Index (Hadoop-BAM 7.4.0 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

addBooleanOption(char, String) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Convenience method for adding a boolean option.
addBooleanOption(String) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Convenience method for adding a boolean option.
addDoubleOption(char, String) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Convenience method for adding a double option.
addDoubleOption(String) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Convenience method for adding a double option.
addIntegerOption(char, String) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Convenience method for adding an integer option.
addIntegerOption(String) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Convenience method for adding an integer option.
addLongOption(char, String) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Convenience method for adding a long integer option.
addLongOption(String) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Convenience method for adding a long integer option.
addNamedOutput(Job, String, Class<? extends OutputFormat>, Class<?>, Class<?>) - Static method in class hadoop.org.apache.hadoop.mapreduce.lib.output.MultipleOutputs: Adds a named output for the job.
addOption(CmdLineParser.Option) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Add the specified Option to the list of accepted options
addStringOption(char, String) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Convenience method for adding a string option.
addStringOption(String) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Convenience method for adding a string option.
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.

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
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(FSDataInputStream) - Constructor for class org.seqdoop.hadoop_bam.util.BGZFSplitGuesser
BooleanOption(char, String) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.BooleanOption
BooleanOption(String) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.BooleanOption
buffer - Variable in class org.seqdoop.hadoop_bam.FastqOutputFormat.FastqRecordWriter

C

cacheAndSetProperties(CmdLineParser) - Method in class org.seqdoop.hadoop_bam.cli.CLIMRBAMPlugin: Should be called before accessing any of the protected data such as samFormat.
cacheAndSetProperties(CmdLineParser) - Method in class org.seqdoop.hadoop_bam.cli.CLIMRPlugin: Should be called before accessing any of the protected data such as verbose.
Cat - Class in org.seqdoop.hadoop_bam.cli.plugins
Cat() - Constructor for class org.seqdoop.hadoop_bam.cli.plugins.Cat
checkOutputSpecs(JobContext) - Method in class org.seqdoop.hadoop_bam.cli.CLIMergingAnySAMOutputFormat
clear() - Method in class org.seqdoop.hadoop_bam.ReferenceFragment
clear() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
CLIMergingAnySAMOutputFormat<K> - Class in org.seqdoop.hadoop_bam.cli
CLIMergingAnySAMOutputFormat() - Constructor for class org.seqdoop.hadoop_bam.cli.CLIMergingAnySAMOutputFormat
CLIMRBAMPlugin - Class in org.seqdoop.hadoop_bam.cli: Like CLIMRPlugin, with added useful defaults for plugins working solely on BAM/SAM files.
CLIMRBAMPlugin(String, String, String, String, List<Pair<CmdLineParser.Option, String>>, String) - Constructor for class org.seqdoop.hadoop_bam.cli.CLIMRBAMPlugin
