for class org.seqdoop.hadoop_bam.util.DataInputWrapper
DataOutputWrapper - Class in org.seqdoop.hadoop_bam.util
DataOutputWrapper(DataOutput) - Constructor for class org.seqdoop.hadoop_bam.util.DataOutputWrapper
decoder - Static variable in class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.HeaderDataCache
DEFAULT_EXTENSION - Static variable in class org.seqdoop.hadoop_bam.util.BGZFCodec
DEFAULT_GRANULARITY - Static variable in class org.seqdoop.hadoop_bam.SplittingBAMIndexer

E

ENABLE_BAI_SPLIT_CALCULATOR - Static variable in class org.seqdoop.hadoop_bam.BAMInputFormat: If set to true, enables the use of BAM indices to calculate splits.
eof() - Method in class org.seqdoop.hadoop_bam.util.SeekableArrayStream: Deprecated.
eof() - Method in class org.seqdoop.hadoop_bam.util.WrapSeekable
equals(Object) - Method in class org.seqdoop.hadoop_bam.ReferenceFragment
equals(Object) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
equals(Object) - Method in class org.seqdoop.hadoop_bam.SplittingBAMIndex

F

FastaInputFormat - Class in org.seqdoop.hadoop_bam: Reads the FASTA reference sequence format.
FastaInputFormat() - Constructor for class org.seqdoop.hadoop_bam.FastaInputFormat
FastaInputFormat.FastaRecordReader - Class in org.seqdoop.hadoop_bam
FastaRecordReader(Configuration, FileSplit) - Constructor for class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader
FastqInputFormat - Class in org.seqdoop.hadoop_bam
FastqInputFormat() - Constructor for class org.seqdoop.hadoop_bam.FastqInputFormat
FastqInputFormat.FastqRecordReader - Class in org.seqdoop.hadoop_bam
FastqOutputFormat - Class in org.seqdoop.hadoop_bam: Output format for the fastq format.
FastqOutputFormat() - Constructor for class org.seqdoop.hadoop_bam.FastqOutputFormat
FastqOutputFormat.FastqRecordWriter - Class in org.seqdoop.hadoop_bam
FastqRecordReader(Configuration, FileSplit) - Constructor for class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader
FastqRecordWriter(Configuration, OutputStream) - Constructor for class org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter
FileVirtualSplit - Class in org.seqdoop.hadoop_bam: Like a FileSplit, but uses BGZF virtual offsets to fit with BlockCompressedInputStream.
FileVirtualSplit() - Constructor for class org.seqdoop.hadoop_bam.FileVirtualSplit
FileVirtualSplit(Path, long, long, String[]) - Constructor for class org.seqdoop.hadoop_bam.FileVirtualSplit
FileVirtualSplit(Path, long, long, String[], long[]) - Constructor for class org.seqdoop.hadoop_bam.FileVirtualSplit
filterPassed - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
FilterPassed_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment
finish(long) - Method in class org.seqdoop.hadoop_bam.SplittingBAMIndexer: Complete the index by writing the input BAM file size to the index, and closing the output stream.
flowcellId - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
FlowcellId_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment
fms() - Method in class org.seqdoop.hadoop_bam.util.Timer: Deprecated.
format - Variable in class org.seqdoop.hadoop_bam.AnySAMOutputFormat
format - Variable in class org.seqdoop.hadoop_bam.VCFOutputFormat
FormatConstants - Class in org.seqdoop.hadoop_bam
FormatConstants.BaseQualityEncoding - Enum in org.seqdoop.hadoop_bam: Encodings for base quality formats.
FormatException - Exception in org.seqdoop.hadoop_bam
FormatException(String) - Constructor for exception org.seqdoop.hadoop_bam.FormatException
fst - Variable in class org.seqdoop.hadoop_bam.util.Pair: Deprecated.

