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