CLIMRPlugin - Class in org.seqdoop.hadoop_bam.cli: Like CLIPlugin, but has lots of useful defaults for MapReduce-using plugins.
CLIMRPlugin(String, String, String, String, List<Pair<CmdLineParser.Option, String>>, String) - Constructor for class org.seqdoop.hadoop_bam.cli.CLIMRPlugin
CLIPlugin - Class in org.seqdoop.hadoop_bam.cli
CLIPlugin(String, String, String, String, List<Pair<CmdLineParser.Option, String>>, String) - Constructor for class org.seqdoop.hadoop_bam.cli.CLIPlugin
close() - Method in class hadoop.org.apache.hadoop.mapreduce.lib.output.MultipleOutputs: Closes all the opened outputs.
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
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
CmdLineParser - Class in org.seqdoop.hadoop_bam.custom.jargs.gnu: Largely GNU-compatible command-line options parser.
CmdLineParser() - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser
CmdLineParser.IllegalOptionValueException - Exception in org.seqdoop.hadoop_bam.custom.jargs.gnu: Thrown when an illegal or missing value is given by the user for an option that takes a value.
CmdLineParser.NotFlagException - Exception in org.seqdoop.hadoop_bam.custom.jargs.gnu: Thrown when the parsed commandline contains multiple concatenated short options, such as -abcd, where one or more requires a value.
CmdLineParser.Option - Class in org.seqdoop.hadoop_bam.custom.jargs.gnu: Representation of a command-line option
CmdLineParser.Option.BooleanOption - Class in org.seqdoop.hadoop_bam.custom.jargs.gnu
CmdLineParser.Option.DoubleOption - Class in org.seqdoop.hadoop_bam.custom.jargs.gnu: An option that expects a floating-point value
CmdLineParser.Option.IntegerOption - Class in org.seqdoop.hadoop_bam.custom.jargs.gnu: An option that expects an integer value
CmdLineParser.Option.LongOption - Class in org.seqdoop.hadoop_bam.custom.jargs.gnu: An option that expects a long integer value
CmdLineParser.Option.StringOption - Class in org.seqdoop.hadoop_bam.custom.jargs.gnu: An option that expects a string value
CmdLineParser.OptionException - Exception in org.seqdoop.hadoop_bam.custom.jargs.gnu: Base class for exceptions that may be thrown when options are parsed
CmdLineParser.UnknownOptionException - Exception in org.seqdoop.hadoop_bam.custom.jargs.gnu: Thrown when the parsed command-line contains an option that is not recognised.
CmdLineParser.UnknownSuboptionException - Exception in org.seqdoop.hadoop_bam.custom.jargs.gnu: Thrown when the parsed commandline contains multiple concatenated short options, such as -abcd, where one is unknown.
command - Variable in class org.seqdoop.hadoop_bam.cli.CLIPlugin
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
configureSampling(Path, String, Configuration) - Static method in class org.seqdoop.hadoop_bam.cli.Utils
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.
correctSAMRecordForMerging(SAMRecord, Configuration) - Static method in class org.seqdoop.hadoop_bam.cli.Utils: Changes the given SAMRecord as appropriate for being placed in a file whose header is getSAMHeaderMerger(conf).getMergedHeader().
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
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.
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.