G

get() - Method in class org.seqdoop.hadoop_bam.SAMRecordWritable
get() - Method in class org.seqdoop.hadoop_bam.VariantContextWritable
getBuilders() - Method in class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.HeaderDataCache
getCodec() - Method in class org.seqdoop.hadoop_bam.LazyVCFGenotypesContext.HeaderDataCache
getCompressorType() - Method in class org.seqdoop.hadoop_bam.util.BGZFCodec
getControlNumber() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getCurrentKey() - Method in class org.seqdoop.hadoop_bam.BAMRecordReader
getCurrentKey() - Method in class org.seqdoop.hadoop_bam.BCFRecordReader
getCurrentKey() - Method in class org.seqdoop.hadoop_bam.CRAMRecordReader
getCurrentKey() - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader: Added to use mapreduce API.
getCurrentKey() - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader: Added to use mapreduce API.
getCurrentKey() - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader: Added to use mapreduce API.
getCurrentKey() - Method in class org.seqdoop.hadoop_bam.SAMRecordReader
getCurrentKey() - Method in class org.seqdoop.hadoop_bam.VCFRecordReader
getCurrentValue() - Method in class org.seqdoop.hadoop_bam.BAMRecordReader
getCurrentValue() - Method in class org.seqdoop.hadoop_bam.BCFRecordReader
getCurrentValue() - Method in class org.seqdoop.hadoop_bam.CRAMRecordReader
getCurrentValue() - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader: Added to use mapreduce API.
getCurrentValue() - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader: Added to use mapreduce API.
getCurrentValue() - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader: Added to use mapreduce API.
getCurrentValue() - Method in class org.seqdoop.hadoop_bam.SAMRecordReader
getCurrentValue() - Method in class org.seqdoop.hadoop_bam.VCFRecordReader
getDefaultExtension() - Method in class org.seqdoop.hadoop_bam.util.BGZFCodec
getEndVirtualOffset() - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit: Exclusive.
getFieldDict() - Method in class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.HeaderDataCache
getFilterPassed() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getFlowcellId() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getFormat(Path) - Method in class org.seqdoop.hadoop_bam.AnySAMInputFormat: Returns the SAMFormat corresponding to the given path.
getFormat(Path) - Method in class org.seqdoop.hadoop_bam.VCFInputFormat: Returns the VCFFormat corresponding to the given path.
getGenoFieldDecoders() - Method in class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.HeaderDataCache
getHeader() - Method in class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat
getHeader() - Method in class org.seqdoop.hadoop_bam.VariantContextWithHeader
getIndexSequence() - Method in class org.seqdoop.hadoop_bam.ReferenceFragment
getIndexSequence() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getInstrument() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getIntervalFilePointers() - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit
getKey(SAMRecord) - Static method in class org.seqdoop.hadoop_bam.BAMRecordReader: Note: this is the only getKey function that handles unmapped reads specially!
getKey(int, int) - Static method in class org.seqdoop.hadoop_bam.BAMRecordReader
getKey0(int, int) - Static method in class org.seqdoop.hadoop_bam.BAMRecordReader
getLane() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getLength() - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit: Inexact due to the nature of virtual offsets.
getLinearIndex(int) - Method in class htsjdk.samtools.LinearBAMIndex
getLocations() - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit
getParser() - Method in class org.seqdoop.hadoop_bam.LazyParsingGenotypesContext
getPath() - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit
getPos() - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader: Returns the current position in the input.
getPos() - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader: Returns the current position in the input.
getPos() - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader: Returns the current position in the input.
getPosition() - Method in class org.seqdoop.hadoop_bam.ReferenceFragment
getProgress() - Method in class org.seqdoop.hadoop_bam.BAMRecordReader: Unless the end has been reached, this only takes file position into account, not the position within the block.
getProgress() - Method in class org.seqdoop.hadoop_bam.BCFRecordReader: For compressed BCF, unless the end has been reached, this is quite inaccurate.
getProgress() - Method in class org.seqdoop.hadoop_bam.CRAMRecordReader
getProgress() - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader: How much of the input has the RecordReader consumed i.e.
getProgress() - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader: How much of the input has the RecordReader consumed i.e.
getProgress() - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader: How much of the input has the RecordReader consumed i.e.
getProgress() - Method in class org.seqdoop.hadoop_bam.SAMRecordReader
getProgress() - Method in class org.seqdoop.hadoop_bam.VCFRecordReader
getQuality() - Method in class org.seqdoop.hadoop_bam.SequencedFragment: Get quality Text object.
getRead() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getRecordWriter(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.FastqOutputFormat
getRecordWriter(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat: setSAMHeader or readSAMHeaderFrom must have been called first.
getRecordWriter(TaskAttemptContext, Path) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat
getRecordWriter(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat: setSAMHeader or readSAMHeaderFrom must have been called first.
getRecordWriter(TaskAttemptContext, Path) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat
getRecordWriter(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat: setSAMHeader or readSAMHeaderFrom must have been called first.
getRecordWriter(TaskAttemptContext, Path) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat
getRecordWriter(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat: setHeader or readHeaderFrom must have been called first.
getRecordWriter(TaskAttemptContext, Path) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat
getRecordWriter(TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.QseqOutputFormat
getReferenceSource(Configuration) - Static method in class org.seqdoop.hadoop_bam.util.SAMHeaderReader
getRunNumber() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getSAMHeader() - Method in class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat
getSAMHeader() - Method in class org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat
getSAMHeader() - Method in class org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat
getSampleNamesInOrder() - Method in class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.HeaderDataCache
getSampleNameToOffset() - Method in class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.HeaderDataCache
getSequence() - Method in class org.seqdoop.hadoop_bam.ReferenceFragment: Get sequence Text object.
getSequence() - Method in class org.seqdoop.hadoop_bam.SequencedFragment: Get sequence Text object.
GetSortedBAMHeader - Class in org.seqdoop.hadoop_bam.util
GetSortedBAMHeader() - Constructor for class org.seqdoop.hadoop_bam.util.GetSortedBAMHeader
getSource() - Method in class org.seqdoop.hadoop_bam.util.SeekableArrayStream: Deprecated.
getSource() - Method in class org.seqdoop.hadoop_bam.util.WrapSeekable
getSplits(JobContext) - Method in class org.seqdoop.hadoop_bam.AnySAMInputFormat: Defers to BAMInputFormat or CRAMInputFormat as appropriate for each individual path.
getSplits(JobContext) - Method in class org.seqdoop.hadoop_bam.BAMInputFormat: The splits returned are FileVirtualSplits.
getSplits(List<InputSplit>, Configuration) - Method in class org.seqdoop.hadoop_bam.BAMInputFormat
getSplits(JobContext) - Method in class org.seqdoop.hadoop_bam.CRAMInputFormat
getSplits(List<InputSplit>, Configuration) - Method in class org.seqdoop.hadoop_bam.CRAMInputFormat
getSplits(JobContext) - Method in class org.seqdoop.hadoop_bam.FastaInputFormat
getSplits(JobContext) - Method in class org.seqdoop.hadoop_bam.util.BGZFSplitFileInputFormat: The splits returned are FileSplits.
getSplits(JobContext) - Method in class org.seqdoop.hadoop_bam.VCFInputFormat: Defers to BCFSplitGuesser as appropriate for each individual path.
getStartVirtualOffset() - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit: Inclusive.
getTile() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getValidationStringency(Configuration) - Static method in class org.seqdoop.hadoop_bam.util.SAMHeaderReader
getVirtualOffsets() - Method in class org.seqdoop.hadoop_bam.SplittingBAMIndex
getWriteHeader() - Method in class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat: Deprecated.
getWriteHeader() - Method in class org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat: Whether the header will be written or not.
getWriteHeader() - Method in class org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat: Whether the header will be written or not.
getXpos() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getYpos() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
guessNextBAMRecordStart(long, long) - Method in class org.seqdoop.hadoop_bam.BAMSplitGuesser: Finds a virtual BAM record position in the physical position range [beg,end).
guessNextBCFRecordStart(long, long) - Method in class org.seqdoop.hadoop_bam.BCFSplitGuesser: Finds a (virtual in the case of BGZF) BCF record position in the physical position range [beg,end).
guessNextBGZFBlockStart(long, long) - Method in class org.seqdoop.hadoop_bam.util.BGZFSplitGuesser

H

hashCode() - Method in class org.seqdoop.hadoop_bam.ReferenceFragment
hashCode() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
hashCode() - Method in class org.seqdoop.hadoop_bam.SplittingBAMIndex
header - Variable in class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat
header - Variable in class org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat
header - Variable in class org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat
header - Variable in class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat
HeaderDataCache() - Constructor for class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.HeaderDataCache
HeaderDataCache() - Constructor for class org.seqdoop.hadoop_bam.LazyVCFGenotypesContext.HeaderDataCache
htsjdk.samtools - package htsjdk.samtools

