Interface Read
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final int
ReadCategorystatic final int
static final int
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Method Summary
Modifier and TypeMethodDescriptionboolean
fragmentIsAligned
(int fragIdx) fragmentIsAlignedint
getNumFragmentsgetReadBasesgetReadBases
(long offset) getReadBasesgetReadBases
(long offset, long length) getReadBasesint
getReadCategorygetReadGroupgetReadIdgetReadNamegetReadQualitiesgetReadQualities
(long offset) getReadQualitiesgetReadQualities
(long offset, long length) getReadQualitiesMethods inherited from interface ngs.Fragment
getFragmentBases, getFragmentBases, getFragmentBases, getFragmentId, getFragmentQualities, getFragmentQualities, getFragmentQualities, isAligned, isPaired
Methods inherited from interface ngs.FragmentIterator
nextFragment
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Field Details
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fullyAligned
static final int fullyAlignedReadCategory- See Also:
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partiallyAligned
static final int partiallyAligned- See Also:
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aligned
static final int aligned- See Also:
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unaligned
static final int unaligned- See Also:
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all
static final int all- See Also:
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Method Details
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getReadId
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getNumFragments
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fragmentIsAligned
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getReadCategory
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getReadGroup
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getReadName
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getReadBases
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getReadBases
getReadBases- Parameters:
offset
- is zero-based and non-negative- Returns:
- sequence bases
- Throws:
ErrorMsg
- upon an error accessing dataIndexOutOfBoundsException
- if offset is invalid
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getReadBases
getReadBases- Parameters:
offset
- is zero-based and non-negativelength
- must be ≥ 0- Returns:
- sequence bases
- Throws:
ErrorMsg
- upon an error accessing dataIndexOutOfBoundsException
- if offset/length are invalid
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getReadQualities
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getReadQualities
getReadQualities- Parameters:
offset
- is zero-based and non-negative- Returns:
- phred quality values using ASCII offset of 33
- Throws:
ErrorMsg
- upon an error accessing dataIndexOutOfBoundsException
- if offset is invalid
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getReadQualities
getReadQualities- Parameters:
offset
- is zero-based and non-negativelength
- must be ≥ 0- Returns:
- phred quality values using ASCII offset of 33
- Throws:
ErrorMsg
- upon an error accessing dataIndexOutOfBoundsException
- if offset/length are invalid
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