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
DEBUG_BAM_SPLITTER - Static variable in class org.seqdoop.hadoop_bam.BAMInputFormat
decoder - Static variable in class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.HeaderDataCache
DEFAULT_GRANULARITY - Static variable in class org.seqdoop.hadoop_bam.SplittingBAMIndexer
DEFAULT_PATH - Static variable in class hadoop.org.apache.hadoop.mapreduce.lib.partition.TotalOrderPartitioner
desc - Variable in class org.seqdoop.hadoop_bam.cli.CLIPlugin
DoubleOption(char, String) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.DoubleOption
DoubleOption(String) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.DoubleOption

E

eof() - Method in class org.seqdoop.hadoop_bam.util.SeekableArrayStream
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
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.
FixMate - Class in org.seqdoop.hadoop_bam.cli.plugins
FixMate() - Constructor for class org.seqdoop.hadoop_bam.cli.plugins.FixMate
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
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
formatOpt - Static variable in class org.seqdoop.hadoop_bam.cli.CLIMRBAMPlugin
Frontend - Class in org.seqdoop.hadoop_bam.cli
Frontend() - Constructor for class org.seqdoop.hadoop_bam.cli.Frontend
fst - Variable in class org.seqdoop.hadoop_bam.util.Pair

G

get() - Method in class org.seqdoop.hadoop_bam.SAMRecordWritable
get() - Method in class org.seqdoop.hadoop_bam.VariantContextWritable
getArgv0() - Static method in class org.seqdoop.hadoop_bam.cli.Utils
getBoolean(CmdLineParser.Option) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser
getBuilders() - Method in class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.HeaderDataCache
getCodec() - Method in class org.seqdoop.hadoop_bam.LazyVCFGenotypesContext.HeaderDataCache
getCommandName() - Method in class org.seqdoop.hadoop_bam.cli.CLIPlugin
getConf() - Method in class hadoop.org.apache.hadoop.mapreduce.lib.partition.TotalOrderPartitioner
getControlNumber() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getCountersEnabled(JobContext) - Static method in class hadoop.org.apache.hadoop.mapreduce.lib.output.MultipleOutputs: Returns if the counters for the named outputs are enabled or not.
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
getDefaultWorkFile(TaskAttemptContext, String) - Method in class org.seqdoop.hadoop_bam.cli.CLIMergingAnySAMOutputFormat
getDescription() - Method in class org.seqdoop.hadoop_bam.cli.CLIPlugin
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
getInt(CmdLineParser.Option, int) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser
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.
getLocations() - Method in class org.seqdoop.hadoop_bam.FileVirtualSplit
getMergeableWorkFile(Path, String, String, TaskAttemptContext, String) - Static method in class org.seqdoop.hadoop_bam.cli.Utils: Returns a name that mergeInto() will recognize as a file to be merged.
getOption() - Method in exception org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.IllegalOptionValueException
getOptionChar() - Method in exception org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.NotFlagException
getOptionName() - Method in exception org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.UnknownOptionException
getOptionValue(CmdLineParser.Option) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Equivalent to getOptionValue(o, null).
getOptionValue(CmdLineParser.Option, Object) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser
getOptionValues(CmdLineParser.Option) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser
getParser() - Method in class org.seqdoop.hadoop_bam.LazyParsingGenotypesContext
getPartition(K, V, int) - Method in class hadoop.org.apache.hadoop.mapreduce.lib.partition.TotalOrderPartitioner
getPartitionFile(Configuration) - Static method in class hadoop.org.apache.hadoop.mapreduce.lib.partition.TotalOrderPartitioner: Get the path to the SequenceFile storing the sorted partition keyset.
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.cli.CLIMergingAnySAMOutputFormat
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
getRemainingArgs() - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser
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
getSAMHeaderMerger(Configuration) - Static method in class org.seqdoop.hadoop_bam.cli.Utils: Computes the merger of the SAM headers in the files listed in HEADERMERGER_INPUTS_PROPERTY.
getSample(InputFormat<K, V>, Job) - Method in class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.IntervalSampler: For each split sampled, emit when the ratio of the number of records retained to the total record count is less than the specified frequency.
getSample(InputFormat<K, V>, Job) - Method in class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.RandomSampler: Randomize the split order, then take the specified number of keys from each split sampled, where each key is selected with the specified probability and possibly replaced by a subsequently selected key when the quota of keys from that split is satisfied.
getSample(InputFormat<K, V>, Job) - Method in interface hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.Sampler: For a given job, collect and return a subset of the keys from the input data.
getSample(InputFormat<K, V>, Job) - Method in class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.SplitSampler: From each split sampled, take the first numSamples / numSplits records.
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
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.
getStringencyOptHelp() - Static method in class org.seqdoop.hadoop_bam.cli.Utils
getSuboption() - Method in exception org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.UnknownSuboptionException
getTile() - Method in class org.seqdoop.hadoop_bam.SequencedFragment
getValidationStringency(Configuration) - Static method in class org.seqdoop.hadoop_bam.util.SAMHeaderReader
getValue() - Method in exception org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.IllegalOptionValueException
getValue(String, Locale) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option
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
go(String[], Configuration) - Static method in class org.seqdoop.hadoop_bam.cli.Frontend
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

hadoop.org.apache.hadoop.mapreduce.lib.output - package hadoop.org.apache.hadoop.mapreduce.lib.output
hadoop.org.apache.hadoop.mapreduce.lib.partition - package hadoop.org.apache.hadoop.mapreduce.lib.partition
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
HEADERMERGER_INPUTS_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.cli.Utils