I

ILLUMINA_MAX - Static variable in class org.seqdoop.hadoop_bam.FormatConstants: Maximum encodable quality score for Illumina Phred+64 encoded base qualities.
ILLUMINA_OFFSET - Static variable in class org.seqdoop.hadoop_bam.FormatConstants: Offset by which Illumina-style ASCII-encoded quality scores are shifted.
index(InputStream, OutputStream, long, int) - Static method in class org.seqdoop.hadoop_bam.SplittingBAMIndexer: Perform indexing on the given BAM file, at the granularity level specified.
indexSequence - Variable in class org.seqdoop.hadoop_bam.ReferenceFragment
indexSequence - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
IndexSequence_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment
inferFromData(InputStream) - Static method in enum org.seqdoop.hadoop_bam.SAMFormat
inferFromData(InputStream) - Static method in enum org.seqdoop.hadoop_bam.VCFFormat: Infers the VCF format by looking at the first few bytes of the input.
inferFromFilePath(Path) - Static method in enum org.seqdoop.hadoop_bam.SAMFormat: Infers the SAM format by looking at the filename of the given path.
inferFromFilePath(String) - Static method in enum org.seqdoop.hadoop_bam.SAMFormat: Infers the SAM format by looking at the extension of the given file name.
inferFromFilePath(Path) - Static method in enum org.seqdoop.hadoop_bam.VCFFormat: Infers the VCF format by looking at the filename of the given path.
inferFromFilePath(String) - Static method in enum org.seqdoop.hadoop_bam.VCFFormat: Infers the VCF format by looking at the extension of the given file name.
initialize(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.BAMRecordReader
initialize(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.BCFRecordReader
initialize(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.CRAMRecordReader
initialize(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader: Added to use mapreduce API.
initialize(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader: Added to use mapreduce API.
initialize(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader: Added to use mapreduce API.
initialize(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.SAMRecordReader
initialize(InputSplit, TaskAttemptContext) - Method in class org.seqdoop.hadoop_bam.VCFRecordReader
instrument - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
Instrument_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment
INTERVALS_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.BAMInputFormat: Filter by region, like -L in SAMtools.
INTERVALS_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.VCFInputFormat: Filter by region, like -L in SAMtools.
isBGZF() - Method in class org.seqdoop.hadoop_bam.BCFSplitGuesser
isGzip(InputStream) - Static method in enum org.seqdoop.hadoop_bam.VCFFormat
isSplitable(JobContext, Path) - Method in class org.seqdoop.hadoop_bam.AnySAMInputFormat: Defers to BAMInputFormat, CRAMInputFormat, or SAMInputFormat as appropriate for the given path.
isSplitable(JobContext, Path) - Method in class org.seqdoop.hadoop_bam.BAMInputFormat
isSplitable(JobContext, Path) - Method in class org.seqdoop.hadoop_bam.CRAMInputFormat
isSplitable(JobContext, Path) - Method in class org.seqdoop.hadoop_bam.FastaInputFormat
isSplitable(JobContext, Path) - Method in class org.seqdoop.hadoop_bam.FastqInputFormat
isSplitable(JobContext, Path) - Method in class org.seqdoop.hadoop_bam.QseqInputFormat
isSplitable(JobContext, Path) - Method in class org.seqdoop.hadoop_bam.SAMInputFormat
isSplitable(JobContext, Path) - Method in class org.seqdoop.hadoop_bam.util.BGZFSplitFileInputFormat
isSplitable(JobContext, Path) - Method in class org.seqdoop.hadoop_bam.VCFInputFormat

K

KeyIgnoringAnySAMOutputFormat<K> - Class in org.seqdoop.hadoop_bam: Writes only the SAM records, not the key.
KeyIgnoringAnySAMOutputFormat(SAMFormat) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat
KeyIgnoringAnySAMOutputFormat(Configuration) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat
KeyIgnoringAnySAMOutputFormat(Configuration, Path) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat
KeyIgnoringBAMOutputFormat<K> - Class in org.seqdoop.hadoop_bam: Writes only the BAM records, not the key.
KeyIgnoringBAMOutputFormat() - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat
KeyIgnoringBAMRecordWriter<K> - Class in org.seqdoop.hadoop_bam: A convenience class that you can use as a RecordWriter for BAM files.
KeyIgnoringBAMRecordWriter(Path, Path, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringBAMRecordWriter
KeyIgnoringBAMRecordWriter(Path, SAMFileHeader, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringBAMRecordWriter
KeyIgnoringBAMRecordWriter(OutputStream, SAMFileHeader, boolean) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringBAMRecordWriter
KeyIgnoringBCFRecordWriter<K> - Class in org.seqdoop.hadoop_bam: A convenience class that you can use as a RecordWriter for BCF files.
KeyIgnoringBCFRecordWriter(Path, Path, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter
KeyIgnoringBCFRecordWriter(Path, VCFHeader, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter
KeyIgnoringBCFRecordWriter(OutputStream, VCFHeader, boolean) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter
KeyIgnoringCRAMOutputFormat<K> - Class in org.seqdoop.hadoop_bam: Writes only the BAM records, not the key.
KeyIgnoringCRAMOutputFormat() - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat
KeyIgnoringCRAMRecordWriter<K> - Class in org.seqdoop.hadoop_bam: A convenience class that you can use as a RecordWriter for CRAM files.
KeyIgnoringCRAMRecordWriter(Path, Path, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringCRAMRecordWriter
KeyIgnoringCRAMRecordWriter(Path, SAMFileHeader, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringCRAMRecordWriter
KeyIgnoringSAMRecordWriter<K> - Class in org.seqdoop.hadoop_bam: A convenience class that you can use as a RecordWriter for SAM files.
KeyIgnoringSAMRecordWriter(Path, Path, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringSAMRecordWriter
KeyIgnoringSAMRecordWriter(Path, SAMFileHeader, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringSAMRecordWriter
KeyIgnoringSAMRecordWriter(OutputStream, SAMFileHeader, boolean) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringSAMRecordWriter
KeyIgnoringVCFOutputFormat<K> - Class in org.seqdoop.hadoop_bam: Writes only the VCF records, not the key.
KeyIgnoringVCFOutputFormat(VCFFormat) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat
KeyIgnoringVCFOutputFormat(Configuration) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat
KeyIgnoringVCFOutputFormat(Configuration, Path) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat
KeyIgnoringVCFRecordWriter<K> - Class in org.seqdoop.hadoop_bam: A convenience class that you can use as a RecordWriter for VCF files.
KeyIgnoringVCFRecordWriter(Path, Path, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringVCFRecordWriter
KeyIgnoringVCFRecordWriter(Path, VCFHeader, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringVCFRecordWriter
KeyIgnoringVCFRecordWriter(OutputStream, VCFHeader, boolean) - Constructor for class org.seqdoop.hadoop_bam.KeyIgnoringVCFRecordWriter

