Package ngs
Interface Fragment
- All Known Subinterfaces:
Alignment
,AlignmentIterator
,FragmentIterator
,Read
,ReadIterator
public interface Fragment
Represents an NGS biological fragment
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Method Summary
Modifier and TypeMethodDescriptiongetFragmentBasesgetFragmentBases
(long offset) getFragmentBasesgetFragmentBases
(long offset, long length) getFragmentBasesgetFragmentIdgetFragmentQualities using ASCII offset of 33getFragmentQualities
(long offset) getFragmentQualities using ASCII offset of 33getFragmentQualities
(long offset, long length) getFragmentQualities using ASCII offset of 33boolean
check to see if Fragment has alignment data (requires interface 1.1)boolean
isPaired()
isPaired
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Method Details
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getFragmentId
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getFragmentBases
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getFragmentBases
getFragmentBases- Parameters:
offset
- is zero-based and non-negative- Returns:
- sequence bases
- Throws:
ErrorMsg
- upon an error accessing dataIndexOutOfBoundsException
- upon invalid offset
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getFragmentBases
getFragmentBases- Parameters:
offset
- is zero-based and non-negativelength
- must be ≥ 0- Returns:
- sequence bases
- Throws:
ErrorMsg
- upon an error accessing dataIndexOutOfBoundsException
- upon invalid offset
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getFragmentQualities
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getFragmentQualities
getFragmentQualities using ASCII offset of 33- Parameters:
offset
- is zero-based and non-negative- Returns:
- phred quality values
- Throws:
ErrorMsg
- upon an error accessing dataIndexOutOfBoundsException
- upon invalid offset
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getFragmentQualities
getFragmentQualities using ASCII offset of 33- Parameters:
offset
- is zero-based and non-negativelength
- must be ≥ 0- Returns:
- phred quality values
- Throws:
ErrorMsg
- upon an error accessing dataIndexOutOfBoundsException
- upon invalid offset/length
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isPaired
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isAligned
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