# Index

A C D E F G H I L M N O P R S U W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

## A

aligned - Static variable in interface ngs.Read
Alignment - Interface in ngs
  Represents an alignment between a Fragment and Reference sub-sequence provides a path to Read and mate Alignment
alignment_minus_strand - Static variable in interface ngs.PileupEvent
alignment_start - Static variable in interface ngs.PileupEvent
alignment_stop - Static variable in interface ngs.PileupEvent
AlignmentIterator - Interface in ngs
  Iterates across a list of Alignments
all - Static variable in interface ngs.Alignment
all - Static variable in interface ngs.Read

## C

clipLeft - Static variable in interface ngs.Alignment
clipRight - Static variable in interface ngs.Alignment

## D

deletion - Static variable in interface ngs.PileupEvent

## E

ErrorMsg - Exception Class in ngs
  A generic NGS error class Holds a message describing what happened
ErrorMsg() - Constructor for exception class ngs.ErrorMsg
ErrorMsg(String) - Constructor for exception class ngs.ErrorMsg
ErrorMsg(ErrorMsg) - Constructor for exception class ngs.ErrorMsg

## F

Fragment - Interface in ngs
  Represents an NGS biological fragment
fragmentIsAligned(int) - Method in interface ngs.Read
  fragmentIsAligned
FragmentIterator - Interface in ngs
  Iterates across a list of Fragments
fullyAligned - Static variable in interface ngs.Read
  ReadCategory

