Serialized Form

Package htsjdk.samtools

Class htsjdk.samtools.Chunk extends java.lang.Object implements Serializable

serialVersionUID:

1L

Serialized Fields

mChunkStart

long mChunkStart

A pointer to the start of a region in a SAM/BAM file. The start is inclusive: start reading from this point.

mChunkEnd

long mChunkEnd

A pointer to the end of a region in a SAM/BAM file. The end is exclusive: this pointer points to one byte past the end of the region of interest inside the file.

Class htsjdk.samtools.FileTruncatedException extends SAMException implements Serializable

Class htsjdk.samtools.SAMException extends java.lang.RuntimeException implements Serializable

Class htsjdk.samtools.SAMFormatException extends SAMException implements Serializable

Class htsjdk.samtools.SAMTestUtil.SanityCheckFailedException extends java.lang.RuntimeException implements Serializable

Package htsjdk.samtools.cram.common

Class htsjdk.samtools.cram.common.NonforgivingPrintStream.PrintStreamError extends java.lang.RuntimeException implements Serializable

Package htsjdk.samtools.cram.encoding.read_features

Class htsjdk.samtools.cram.encoding.read_features.BaseChange extends java.lang.Object implements Serializable

Serialized Fields

change

int change

Class htsjdk.samtools.cram.encoding.read_features.BaseQualityScore extends java.lang.Object implements Serializable

Serialized Fields

position

int position

qualityScore

byte qualityScore

Class htsjdk.samtools.cram.encoding.read_features.Deletion extends java.lang.Object implements Serializable

Serialized Fields

position

int position

length

int length

Class htsjdk.samtools.cram.encoding.read_features.HardClip extends java.lang.Object implements Serializable

Serialized Fields

position

int position

length

int length

Class htsjdk.samtools.cram.encoding.read_features.InsertBase extends java.lang.Object implements Serializable

Serialized Fields

position

int position

base

byte base

Class htsjdk.samtools.cram.encoding.read_features.Insertion extends java.lang.Object implements Serializable

Serialized Fields

position

int position

sequence

byte[] sequence

Class htsjdk.samtools.cram.encoding.read_features.Padding extends java.lang.Object implements Serializable

Serialized Fields

position

int position

length

int length

Class htsjdk.samtools.cram.encoding.read_features.ReadBase extends java.lang.Object implements Serializable

Serialized Fields

position

int position

base

byte base

qualityScore

byte qualityScore

Class htsjdk.samtools.cram.encoding.read_features.RefSkip extends java.lang.Object implements Serializable

Serialized Fields

position

int position

length

int length

Class htsjdk.samtools.cram.encoding.read_features.SoftClip extends java.lang.Object implements Serializable

Serialized Fields

position

int position

sequence

byte[] sequence

Class htsjdk.samtools.cram.encoding.read_features.Substitution extends java.lang.Object implements Serializable

Serialized Fields

position

int position

base

byte base

refernceBase

byte refernceBase

baseChange

BaseChange baseChange

code

byte code

Package htsjdk.samtools.cram.mask

Class htsjdk.samtools.cram.mask.ReadMaskException extends java.lang.Exception implements Serializable

Class htsjdk.samtools.cram.mask.ReadMaskFormatException extends ReadMaskException implements Serializable

Package htsjdk.samtools.util

Class htsjdk.samtools.util.CollectionUtil.DefaultingMap extends java.util.HashMap<K,V> implements Serializable

Serialized Fields

defaultGenerator

CollectionUtil.DefaultingMap.Factory<V,K> defaultGenerator

injectValueOnDefault

boolean injectValueOnDefault

Class htsjdk.samtools.util.CollectionUtil.MultiMap extends java.util.HashMap<K,java.util.Collection<V>> implements Serializable

Class htsjdk.samtools.util.DateParser.InvalidDateException extends SAMException implements Serializable

Class htsjdk.samtools.util.Histogram extends java.util.TreeMap<K extends java.lang.Comparable,Histogram.Bin> implements Serializable

Serialized Fields

binLabel

java.lang.String binLabel

valueLabel

java.lang.String valueLabel

mean

java.lang.Double mean

Class htsjdk.samtools.util.Iso8601Date extends java.util.Date implements Serializable

Class htsjdk.samtools.util.ListMap extends java.util.HashMap<K,java.util.List<V>> implements Serializable

Class htsjdk.samtools.util.RelativeIso8601Date extends Iso8601Date implements Serializable

Serialized Fields

doSetTimeNextQuery

boolean doSetTimeNextQuery

Flag that indicates this instance is lazy and has not yet been queried (and so its value should be updated at the next query).

Class htsjdk.samtools.util.RuntimeEOFException extends SAMException implements Serializable

Class htsjdk.samtools.util.RuntimeIOException extends SAMException implements Serializable

Class htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException extends SAMException implements Serializable

Package htsjdk.tribble

Class htsjdk.tribble.TribbleException extends java.lang.RuntimeException implements Serializable

Serialized Fields

source

java.lang.String source

Class htsjdk.tribble.TribbleException.FeatureFileDoesntExist extends TribbleException implements Serializable

Class htsjdk.tribble.TribbleException.InternalCodecException extends TribbleException implements Serializable

Class htsjdk.tribble.TribbleException.InvalidDecodeLine extends TribbleException implements Serializable

Class htsjdk.tribble.TribbleException.InvalidHeader extends TribbleException implements Serializable

Class htsjdk.tribble.TribbleException.MalformedFeatureFile extends TribbleException implements Serializable

Class htsjdk.tribble.TribbleException.TabixReaderFailure extends TribbleException implements Serializable

Class htsjdk.tribble.TribbleException.UnableToCreateCorrectIndexType extends TribbleException implements Serializable

Class htsjdk.tribble.TribbleException.UnableToReadIndexFile extends TribbleException implements Serializable

Package htsjdk.tribble.exception

Class htsjdk.tribble.exception.CodecLineParsingException extends java.lang.RuntimeException implements Serializable

Class htsjdk.tribble.exception.UnsortedFileException extends java.lang.RuntimeException implements Serializable