Package ngs
Interface Fragment
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- All Known Subinterfaces:
Alignment
,AlignmentIterator
,FragmentIterator
,Read
,ReadIterator
public interface Fragment
Represents an NGS biological fragment
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.String
getFragmentBases()
getFragmentBasesjava.lang.String
getFragmentBases(long offset)
getFragmentBasesjava.lang.String
getFragmentBases(long offset, long length)
getFragmentBasesjava.lang.String
getFragmentId()
getFragmentIdjava.lang.String
getFragmentQualities()
getFragmentQualities using ASCII offset of 33java.lang.String
getFragmentQualities(long offset)
getFragmentQualities using ASCII offset of 33java.lang.String
getFragmentQualities(long offset, long length)
getFragmentQualities using ASCII offset of 33boolean
isAligned()
check to see if Fragment has alignment data (requires interface 1.1)boolean
isPaired()
isPaired
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Method Detail
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getFragmentId
java.lang.String getFragmentId() throws ErrorMsg
getFragmentId- Returns:
- the unique ID of the fragment
- Throws:
ErrorMsg
- upon an error accessing data
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getFragmentBases
java.lang.String getFragmentBases() throws ErrorMsg
getFragmentBases- Returns:
- sequence bases
- Throws:
ErrorMsg
- upon an error accessing data
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getFragmentBases
java.lang.String getFragmentBases(long offset) throws ErrorMsg, java.lang.IndexOutOfBoundsException
getFragmentBases- Parameters:
offset
- is zero-based and non-negative- Returns:
- sequence bases
- Throws:
ErrorMsg
- upon an error accessing datajava.lang.IndexOutOfBoundsException
- upon invalid offset
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getFragmentBases
java.lang.String getFragmentBases(long offset, long length) throws ErrorMsg, java.lang.IndexOutOfBoundsException
getFragmentBases- Parameters:
offset
- is zero-based and non-negativelength
- must be ≥ 0- Returns:
- sequence bases
- Throws:
ErrorMsg
- upon an error accessing datajava.lang.IndexOutOfBoundsException
- upon invalid offset
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getFragmentQualities
java.lang.String getFragmentQualities() throws ErrorMsg
getFragmentQualities using ASCII offset of 33- Returns:
- phred quality values for the whole fragment
- Throws:
ErrorMsg
- upon an error accessing data
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getFragmentQualities
java.lang.String getFragmentQualities(long offset) throws ErrorMsg, java.lang.IndexOutOfBoundsException
getFragmentQualities using ASCII offset of 33- Parameters:
offset
- is zero-based and non-negative- Returns:
- phred quality values
- Throws:
ErrorMsg
- upon an error accessing datajava.lang.IndexOutOfBoundsException
- upon invalid offset
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getFragmentQualities
java.lang.String getFragmentQualities(long offset, long length) throws ErrorMsg, java.lang.IndexOutOfBoundsException
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 datajava.lang.IndexOutOfBoundsException
- upon invalid offset/length
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isPaired
boolean isPaired() throws ErrorMsg
isPaired- Returns:
- true if fragment has a mate
- Throws:
ErrorMsg
- upon an error accessing data
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