## G

getAlignedFragmentBases() - Method in interface ngs.Alignment
  getAlignedFragmentBases
getAlignment(String) - Method in interface ngs.ReadCollection
  Access a single Alignment by id.
getAlignment(String) - Method in interface ngs.Reference
  getAlignment
getAlignmentBase() - Method in interface ngs.PileupEvent
  getAlignmentBase
getAlignmentCategory() - Method in interface ngs.Alignment
  Alignments are categorized as primary or secondary (alternate).
getAlignmentCount() - Method in interface ngs.ReadCollection
  Count all Alignments within the ReadCollection
getAlignmentCount() - Method in interface ngs.Reference
  Count all Alignments within the Reference
getAlignmentCount(int) - Method in interface ngs.ReadCollection
  Count selected Alignments within the ReadCollection
getAlignmentCount(int) - Method in interface ngs.Reference
  Count selected Alignments within the Reference
getAlignmentId() - Method in interface ngs.Alignment
  Retrieve an identifying String that can be used for later access.
getAlignmentId() - Method in interface ngs.PileupEvent
  getAlignmentId
getAlignmentLength() - Method in interface ngs.Alignment
  Retrieve the projected length of an Alignment projected upon Reference.
getAlignmentPosition() - Method in interface ngs.Alignment
  Retrieve the Alignment's starting position on the Reference
getAlignmentPosition() - Method in interface ngs.PileupEvent
  getAlignmentPosition
getAlignmentQuality() - Method in interface ngs.PileupEvent
  getAlignmentQuality
getAlignmentRange(long, long) - Method in interface ngs.ReadCollection
  getAlignmentRange
getAlignmentRange(long, long, int) - Method in interface ngs.ReadCollection
  getAlignmentRange
getAlignments(int) - Method in interface ngs.ReadCollection
  Select Alignments by AlignmentCategory.
getAlignments(int) - Method in interface ngs.Reference
  getAlignments
getAlignmentSlice(long, long) - Method in interface ngs.Reference
  getAlignmentSlice
getAlignmentSlice(long, long, int) - Method in interface ngs.Reference
  getAlignmentSlice
getAsDouble(String) - Method in interface ngs.Statistics
  getAsDouble
getAsI64(String) - Method in interface ngs.Statistics
  getAsI64
getAsString(String) - Method in interface ngs.Statistics
  getAsString
getAsU64(String) - Method in interface ngs.Statistics
  getAsU64
getCanonicalName() - Method in interface ngs.Reference
  getCanonicalName
getCanonicalName() - Method in interface ngs.ReferenceSequence
  getCanonicalName
getClippedFragmentBases() - Method in interface ngs.Alignment
  getClippedFragmentBases
getClippedFragmentQualities() - Method in interface ngs.Alignment
  getClippedFragmentQualities
getCommonName() - Method in interface ngs.Reference
  getCommonName
getEventIndelType() - Method in interface ngs.PileupEvent
  getEventIndelType
getEventRepeatCount() - Method in interface ngs.PileupEvent
  getEventRepeatCount
getEventType() - Method in interface ngs.PileupEvent
  getEventType
getFilteredAlignmentSlice(long, long, int, int, int) - Method in interface ngs.Reference
  getFilteredAlignmentSlice Behaves like "getAlignmentSlice" except that supported filters are applied to selection
getFilteredPileups(int, int, int) - Method in interface ngs.Reference
  getFilteredPileups Filtered according to criteria in parameters
getFilteredPileupSlice(long, long, int, int, int) - Method in interface ngs.Reference
  getFilteredPileupSlice Creates a PileupIterator on a slice (window) of reference filtered according to criteria in parameters
getFirstAlignmentPosition() - Method in interface ngs.PileupEvent
  getFirstAlignmentPosition
getFragmentBases() - Method in interface ngs.Fragment
  getFragmentBases
getFragmentBases(long) - Method in interface ngs.Fragment
  getFragmentBases
getFragmentBases(long, long) - Method in interface ngs.Fragment
  getFragmentBases
getFragmentId() - Method in interface ngs.Fragment
  getFragmentId
getFragmentQualities() - Method in interface ngs.Fragment
  getFragmentQualities using ASCII offset of 33
getFragmentQualities(long) - Method in interface ngs.Fragment
  getFragmentQualities using ASCII offset of 33
getFragmentQualities(long, long) - Method in interface ngs.Fragment
  getFragmentQualities using ASCII offset of 33
getInitializationError() - Static method in class gov.nih.nlm.ncbi.ngs.NGS
  Returns exception which occurred during initialization If the exception is a subclass of LibraryLoadError, then there was a problem with loading native libraries
getInsertionBases() - Method in interface ngs.PileupEvent
  getInsertionBases
getInsertionQualities() - Method in interface ngs.PileupEvent
  getInsertionQualities
getIsCircular() - Method in interface ngs.Reference
  getIsCircular
getIsCircular() - Method in interface ngs.ReferenceSequence
  getIsCircular
getIsLocal() - Method in interface ngs.Reference
  getIsLocal
getIsReversedOrientation() - Method in interface ngs.Alignment
  Test if orientation is reversed with respect to the Reference sequence.
getLastAlignmentPosition() - Method in interface ngs.PileupEvent
  getLastAlignmentPosition
getLength() - Method in interface ngs.Reference
  getLength
getLength() - Method in interface ngs.ReferenceSequence
  getLength
getLongCigar(boolean) - Method in interface ngs.Alignment
  getLongCigar
getMappingQuality() - Method in interface ngs.Alignment
  getMappingQuality
getMappingQuality() - Method in interface ngs.PileupEvent
  getMappingQuality
getMateAlignment() - Method in interface ngs.Alignment
  getMateAlignment
getMateAlignmentId() - Method in interface ngs.Alignment
  getMateAlignmentId
getMateIsReversedOrientation() - Method in interface ngs.Alignment
  getMateIsReversedOrientation
getMateReferenceSpec() - Method in interface ngs.Alignment
  getMateReferenceSpec
getName() - Method in interface ngs.ReadCollection
  Access the simple name of the ReadCollection.
getName() - Method in interface ngs.ReadGroup
  getName
getNumFragments() - Method in interface ngs.Read
  getNumFragments
getPackageVersion() - Static method in class ngs.Package
getPileupDepth() - Method in interface ngs.Pileup
  getPileupDepth
getPileups(int) - Method in interface ngs.Reference
  getPileups
getPileupSlice(long, long) - Method in interface ngs.Reference
  getPileupSlice Creates a PileupIterator on a slice (window) of reference
getPileupSlice(long, long, int) - Method in interface ngs.Reference
  getPileupSlice Creates a PileupIterator on a slice (window) of reference
getRead(String) - Method in interface ngs.ReadCollection
  getRead
getReadBases() - Method in interface ngs.Read
  getReadBases
getReadBases(long) - Method in interface ngs.Read
  getReadBases
getReadBases(long, long) - Method in interface ngs.Read
  getReadBases
getReadCategory() - Method in interface ngs.Read
  getReadCategory
getReadCount() - Method in interface ngs.ReadCollection
  getReadCount
getReadCount(int) - Method in interface ngs.ReadCollection
  getReadCount
getReadGroup() - Method in interface ngs.Alignment
  getReadGroup
getReadGroup() - Method in interface ngs.Read
  getReadGroup
getReadGroup(String) - Method in interface ngs.ReadCollection
  Access a single ReadGroup by name.
getReadGroups() - Method in interface ngs.ReadCollection
  Access all non-empty ReadGroups.
getReadId() - Method in interface ngs.Alignment
  getReadId
getReadId() - Method in interface ngs.Read
  getReadId
getReadName() - Method in interface ngs.Read
  getReadName
getReadQualities() - Method in interface ngs.Read
  getReadQualities
getReadQualities(long) - Method in interface ngs.Read
  getReadQualities
getReadQualities(long, long) - Method in interface ngs.Read
  getReadQualities
getReadRange(long, long) - Method in interface ngs.ReadCollection
  getReadRange
getReadRange(long, long, int) - Method in interface ngs.ReadCollection
  getReadRange
getReads(int) - Method in interface ngs.ReadCollection
  getReads
getReference(String) - Method in interface ngs.ReadCollection
  Access a single Reference by name spec.
getReferenceBase() - Method in interface ngs.Pileup
getReferenceBases() - Method in interface ngs.Alignment
  getReferenceBases
getReferenceBases(long) - Method in interface ngs.Reference
  getReferenceBases
getReferenceBases(long) - Method in interface ngs.ReferenceSequence
  getReferenceBases
getReferenceBases(long, long) - Method in interface ngs.Reference
  getReferenceBases
getReferenceBases(long, long) - Method in interface ngs.ReferenceSequence
  getReferenceBases
getReferenceChunk(long) - Method in interface ngs.Reference
  getReferenceChunk
getReferenceChunk(long) - Method in interface ngs.ReferenceSequence
  getReferenceChunk
getReferenceChunk(long, long) - Method in interface ngs.Reference
  getReferenceChunk
getReferenceChunk(long, long) - Method in interface ngs.ReferenceSequence
  getReferenceChunk
getReferencePosition() - Method in interface ngs.Pileup
  getReferencePosition
getReferences() - Method in interface ngs.ReadCollection
  Access all References having aligned Reads.
getReferenceSpec() - Method in interface ngs.Alignment
  getReferenceSpec
getReferenceSpec() - Method in interface ngs.Pileup
  getReferenceSpec
getRNAOrientation() - Method in interface ngs.Alignment
  getRNAOrientation
getShortCigar(boolean) - Method in interface ngs.Alignment
  getShortCigar
getSoftClip(int) - Method in interface ngs.Alignment
  getSoftClip
getStatistics() - Method in interface ngs.ReadGroup
  getStatistics
getTemplateLength() - Method in interface ngs.Alignment
  getTemplateLength
getValueType(String) - Method in interface ngs.Statistics
  getValueType
gov.nih.nlm.ncbi.ngs - package gov.nih.nlm.ncbi.ngs