I

IllegalOptionValueException(CmdLineParser.Option, String) - Constructor for exception org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.IllegalOptionValueException
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 - Class in org.seqdoop.hadoop_bam.cli.plugins
Index() - Constructor for class org.seqdoop.hadoop_bam.cli.plugins.Index
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
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
InputSampler<K,V> - Class in hadoop.org.apache.hadoop.mapreduce.lib.partition: Utility for collecting samples and writing a partition file for TotalOrderPartitioner.
InputSampler(Configuration) - Constructor for class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler
InputSampler.IntervalSampler<K,V> - Class in hadoop.org.apache.hadoop.mapreduce.lib.partition: Sample from s splits at regular intervals.
InputSampler.RandomSampler<K,V> - Class in hadoop.org.apache.hadoop.mapreduce.lib.partition: Sample from random points in the input.
InputSampler.Sampler<K,V> - Interface in hadoop.org.apache.hadoop.mapreduce.lib.partition: Interface to sample using an InputFormat.
InputSampler.SplitSampler<K,V> - Class in hadoop.org.apache.hadoop.mapreduce.lib.partition: Samples the first n records from s splits.
instrument - Variable in class org.seqdoop.hadoop_bam.SequencedFragment
Instrument_Present - Static variable in class org.seqdoop.hadoop_bam.SequencedFragment
IntegerOption(char, String) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.IntegerOption
IntegerOption(String) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.IntegerOption
INTERVALS_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.BAMInputFormat: Filter by region, like -L in SAMtools.
IntervalSampler(double) - Constructor for class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.IntervalSampler: Create a new IntervalSampler sampling all splits.
IntervalSampler(double, int) - Constructor for class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.IntervalSampler: Create a new IntervalSampler.
isBGZF() - Method in class org.seqdoop.hadoop_bam.BCFSplitGuesser
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

K

KEEP_PAIRED_READS_TOGETHER_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.BAMInputFormat: If set to true, ensure that for paired reads both reads in a pair are always in the same split for queryname-sorted BAM files.
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
length() - Method in class org.seqdoop.hadoop_bam.util.WrapSeekable
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
longDesc - Variable in class org.seqdoop.hadoop_bam.cli.CLIPlugin
longForm() - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option
LongOption(char, String) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.LongOption
LongOption(String) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.LongOption
lowLevelFastqRead(Text, SequencedFragment) - Method in class org.seqdoop.hadoop_bam.FastqInputFormat.FastqRecordReader

M

main(String[]) - Static method in class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler
main(String[]) - Static method in class org.seqdoop.hadoop_bam.BAMSplitGuesser
main(String[]) - Static method in class org.seqdoop.hadoop_bam.BCFSplitGuesser
main(List<String>) - Method in class org.seqdoop.hadoop_bam.cli.CLIPlugin
main(String[]) - Static method in class org.seqdoop.hadoop_bam.cli.Frontend
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
mergeInto(OutputStream, Path, String, String, Configuration, String) - Static method in class org.seqdoop.hadoop_bam.cli.Utils: Merges the files in the given directory that have names given by getMergeableWorkFile() into out.
mergeSAMInto(Path, Path, String, String, SAMFormat, Configuration, String) - Static method in class org.seqdoop.hadoop_bam.cli.Utils: Merges the files in the given directory that have names given by getMergeableWorkFile() into out in the given SAMFormat, using getSAMHeaderMerger().getMergedHeader() as the header.
MultipleOutputs<KEYOUT,VALUEOUT> - Class in hadoop.org.apache.hadoop.mapreduce.lib.output: The MultipleOutputs class simplifies writing output data to multiple outputs
MultipleOutputs(TaskInputOutputContext<?, ?, KEYOUT, VALUEOUT>) - Constructor for class hadoop.org.apache.hadoop.mapreduce.lib.output.MultipleOutputs: Creates and initializes multiple outputs support, it should be instantiated in the Mapper/Reducer setup method.
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
noTrustExtsOpt - Static variable in class org.seqdoop.hadoop_bam.cli.CLIMRBAMPlugin

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
Option(String, boolean) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option
Option(char, String, boolean) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option
optionDescriptions - Variable in class org.seqdoop.hadoop_bam.cli.CLIPlugin
org.seqdoop.hadoop_bam - package org.seqdoop.hadoop_bam
org.seqdoop.hadoop_bam.cli - package org.seqdoop.hadoop_bam.cli
org.seqdoop.hadoop_bam.cli.plugins - package org.seqdoop.hadoop_bam.cli.plugins
org.seqdoop.hadoop_bam.cli.plugins.chipster - package org.seqdoop.hadoop_bam.cli.plugins.chipster
org.seqdoop.hadoop_bam.custom.jargs.gnu - package org.seqdoop.hadoop_bam.custom.jargs.gnu
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
outPath - Variable in class org.seqdoop.hadoop_bam.cli.CLIMRPlugin
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.
outputPathOpt - Static variable in class org.seqdoop.hadoop_bam.cli.CLIMRPlugin

