Package ngs
Interface Read
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- All Superinterfaces:
Fragment
,FragmentIterator
- All Known Subinterfaces:
ReadIterator
public interface Read extends FragmentIterator
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Field Summary
Fields Modifier and Type Field Description static int
aligned
static int
all
static int
fullyAligned
ReadCategorystatic int
partiallyAligned
static int
unaligned
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description boolean
fragmentIsAligned(int fragIdx)
fragmentIsAlignedint
getNumFragments()
getNumFragmentsjava.lang.String
getReadBases()
getReadBasesjava.lang.String
getReadBases(long offset)
getReadBasesjava.lang.String
getReadBases(long offset, long length)
getReadBasesint
getReadCategory()
getReadCategoryjava.lang.String
getReadGroup()
getReadGroupjava.lang.String
getReadId()
getReadIdjava.lang.String
getReadName()
getReadNamejava.lang.String
getReadQualities()
getReadQualitiesjava.lang.String
getReadQualities(long offset)
getReadQualitiesjava.lang.String
getReadQualities(long offset, long length)
getReadQualities-
Methods inherited from interface ngs.Fragment
getFragmentBases, getFragmentBases, getFragmentBases, getFragmentId, getFragmentQualities, getFragmentQualities, getFragmentQualities, isAligned, isPaired
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Methods inherited from interface ngs.FragmentIterator
nextFragment
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Field Detail
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fullyAligned
static final int fullyAligned
ReadCategory- See Also:
- Constant Field Values
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partiallyAligned
static final int partiallyAligned
- See Also:
- Constant Field Values
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aligned
static final int aligned
- See Also:
- Constant Field Values
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unaligned
static final int unaligned
- See Also:
- Constant Field Values
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all
static final int all
- See Also:
- Constant Field Values
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Method Detail
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getReadId
java.lang.String getReadId() throws ErrorMsg
getReadId- Returns:
- the ID-String of the Read
- Throws:
ErrorMsg
- upon an error accessing data
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getNumFragments
int getNumFragments() throws ErrorMsg
getNumFragments- Returns:
- the number of biological Fragments contained in the read
- Throws:
ErrorMsg
- upon an error accessing data
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fragmentIsAligned
boolean fragmentIsAligned(int fragIdx) throws ErrorMsg
fragmentIsAligned- Parameters:
fragIdx
- is a zero-based and non-negative fragment index- Returns:
- true if a fragment is aligned
- Throws:
ErrorMsg
- upon an error accessing data
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getReadCategory
int getReadCategory() throws ErrorMsg
getReadCategory- Returns:
- the category of the read
- Throws:
ErrorMsg
- upon an error accessing data
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getReadGroup
java.lang.String getReadGroup() throws ErrorMsg
getReadGroup- Returns:
- the read-group of the read
- Throws:
ErrorMsg
- upon an error accessing data
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getReadName
java.lang.String getReadName() throws ErrorMsg
getReadName- Returns:
- the name of thethe read
- Throws:
ErrorMsg
- upon an error accessing data
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getReadBases
java.lang.String getReadBases() throws ErrorMsg
getReadBases- Returns:
- sequence bases
- Throws:
ErrorMsg
- upon an error accessing data
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getReadBases
java.lang.String getReadBases(long offset) throws ErrorMsg, java.lang.IndexOutOfBoundsException
getReadBases- Parameters:
offset
- is zero-based and non-negative- Returns:
- sequence bases
- Throws:
ErrorMsg
- upon an error accessing datajava.lang.IndexOutOfBoundsException
- if offset is invalid
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getReadBases
java.lang.String getReadBases(long offset, long length) throws ErrorMsg, java.lang.IndexOutOfBoundsException
getReadBases- Parameters:
offset
- is zero-based and non-negativelength
- must be ≥ 0- Returns:
- sequence bases
- Throws:
ErrorMsg
- upon an error accessing datajava.lang.IndexOutOfBoundsException
- if offset/length are invalid
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getReadQualities
java.lang.String getReadQualities() throws ErrorMsg
getReadQualities- Returns:
- phred quality values using ASCII offset of 33
- Throws:
ErrorMsg
- upon an error accessing data
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getReadQualities
java.lang.String getReadQualities(long offset) throws ErrorMsg, java.lang.IndexOutOfBoundsException
getReadQualities- Parameters:
offset
- is zero-based and non-negative- Returns:
- phred quality values using ASCII offset of 33
- Throws:
ErrorMsg
- upon an error accessing datajava.lang.IndexOutOfBoundsException
- if offset is invalid
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getReadQualities
java.lang.String getReadQualities(long offset, long length) throws ErrorMsg, java.lang.IndexOutOfBoundsException
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 datajava.lang.IndexOutOfBoundsException
- if offset/length are invalid
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