L

lane - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
Lane_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment
LazyBAMRecordFactory - Class in org.seqdoop.hadoop_bam: A factory for the kind of lazy BAMRecord used internally.
LazyBAMRecordFactory() - Constructor for class org.seqdoop.hadoop_bam.LazyBAMRecordFactory
LazyBCFGenotypesContext - Class in org.seqdoop.hadoop_bam
LazyBCFGenotypesContext(List<Allele>, int, byte[], int) - Constructor for class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext: Takes ownership of the given byte[]: don't modify its contents.
LazyBCFGenotypesContext.HeaderDataCache - Class in org.seqdoop.hadoop_bam
LazyBCFGenotypesContext.Parser - Class in org.seqdoop.hadoop_bam
LazyParsingGenotypesContext - Class in org.seqdoop.hadoop_bam: You need to call getParser().setHeader() here before trying to decode() a GenotypesContext in any VariantContext that came about via VariantContextWritable.readFields().
LazyParsingGenotypesContext(LazyParsingGenotypesContext.Parser, byte[], int) - Constructor for class org.seqdoop.hadoop_bam.LazyParsingGenotypesContext
LazyParsingGenotypesContext.HeaderDataCache - Interface in org.seqdoop.hadoop_bam
LazyParsingGenotypesContext.Parser - Class in org.seqdoop.hadoop_bam
LazyVCFGenotypesContext - Class in org.seqdoop.hadoop_bam
LazyVCFGenotypesContext(List<Allele>, String, int, byte[], int) - Constructor for class org.seqdoop.hadoop_bam.LazyVCFGenotypesContext: Takes ownership of the given byte[]: don't modify its contents.
LazyVCFGenotypesContext.HeaderDataCache - Class in org.seqdoop.hadoop_bam
LazyVCFGenotypesContext.Parser - Class in org.seqdoop.hadoop_bam
length() - Method in class org.seqdoop.hadoop_bam.util.SeekableArrayStream: Deprecated.
length() - Method in class org.seqdoop.hadoop_bam.util.WrapSeekable
LinearBAMIndex - Class in htsjdk.samtools: The htsjdk APIs for accessing the linear BAM index are private...
LinearBAMIndex(SeekableStream, SAMSequenceDictionary) - Constructor for class htsjdk.samtools.LinearBAMIndex
LineReader - Class in org.seqdoop.hadoop_bam: A class that provides a line reader from an input stream.
LineReader(InputStream) - Constructor for class org.seqdoop.hadoop_bam.LineReader: Create a line reader that reads from the given stream using the default buffer-size (64k).
LineReader(InputStream, int) - Constructor for class org.seqdoop.hadoop_bam.LineReader: Create a line reader that reads from the given stream using the given buffer-size.
LineReader(InputStream, Configuration) - Constructor for class org.seqdoop.hadoop_bam.LineReader: Create a line reader that reads from the given stream using the io.file.buffer.size specified in the given Configuration.
loadBuffer() - Method in class org.seqdoop.hadoop_bam.LineReader
lowLevelFastqRead(Text, SequencedFragment) - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader

M

main(String[]) - Static method in class org.seqdoop.hadoop_bam.BAMSplitGuesser
main(String[]) - Static method in class org.seqdoop.hadoop_bam.BCFSplitGuesser
main(String[]) - Static method in class org.seqdoop.hadoop_bam.SplittingBAMIndex: Writes some statistics about each splitting BAM index file given as an argument.
main(String[]) - Static method in class org.seqdoop.hadoop_bam.SplittingBAMIndexer
main(String[]) - Static method in class org.seqdoop.hadoop_bam.util.BGZFBlockIndex: Writes some statistics about each BGZF block index file given as an argument.
main(String[]) - Static method in class org.seqdoop.hadoop_bam.util.BGZFBlockIndexer
main(String[]) - Static method in class org.seqdoop.hadoop_bam.util.GetSortedBAMHeader
makeId(SequencedFragment) - Method in class org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter
makePositionMessage(long) - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader
makePositionMessage() - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader
makePositionMessage() - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader
makePositionMessage(long) - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader
makePositionMessage() - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader
MAX_LINE_LENGTH - Static variable in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader
MAX_LINE_LENGTH - Static variable in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader
mergeParts(String, String, SAMFormat, SAMFileHeader) - Static method in class org.seqdoop.hadoop_bam.util.SAMFileMerger: Merge part file shards produced by KeyIgnoringAnySAMOutputFormat into a single file with the given header.
mergeParts(String, String, VCFHeader) - Static method in class org.seqdoop.hadoop_bam.util.VCFFileMerger: Merge part file shards produced by KeyIgnoringVCFOutputFormat into a single file with the given header.
MurmurHash3 - Class in org.seqdoop.hadoop_bam.util: This class implements a hash function giving the first 64 bits of the MurmurHash3_x64_128 hash.
MurmurHash3() - Constructor for class org.seqdoop.hadoop_bam.util.MurmurHash3
murmurhash3(byte[], int) - Static method in class org.seqdoop.hadoop_bam.util.MurmurHash3
murmurhash3(CharSequence, int) - Static method in class org.seqdoop.hadoop_bam.util.MurmurHash3: This version hashes the characters directly.