P

Pair<A,B> - Class in org.seqdoop.hadoop_bam.util
Pair(A, B) - Constructor for class org.seqdoop.hadoop_bam.util.Pair
parse(List<String>) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Extract the options and non-option arguments from the given list of command-line arguments.
parse(List<String>, Locale) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser: Extract the options and non-option arguments from the given list of command-line arguments.
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
parseValue(String, Locale) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.DoubleOption
parseValue(String, Locale) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.IntegerOption
parseValue(String, Locale) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.LongOption
parseValue(String, Locale) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option: Override to extract and convert an option value passed on the command-line
parseValue(String, Locale) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.StringOption
position - Variable in class org.seqdoop.hadoop_bam.ReferenceFragment
position() - Method in class org.seqdoop.hadoop_bam.util.SeekableArrayStream
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
printUsage(PrintStream) - Method in class org.seqdoop.hadoop_bam.cli.CLIPlugin
printWrapped(PrintStream, String) - Static method in class org.seqdoop.hadoop_bam.cli.Utils
printWrapped(PrintStream, String, int) - Static method in class org.seqdoop.hadoop_bam.cli.Utils
printWrapped(PrintStream, String, int, int) - Static method in class org.seqdoop.hadoop_bam.cli.Utils
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

RandomSampler(double, int) - Constructor for class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.RandomSampler: Create a new RandomSampler sampling all splits.
RandomSampler(double, int, int) - Constructor for class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.RandomSampler: Create a new RandomSampler.
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
read() - Method in class org.seqdoop.hadoop_bam.util.SeekableArrayStream
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.
reducersOpt - Static variable in class org.seqdoop.hadoop_bam.cli.CLIMRPlugin
reduceTasks - Variable in class org.seqdoop.hadoop_bam.cli.CLIMRPlugin
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(String[]) - Method in class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler: Driver for InputSampler from the command line.
run(CmdLineParser) - Method in class org.seqdoop.hadoop_bam.cli.CLIPlugin
run(CmdLineParser) - Method in class org.seqdoop.hadoop_bam.cli.plugins.Cat
run(CmdLineParser) - Method in class org.seqdoop.hadoop_bam.cli.plugins.chipster.Summarize
run(CmdLineParser) - Method in class org.seqdoop.hadoop_bam.cli.plugins.chipster.SummarySort
run(CmdLineParser) - Method in class org.seqdoop.hadoop_bam.cli.plugins.FixMate
run(CmdLineParser) - Method in class org.seqdoop.hadoop_bam.cli.plugins.Index
run(CmdLineParser) - Method in class org.seqdoop.hadoop_bam.cli.plugins.Sort
run(CmdLineParser) - Method in class org.seqdoop.hadoop_bam.cli.plugins.VCFSort
run(CmdLineParser) - Method in class org.seqdoop.hadoop_bam.cli.plugins.View
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

samFormat - Variable in class org.seqdoop.hadoop_bam.cli.CLIMRBAMPlugin
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
seek(long) - Method in class org.seqdoop.hadoop_bam.util.WrapSeekable
SeekableArrayStream - Class in org.seqdoop.hadoop_bam.util
SeekableArrayStream(byte[]) - Constructor for class org.seqdoop.hadoop_bam.util.SeekableArrayStream
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
setArgv0Class(Class<?>) - Static method in class org.seqdoop.hadoop_bam.cli.Utils
setConf(Configuration) - Method in class hadoop.org.apache.hadoop.mapreduce.lib.partition.TotalOrderPartitioner: Read in the partition file and build indexing data structures.
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
setCountersEnabled(Job, boolean) - Static method in class hadoop.org.apache.hadoop.mapreduce.lib.output.MultipleOutputs: Enables or disables counters for the named outputs.
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
setHeaderMergerSortOrder(Configuration, SAMFileHeader.SortOrder) - Static method in class org.seqdoop.hadoop_bam.cli.Utils
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
setLane(Integer) - Method in class org.seqdoop.hadoop_bam.SequencedFragment
setLongForm(String) - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option
setPartitionFile(Configuration, Path) - Static method in class hadoop.org.apache.hadoop.mapreduce.lib.partition.TotalOrderPartitioner: Set the path to the SequenceFile storing the sorted partition keyset.
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
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
shortForm() - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option
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
Sort - Class in org.seqdoop.hadoop_bam.cli.plugins
Sort() - Constructor for class org.seqdoop.hadoop_bam.cli.plugins.Sort
SplitSampler(int) - Constructor for class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.SplitSampler: Create a SplitSampler sampling all splits.
SplitSampler(int, int) - Constructor for class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.SplitSampler: Create a new SplitSampler.
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
stopNs() - Method in class org.seqdoop.hadoop_bam.util.Timer
stopS() - Method in class org.seqdoop.hadoop_bam.util.Timer
StringOption(char, String) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.StringOption
StringOption(String) - Constructor for class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.StringOption
Summarize - Class in org.seqdoop.hadoop_bam.cli.plugins.chipster
Summarize() - Constructor for class org.seqdoop.hadoop_bam.cli.plugins.chipster.Summarize
SummarySort - Class in org.seqdoop.hadoop_bam.cli.plugins.chipster
SummarySort() - Constructor for class org.seqdoop.hadoop_bam.cli.plugins.chipster.SummarySort

