Package ngs
Interface Read
- All Superinterfaces:
Fragment,FragmentIterator
- All Known Subinterfaces:
ReadIterator
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final intstatic final intstatic final intReadCategorystatic final intstatic final int -
Method Summary
Modifier and TypeMethodDescriptionbooleanfragmentIsAligned(int fragIdx) fragmentIsAlignedintgetNumFragmentsgetReadBasesgetReadBases(long offset) getReadBasesgetReadBases(long offset, long length) getReadBasesintgetReadCategorygetReadGroupgetReadIdgetReadNamegetReadQualitiesgetReadQualities(long offset) getReadQualitiesgetReadQualities(long offset, long length) getReadQualitiesMethods inherited from interface ngs.Fragment
getFragmentBases, getFragmentBases, getFragmentBases, getFragmentId, getFragmentQualities, getFragmentQualities, getFragmentQualities, isAligned, isPairedMethods inherited from interface ngs.FragmentIterator
nextFragment
-
Field Details
-
fullyAligned
static final int fullyAlignedReadCategory- See Also:
-
partiallyAligned
static final int partiallyAligned- See Also:
-
aligned
static final int aligned- See Also:
-
unaligned
static final int unaligned- See Also:
-
all
static final int all- See Also:
-
-
Method Details
-
getReadId
getReadId- Returns:
- the ID-String of the Read
- Throws:
ErrorMsg- upon an error accessing data
-
getNumFragments
getNumFragments- Returns:
- the number of biological Fragments contained in the read
- Throws:
ErrorMsg- upon an error accessing data
-
fragmentIsAligned
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
-
getReadCategory
getReadCategory- Returns:
- the category of the read
- Throws:
ErrorMsg- upon an error accessing data
-
getReadGroup
getReadGroup- Returns:
- the read-group of the read
- Throws:
ErrorMsg- upon an error accessing data
-
getReadName
getReadName- Returns:
- the name of thethe read
- Throws:
ErrorMsg- upon an error accessing data
-
getReadBases
getReadBases- Returns:
- sequence bases
- Throws:
ErrorMsg- upon an error accessing data
-
getReadBases
getReadBases- Parameters:
offset- is zero-based and non-negative- Returns:
- sequence bases
- Throws:
ErrorMsg- upon an error accessing dataIndexOutOfBoundsException- if offset is invalid
-
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
-
getReadQualities
getReadQualities- Returns:
- phred quality values using ASCII offset of 33
- Throws:
ErrorMsg- upon an error accessing data
-
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
-
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
-