## H

hasMate() - Method in interface ngs.Alignment
  hasMate
hasReadGroup(String) - Method in interface ngs.ReadCollection
hasReference(String) - Method in interface ngs.ReadCollection

## I

insertion - Static variable in interface ngs.PileupEvent
insertion_before_deletion - Static variable in interface ngs.PileupEvent
insertion_before_match - Static variable in interface ngs.PileupEvent
insertion_before_mismatch - Static variable in interface ngs.PileupEvent
int64 - Static variable in interface ngs.Statistics
intron_minus - Static variable in interface ngs.PileupEvent
intron_plus - Static variable in interface ngs.PileupEvent
intron_unknown - Static variable in interface ngs.PileupEvent
isAligned() - Method in interface ngs.Fragment
  check to see if Fragment has alignment data (requires interface 1.1)
isPaired() - Method in interface ngs.Fragment
  isPaired
isSupported() - Static method in class gov.nih.nlm.ncbi.ngs.NGS
  Check to see if NGS SDK is supported by current environment
isValid(String) - Static method in class gov.nih.nlm.ncbi.ngs.NGS
  Check to see if spec string represents an SRA archive

## L

LibDependencies - Class in gov.nih.nlm.ncbi.ngs
LibDependencies() - Constructor for class gov.nih.nlm.ncbi.ngs.LibDependencies