N

next(Text, ReferenceFragment) - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader: Reads the next key/value pair from the input for processing.
next(Text, SequencedFragment) - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader: Reads the next key/value pair from the input for processing.
next(Text, SequencedFragment) - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader: Reads the next key/value pair from the input for processing.
nextAlignment(long) - Method in class org.seqdoop.hadoop_bam.SplittingBAMIndex
nextBlock(long) - Method in class org.seqdoop.hadoop_bam.util.BGZFBlockIndex
nextKeyValue() - Method in class org.seqdoop.hadoop_bam.BAMRecordReader
nextKeyValue() - Method in class org.seqdoop.hadoop_bam.BCFRecordReader
nextKeyValue() - Method in class org.seqdoop.hadoop_bam.CRAMRecordReader
nextKeyValue() - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader: Added to use mapreduce API.
nextKeyValue() - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader: Added to use mapreduce API.
nextKeyValue() - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader: Added to use mapreduce API.
nextKeyValue() - Method in class org.seqdoop.hadoop_bam.SAMRecordReader
nextKeyValue() - Method in class org.seqdoop.hadoop_bam.VCFRecordReader
NIOFileUtil - Class in org.seqdoop.hadoop_bam.util

O

openPath(FileSystem, Path) - Static method in class org.seqdoop.hadoop_bam.util.WrapSeekable: A helper for the common use case.
openPath(Configuration, Path) - Static method in class org.seqdoop.hadoop_bam.util.WrapSeekable
org.seqdoop.hadoop_bam - package org.seqdoop.hadoop_bam
org.seqdoop.hadoop_bam.util - package org.seqdoop.hadoop_bam.util
out - Variable in class org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter
out - Variable in class org.seqdoop.hadoop_bam.QseqOutputFormat.QseqRecordWriter
OUTPUT_FILE_EXTENSION - Static variable in class org.seqdoop.hadoop_bam.SplittingBAMIndexer
OUTPUT_SAM_FORMAT_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.AnySAMOutputFormat: A string property defining the output format to use.
OUTPUT_VCF_FORMAT_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.VCFOutputFormat: A string property defining the output format to use.

P

Pair<A,B> - Class in org.seqdoop.hadoop_bam.util: Deprecated.
This class will be removed in the next major version release (8.0).
Pair(A, B) - Constructor for class org.seqdoop.hadoop_bam.util.Pair: Deprecated.
parse(Object) - Method in class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.Parser
parse(Object) - Method in class org.seqdoop.hadoop_bam.LazyVCFGenotypesContext.Parser
parseBoolean(String, boolean) - Static method in class org.seqdoop.hadoop_bam.util.ConfHelper: Convert a string to a boolean.
parseBoolean(Configuration, String, boolean) - Static method in class org.seqdoop.hadoop_bam.util.ConfHelper
Parser(List<Allele>, int) - Constructor for class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.Parser
Parser() - Constructor for class org.seqdoop.hadoop_bam.LazyParsingGenotypesContext.Parser
Parser(List<Allele>, String, int) - Constructor for class org.seqdoop.hadoop_bam.LazyVCFGenotypesContext.Parser
position - Variable in class org.seqdoop.hadoop_bam.ReferenceFragment
position() - Method in class org.seqdoop.hadoop_bam.util.SeekableArrayStream: Deprecated.
position() - Method in class org.seqdoop.hadoop_bam.util.WrapSeekable
prepareForRecords(OutputStream, SAMFormat, SAMFileHeader) - Method in class org.seqdoop.hadoop_bam.util.SAMOutputPreparer: Prepares the given output stream for writing of SAMRecords in the given format.
prevAlignment(long) - Method in class org.seqdoop.hadoop_bam.SplittingBAMIndex
prevBlock(long) - Method in class org.seqdoop.hadoop_bam.util.BGZFBlockIndex
processAlignment(SAMRecord) - Method in class org.seqdoop.hadoop_bam.SplittingBAMIndexer: Process the given record for the index.

Q

QseqInputFormat - Class in org.seqdoop.hadoop_bam: Reads the Illumina qseq sequence format.
QseqInputFormat() - Constructor for class org.seqdoop.hadoop_bam.QseqInputFormat
QseqInputFormat.QseqRecordReader - Class in org.seqdoop.hadoop_bam
QseqOutputFormat - Class in org.seqdoop.hadoop_bam: Output format for Illumina qseq format.
QseqOutputFormat() - Constructor for class org.seqdoop.hadoop_bam.QseqOutputFormat
QseqOutputFormat.QseqRecordWriter - Class in org.seqdoop.hadoop_bam
QseqRecordReader(Configuration, FileSplit) - Constructor for class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader
QseqRecordWriter(Configuration, OutputStream) - Constructor for class org.seqdoop.hadoop_bam.QseqOutputFormat.QseqRecordWriter
quality - Variable in class org.seqdoop.hadoop_bam.SequencedFragment

R

read - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
read(byte[], int, int) - Method in class org.seqdoop.hadoop_bam.util.DataInputWrapper
read() - Method in class org.seqdoop.hadoop_bam.util.DataInputWrapper
read(byte[], int, int) - Method in class org.seqdoop.hadoop_bam.util.SeekableArrayStream: Deprecated.
read() - Method in class org.seqdoop.hadoop_bam.util.SeekableArrayStream: Deprecated.
read() - Method in class org.seqdoop.hadoop_bam.util.WrapSeekable
read(byte[], int, int) - Method in class org.seqdoop.hadoop_bam.util.WrapSeekable
read(DataInput) - Static method in class org.seqdoop.hadoop_bam.VariantContextCodec
Read_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment
readFields(DataInput) - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit
readFields(DataInput) - Method in class org.seqdoop.hadoop_bam.ReferenceFragment
readFields(DataInput) - Method in class org.seqdoop.hadoop_bam.SAMRecordWritable
readFields(DataInput) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
readFields(DataInput) - Method in class org.seqdoop.hadoop_bam.VariantContextWritable
readHeaderFrom(Path, FileSystem) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat
readHeaderFrom(SeekableStream) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat
readHeaderFrom(SeekableStream) - Static method in class org.seqdoop.hadoop_bam.util.VCFHeaderReader
readIndex(InputStream) - Method in class org.seqdoop.hadoop_bam.SplittingBAMIndex
readIndex(InputStream) - Method in class org.seqdoop.hadoop_bam.util.BGZFBlockIndex
readLine(Text, int, int) - Method in class org.seqdoop.hadoop_bam.LineReader: Read one line from the InputStream into the given Text.
readLine(Text, int) - Method in class org.seqdoop.hadoop_bam.LineReader: Read from the InputStream into the given Text.
readLine(Text) - Method in class org.seqdoop.hadoop_bam.LineReader: Read from the InputStream into the given Text.
readSAMHeaderFrom(Path, Configuration) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat
readSAMHeaderFrom(InputStream, Configuration) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat
readSAMHeaderFrom(Path, Configuration) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat
readSAMHeaderFrom(InputStream, Configuration) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat
readSAMHeaderFrom(Path, Configuration) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat
readSAMHeaderFrom(InputStream, Configuration) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat
readSAMHeaderFrom(Path, Configuration) - Static method in class org.seqdoop.hadoop_bam.util.SAMHeaderReader
readSAMHeaderFrom(InputStream, Configuration) - Static method in class org.seqdoop.hadoop_bam.util.SAMHeaderReader: Does not close the stream.
REFERENCE_SOURCE_PATH_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.CRAMInputFormat
ReferenceFragment - Class in org.seqdoop.hadoop_bam
ReferenceFragment() - Constructor for class org.seqdoop.hadoop_bam.ReferenceFragment
run(Configuration) - Static method in class org.seqdoop.hadoop_bam.SplittingBAMIndexer: Invoke a new SplittingBAMIndexer object, operating on the supplied Configuration object instead of a supplied argument list
runNumber - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
RunNumber_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment

S

SAMFileMerger - Class in org.seqdoop.hadoop_bam.util: Merges headerless BAM or CRAM files produced by KeyIgnoringAnySAMOutputFormat into a single file.
SAMFormat - Enum in org.seqdoop.hadoop_bam: Describes a SAM format.
SAMHeaderReader - Class in org.seqdoop.hadoop_bam.util
SAMHeaderReader() - Constructor for class org.seqdoop.hadoop_bam.util.SAMHeaderReader
SAMInputFormat - Class in org.seqdoop.hadoop_bam: An InputFormat for SAM files.
SAMInputFormat() - Constructor for class org.seqdoop.hadoop_bam.SAMInputFormat
SAMOutputPreparer - Class in org.seqdoop.hadoop_bam.util
SAMOutputPreparer() - Constructor for class org.seqdoop.hadoop_bam.util.SAMOutputPreparer
SAMRecordReader - Class in org.seqdoop.hadoop_bam: See BAMRecordReader for the meaning of the key.
SAMRecordReader() - Constructor for class org.seqdoop.hadoop_bam.SAMRecordReader
SAMRecordWritable - Class in org.seqdoop.hadoop_bam: A Writable SAMRecord.
SAMRecordWritable() - Constructor for class org.seqdoop.hadoop_bam.SAMRecordWritable
SAMRecordWriter<K> - Class in org.seqdoop.hadoop_bam: A base RecordWriter for SAM records.
SAMRecordWriter(Path, Path, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.SAMRecordWriter: A SAMFileHeader is read from the input Path.
SAMRecordWriter(Path, SAMFileHeader, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.SAMRecordWriter
SAMRecordWriter(OutputStream, SAMFileHeader, boolean) - Constructor for class org.seqdoop.hadoop_bam.SAMRecordWriter
SANGER_MAX - Static variable in class org.seqdoop.hadoop_bam.FormatConstants: Maximum encodable quality score for Sanger Phred+33 encoded base qualities.
SANGER_OFFSET - Static variable in class org.seqdoop.hadoop_bam.FormatConstants: Offset by which Sanger-style ASCII-encoded quality scores are shifted.
sBuilder - Variable in class org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter
sBuilder - Variable in class org.seqdoop.hadoop_bam.QseqOutputFormat.QseqRecordWriter
seek(long) - Method in class org.seqdoop.hadoop_bam.util.SeekableArrayStream: Deprecated.
seek(long) - Method in class org.seqdoop.hadoop_bam.util.WrapSeekable
SeekableArrayStream - Class in org.seqdoop.hadoop_bam.util: Deprecated.
Use ByteArraySeekableStream. This class will be removed in the next major version release (8.0).
SeekableArrayStream(byte[]) - Constructor for class org.seqdoop.hadoop_bam.util.SeekableArrayStream: Deprecated.
sequence - Variable in class org.seqdoop.hadoop_bam.ReferenceFragment
sequence - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
SequencedFragment - Class in org.seqdoop.hadoop_bam
SequencedFragment() - Constructor for class org.seqdoop.hadoop_bam.SequencedFragment
set(SAMRecord) - Method in class org.seqdoop.hadoop_bam.SAMRecordWritable
set(VariantContext) - Method in class org.seqdoop.hadoop_bam.VariantContextWritable
set(VariantContext, VCFHeader) - Method in class org.seqdoop.hadoop_bam.VariantContextWritable
setConf(Configuration) - Method in class org.seqdoop.hadoop_bam.FastaInputFormat.FastaRecordReader
setConf(Configuration) - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader
setConf(Configuration) - Method in class org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter
setConf(Configuration) - Method in class org.seqdoop.hadoop_bam.QseqInputFormat.QseqRecordReader
setConf(Configuration) - Method in class org.seqdoop.hadoop_bam.QseqOutputFormat.QseqRecordWriter
setControlNumber(Integer) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setEnableBAISplitCalculator(Configuration, boolean) - Static method in class org.seqdoop.hadoop_bam.BAMInputFormat: Enables or disables the split calculator that uses the BAM index to calculate splits.
setEndVirtualOffset(long) - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit
setFilterPassed(Boolean) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setFlowcellId(String) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setHeader(VCFHeader) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat
setHeader(VCFHeader) - Method in class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.HeaderDataCache
setHeader(VCFHeader) - Method in interface org.seqdoop.hadoop_bam.LazyParsingGenotypesContext.HeaderDataCache
setHeader(VCFHeader) - Method in class org.seqdoop.hadoop_bam.LazyVCFGenotypesContext.HeaderDataCache
setHeaderDataCache(LazyParsingGenotypesContext.HeaderDataCache) - Method in class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.Parser
setHeaderDataCache(LazyParsingGenotypesContext.HeaderDataCache) - Method in class org.seqdoop.hadoop_bam.LazyParsingGenotypesContext.Parser
setHeaderDataCache(LazyParsingGenotypesContext.HeaderDataCache) - Method in class org.seqdoop.hadoop_bam.LazyVCFGenotypesContext.Parser
setIndexSequence(String) - Method in class org.seqdoop.hadoop_bam.ReferenceFragment
setIndexSequence(String) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setInputHeader(VCFHeader) - Method in class org.seqdoop.hadoop_bam.BCFRecordWriter: Used for lazy decoding of genotype data.
setInputHeader(VCFHeader) - Method in class org.seqdoop.hadoop_bam.VCFRecordWriter: Used for lazy decoding of genotype data.
setInstrument(String) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setIntervals(Configuration, List<T>) - Static method in class org.seqdoop.hadoop_bam.BAMInputFormat: Only include reads that overlap the given intervals.
setIntervals(Configuration, List<T>) - Static method in class org.seqdoop.hadoop_bam.VCFInputFormat
setLane(Integer) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setPosition(Integer) - Method in class org.seqdoop.hadoop_bam.ReferenceFragment: Get quality Text object.
setQuality(Text) - Method in class org.seqdoop.hadoop_bam.SequencedFragment: Set quality.
setRead(Integer) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setRunNumber(Integer) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setSAMHeader(SAMFileHeader) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat
setSAMHeader(SAMFileHeader) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat
setSAMHeader(SAMFileHeader) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat
setSequence(Text) - Method in class org.seqdoop.hadoop_bam.ReferenceFragment
setSequence(Text) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setStartVirtualOffset(long) - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit
setTile(Integer) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setTraversalParameters(Configuration, List<T>, boolean) - Static method in class org.seqdoop.hadoop_bam.BAMInputFormat: Only include reads that overlap the given intervals (if specified) and unplaced unmapped reads (if true).
setWriteHeader(boolean) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat: Deprecated.
setWriteHeader(boolean) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat: Set whether the header will be written or not.
setWriteHeader(boolean) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringCRAMOutputFormat: Set whether the header will be written or not.
setXpos(Integer) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setYpos(Integer) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
size() - Method in class org.seqdoop.hadoop_bam.SplittingBAMIndex
size() - Method in class org.seqdoop.hadoop_bam.util.BGZFBlockIndex
skip(long) - Method in class org.seqdoop.hadoop_bam.LineReader: Skip n bytes from the InputStream.
skip(long) - Method in class org.seqdoop.hadoop_bam.util.DataInputWrapper
snd - Variable in class org.seqdoop.hadoop_bam.util.Pair: Deprecated.
SplittingBAMIndex - Class in org.seqdoop.hadoop_bam: An index into BAM files, for BAMInputFormat.
SplittingBAMIndex() - Constructor for class org.seqdoop.hadoop_bam.SplittingBAMIndex
SplittingBAMIndex(File) - Constructor for class org.seqdoop.hadoop_bam.SplittingBAMIndex
SplittingBAMIndex(InputStream) - Constructor for class org.seqdoop.hadoop_bam.SplittingBAMIndex
SplittingBAMIndexer - Class in org.seqdoop.hadoop_bam: An indexing tool and API for BAM files, making them palatable to BAMInputFormat.
SplittingBAMIndexer(int) - Constructor for class org.seqdoop.hadoop_bam.SplittingBAMIndexer: Deprecated.
use one of the other constructors to create an index while building a BAM file or SplittingBAMIndexer.index(InputStream, OutputStream, long, int) for an existing BAM file.
SplittingBAMIndexer(OutputStream) - Constructor for class org.seqdoop.hadoop_bam.SplittingBAMIndexer: Prepare to index a BAM file.
SplittingBAMIndexer(OutputStream, int) - Constructor for class org.seqdoop.hadoop_bam.SplittingBAMIndexer: Prepare to index a BAM file.
start() - Method in class org.seqdoop.hadoop_bam.util.Timer: Deprecated.
stopNs() - Method in class org.seqdoop.hadoop_bam.util.Timer: Deprecated.
stopS() - Method in class org.seqdoop.hadoop_bam.util.Timer: Deprecated.