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
Timer() - Constructor for class org.seqdoop.hadoop_bam.util.Timer
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.
toStringency(Object, String) - Static method in class org.seqdoop.hadoop_bam.cli.Utils: Sets the default validation stringency in addition to returning it.
TotalOrderPartitioner<K extends org.apache.hadoop.io.WritableComparable<?>,V> - Class in hadoop.org.apache.hadoop.mapreduce.lib.partition: Partitioner effecting a total order by reading split points from an externally generated source.
TotalOrderPartitioner() - Constructor for class hadoop.org.apache.hadoop.mapreduce.lib.partition.TotalOrderPartitioner
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

usage(PrintStream, Map<String, CLIPlugin>) - Static method in class org.seqdoop.hadoop_bam.cli.Frontend
usageTail - Variable in class org.seqdoop.hadoop_bam.cli.CLIPlugin
UTF8 - Static variable in class org.seqdoop.hadoop_bam.FastaInputFormat
UTF8 - Static variable in class org.seqdoop.hadoop_bam.FastqOutputFormat
Utils - Class in org.seqdoop.hadoop_bam.cli
Utils() - Constructor for class org.seqdoop.hadoop_bam.cli.Utils

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
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
VCFSort - Class in org.seqdoop.hadoop_bam.cli.plugins
VCFSort() - Constructor for class org.seqdoop.hadoop_bam.cli.plugins.VCFSort
verbose - Variable in class org.seqdoop.hadoop_bam.cli.CLIMRPlugin
verboseOpt - Static variable in class org.seqdoop.hadoop_bam.cli.CLIMRPlugin
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.
version - Variable in class org.seqdoop.hadoop_bam.cli.CLIPlugin
VERSION_MAJOR - Static variable in class org.seqdoop.hadoop_bam.cli.Frontend
VERSION_MINOR - Static variable in class org.seqdoop.hadoop_bam.cli.Frontend
View - Class in org.seqdoop.hadoop_bam.cli.plugins
View() - Constructor for class org.seqdoop.hadoop_bam.cli.plugins.View

W

wantsValue() - Method in class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option: Tells whether or not this option wants a value
WORK_FILENAME_PROPERTY - Static variable in class org.seqdoop.hadoop_bam.cli.Utils
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(String, K, V) - Method in class hadoop.org.apache.hadoop.mapreduce.lib.output.MultipleOutputs: Write key and value to the namedOutput.
write(String, K, V, String) - Method in class hadoop.org.apache.hadoop.mapreduce.lib.output.MultipleOutputs: Write key and value to baseOutputPath using the namedOutput.
write(KEYOUT, VALUEOUT, String) - Method in class hadoop.org.apache.hadoop.mapreduce.lib.output.MultipleOutputs: Write key value to an output file name.
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.
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
writePartitionFile(Job, InputSampler.Sampler<K, V>) - Static method in class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler: Write a partition file for the given job, using the Sampler provided.
writeRecord(VariantContext) - Method in class org.seqdoop.hadoop_bam.BCFRecordWriter
writeRecord(VariantContext) - Method in class org.seqdoop.hadoop_bam.VCFRecordWriter

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