## M

main(String[]) - Static method in class gov.nih.nlm.ncbi.ngs.NGS
match - Static variable in interface ngs.PileupEvent
  EventType
maxMapQuality - Static variable in interface ngs.Alignment
minMapQuality - Static variable in interface ngs.Alignment
mismatch - Static variable in interface ngs.PileupEvent

## N

NCBI_VDB - Static variable in class gov.nih.nlm.ncbi.ngs.LibDependencies
nextAlignment() - Method in interface ngs.AlignmentIterator
  Advance to first alignment on initial invocation Advance to next Alignment subsequently
nextFragment() - Method in interface ngs.FragmentIterator
  Advance to next Fragment
nextPath(String) - Method in interface ngs.Statistics
  nextPath advance to next path in container
nextPileup() - Method in interface ngs.PileupIterator
  Advance to first Pileup on initial invocation advance to next Pileup subsequently
nextPileupEvent() - Method in interface ngs.PileupEventIterator
  Advance to first PileupEvent on initial invocation advance to next PileupEvent subsequently
nextRead() - Method in interface ngs.ReadIterator
  Advance to first Read on initial invocation advance to next Read subsequently
nextReadGroup() - Method in interface ngs.ReadGroupIterator
  Advance to first ReadGroup on initial invocation Advance to next ReadGroup subsequently
nextReference() - Method in interface ngs.ReferenceIterator
  Advance to first Reference on initial invocation Advance to next Reference subsequently
ngs - package ngs
NGS - Class in gov.nih.nlm.ncbi.ngs
NGS() - Constructor for class gov.nih.nlm.ncbi.ngs.NGS
NGS_SDK - Static variable in class gov.nih.nlm.ncbi.ngs.LibDependencies
none - Static variable in interface ngs.Statistics
  ValueType
normal_indel - Static variable in interface ngs.PileupEvent
  EventIndelType
noWraparound - Static variable in interface ngs.Alignment

## O

openReadCollection(String) - Static method in class gov.nih.nlm.ncbi.ngs.NGS
  Create an object representing a named collection of reads
openReferenceSequence(String) - Static method in class gov.nih.nlm.ncbi.ngs.NGS
  Create an object representing a named reference sequence

## P

Package - Class in ngs
  Represents the NGS software package
Package() - Constructor for class ngs.Package
partiallyAligned - Static variable in interface ngs.Read
passDuplicates - Static variable in interface ngs.Alignment
passFailed - Static variable in interface ngs.Alignment
Pileup - Interface in ngs
  Represents a slice through a stack of Alignments at a given position on the Reference
PileupEvent - Interface in ngs
  Represents a single cell of a sparse 2D matrix with Reference coordinates on one axis and stacked Alignments on the other axis
PileupEventIterator - Interface in ngs
  Iterates across a list of PileupEvents
PileupIterator - Interface in ngs
  Iterates across a list of Pileups
primaryAlignment - Static variable in interface ngs.Alignment

## R

Read - Interface in ngs
read_gap - Static variable in interface ngs.PileupEvent
read_overlap - Static variable in interface ngs.PileupEvent
ReadCollection - Interface in ngs
  Represents an NGS-capable object with a collection of Reads, References and Alignments.
ReadGroup - Interface in ngs
  Represents an NGS-capable object with a group of Reads
ReadGroupIterator - Interface in ngs
  Iterates across a list of ReadGroups
ReadIterator - Interface in ngs
real - Static variable in interface ngs.Statistics
Reference - Interface in ngs
  Represents a reference sequence
ReferenceIterator - Interface in ngs
  Iterates across a list of References
ReferenceSequence - Interface in ngs
  Represents a reference sequence standalone object
replacement - Static variable in interface ngs.PileupEvent
resetPileupEvent() - Method in interface ngs.PileupEventIterator
  resets to initial iterator state the next call to "nextPileupEvent" will advance to first event

## S

secondaryAlignment - Static variable in interface ngs.Alignment
setAppVersionString(String) - Static method in class gov.nih.nlm.ncbi.ngs.NGS
  Updates User-Agent header in HTTP communications
startWithinSlice - Static variable in interface ngs.Alignment
Statistics - Interface in ngs
  Statistical data container
string - Static variable in interface ngs.Statistics

## U

uint64 - Static variable in interface ngs.Statistics
unaligned - Static variable in interface ngs.Read

## W

what() - Method in exception class ngs.ErrorMsg

A C D E F G H I L M N O P R S U W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form