T

tile - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
Tile_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment
Timer - Class in org.seqdoop.hadoop_bam.util: Deprecated.
This class will be removed in the next major version release (8.0).
Timer() - Constructor for class org.seqdoop.hadoop_bam.util.Timer: Deprecated.
toString() - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit
toString() - Method in class org.seqdoop.hadoop_bam.ReferenceFragment: Recreates a pseudo fasta record with the fields available.
toString() - Method in class org.seqdoop.hadoop_bam.SAMRecordWritable
toString() - Method in class org.seqdoop.hadoop_bam.SequencedFragment: Recreates a pseudo qseq record with the fields available.
toString() - Method in class org.seqdoop.hadoop_bam.SplittingBAMIndex
TRAVERSE_UNPLACED_UNMAPPED_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.BAMInputFormat: If set to true, include unplaced unmapped reads (that is, unmapped reads with no position).
TRUST_EXTS_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.AnySAMInputFormat: A Boolean property: are file extensions trusted? The default is true.
TRUST_EXTS_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.VCFInputFormat: Whether file extensions are to be trusted, defaults to true.

U

unsetTraversalParameters(Configuration) - Static method in class org.seqdoop.hadoop_bam.BAMInputFormat: Reset traversal parameters so that all reads are included.
UTF8 - Static variable in class org.seqdoop.hadoop_bam.FastaInputFormat
UTF8 - Static variable in class org.seqdoop.hadoop_bam.FastqOutputFormat

V

VALIDATION_STRINGENCY_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.util.SAMHeaderReader: A String property corresponding to a ValidationStringency value.
valueOf(String) - Static method in enum org.seqdoop.hadoop_bam.FormatConstants.BaseQualityEncoding: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.seqdoop.hadoop_bam.SAMFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.seqdoop.hadoop_bam.VCFFormat: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.seqdoop.hadoop_bam.FormatConstants.BaseQualityEncoding: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.seqdoop.hadoop_bam.SAMFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.seqdoop.hadoop_bam.VCFFormat: Returns an array containing the constants of this enum type, in the order they are declared.
VariantContextCodec - Class in org.seqdoop.hadoop_bam
VariantContextCodec() - Constructor for class org.seqdoop.hadoop_bam.VariantContextCodec
VariantContextWithHeader - Class in org.seqdoop.hadoop_bam
VariantContextWithHeader(VariantContext, VCFHeader) - Constructor for class org.seqdoop.hadoop_bam.VariantContextWithHeader
VariantContextWritable - Class in org.seqdoop.hadoop_bam: VariantContexts read here have LazyGenotypesContexts, which need to have a header set before the genotype data in the VariantContexts can be decoded.
VariantContextWritable() - Constructor for class org.seqdoop.hadoop_bam.VariantContextWritable
VCFFileMerger - Class in org.seqdoop.hadoop_bam.util: Merges headerless VCF files produced by KeyIgnoringVCFOutputFormat into a single file.
VCFFileMerger() - Constructor for class org.seqdoop.hadoop_bam.util.VCFFileMerger
VCFFormat - Enum in org.seqdoop.hadoop_bam: Describes a VCF format.
VCFHeaderReader - Class in org.seqdoop.hadoop_bam.util: Can read a VCF header without being told beforehand whether the input is VCF or BCF.
VCFHeaderReader() - Constructor for class org.seqdoop.hadoop_bam.util.VCFHeaderReader
VCFInputFormat - Class in org.seqdoop.hadoop_bam: An InputFormat for VCF files.
VCFInputFormat() - Constructor for class org.seqdoop.hadoop_bam.VCFInputFormat: Creates a new input format, which will use the Configuration from the first public method called.
VCFInputFormat(Configuration) - Constructor for class org.seqdoop.hadoop_bam.VCFInputFormat: Creates a new input format, reading VCFInputFormat.TRUST_EXTS_PROPERTY from the given Configuration.
VCFInputFormat(Map<Path, VCFFormat>) - Constructor for class org.seqdoop.hadoop_bam.VCFInputFormat: Creates a new input format, trusting the given Map to define the file-to-format associations.
VCFOutputFormat<K> - Class in org.seqdoop.hadoop_bam: An abstract OutputFormat for VCF and BCF files.
VCFOutputFormat(Configuration) - Constructor for class org.seqdoop.hadoop_bam.VCFOutputFormat: Creates a new output format, reading VCFOutputFormat.OUTPUT_VCF_FORMAT_PROPERTY from the given Configuration.
VCFOutputFormat(VCFFormat) - Constructor for class org.seqdoop.hadoop_bam.VCFOutputFormat: Creates a new output format for the given VCF format.
VCFRecordReader - Class in org.seqdoop.hadoop_bam: The key is the bitwise OR of the chromosome index in the upper 32 bits and the 0-based leftmost coordinate in the lower.
VCFRecordReader() - Constructor for class org.seqdoop.hadoop_bam.VCFRecordReader
VCFRecordWriter<K> - Class in org.seqdoop.hadoop_bam: A base RecordWriter for VCF.
VCFRecordWriter(Path, Path, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.VCFRecordWriter: A VCFHeader is read from the input Path.
VCFRecordWriter(Path, VCFHeader, boolean, TaskAttemptContext) - Constructor for class org.seqdoop.hadoop_bam.VCFRecordWriter
VCFRecordWriter(OutputStream, VCFHeader, boolean) - Constructor for class org.seqdoop.hadoop_bam.VCFRecordWriter
verifyQuality(Text, FormatConstants.BaseQualityEncoding) - Static method in class org.seqdoop.hadoop_bam.SequencedFragment: Verify that the given quality bytes are within the range allowed for the specified encoding.

W

WrapSeekable<S extends InputStream & org.apache.hadoop.fs.Seekable> - Class in org.seqdoop.hadoop_bam.util: Wraps Hadoop's "seekable stream" abstraction so that we can give such a one to BlockCompressedInputStream and retain seekability.
WrapSeekable(S, long, Path) - Constructor for class org.seqdoop.hadoop_bam.util.WrapSeekable
write(Text, SequencedFragment) - Method in class org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter
write(DataOutput) - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit
write(K, SAMRecordWritable) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringBAMRecordWriter
write(K, VariantContextWritable) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter
write(K, SAMRecordWritable) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringCRAMRecordWriter
write(K, SAMRecordWritable) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringSAMRecordWriter
write(K, VariantContextWritable) - Method in class org.seqdoop.hadoop_bam.KeyIgnoringVCFRecordWriter
write(Text, SequencedFragment) - Method in class org.seqdoop.hadoop_bam.QseqOutputFormat.QseqRecordWriter
write(DataOutput) - Method in class org.seqdoop.hadoop_bam.ReferenceFragment
write(DataOutput) - Method in class org.seqdoop.hadoop_bam.SAMRecordWritable
write(DataOutput) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
write(int) - Method in class org.seqdoop.hadoop_bam.util.DataOutputWrapper
write(byte[], int, int) - Method in class org.seqdoop.hadoop_bam.util.DataOutputWrapper
write(DataOutput, VariantContext) - Static method in class org.seqdoop.hadoop_bam.VariantContextCodec
write(DataOutput) - Method in class org.seqdoop.hadoop_bam.VariantContextWritable
WRITE_HEADER_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat: Whether the header will be written, defaults to true.
WRITE_HEADER_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat: Whether the header will be written, defaults to true.
WRITE_SPLITTING_BAI - Static variable in class org.seqdoop.hadoop_bam.BAMOutputFormat: If set to true, write .splitting-bai files for every BAM file (defaults to false).
writeAlignment(SAMRecord) - Method in class org.seqdoop.hadoop_bam.BAMRecordWriter
writeAlignment(SAMRecord) - Method in class org.seqdoop.hadoop_bam.CRAMRecordWriter
writeAlignment(SAMRecord) - Method in class org.seqdoop.hadoop_bam.SAMRecordWriter
writeRecord(VariantContext) - Method in class org.seqdoop.hadoop_bam.BCFRecordWriter
writeRecord(VariantContext) - Method in class org.seqdoop.hadoop_bam.VCFRecordWriter
writeVirtualOffset(long) - Method in class org.seqdoop.hadoop_bam.SplittingBAMIndexer: Write the given virtual offset to the index.

X

xpos - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
Xpos_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment

Y

ypos - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
Ypos_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment

A B C D E F G H I K L M N O P Q R S T U V W X Y