Package ngs

# Interface Fragment

All Known Subinterfaces:
  `Alignment`, `AlignmentIterator`, `FragmentIterator`, `Read`, `ReadIterator`

public interface Fragment
Represents an NGS biological fragment

## Method Summary

Modifier and Type
Method
Description
`String`
`getFragmentBases()`
getFragmentBases
`String`
`getFragmentBases(long offset)`
getFragmentBases
`String`
`getFragmentBases(long offset, long length)`
getFragmentBases
`String`
`getFragmentId()`
getFragmentId
`String`
`getFragmentQualities()`
getFragmentQualities using ASCII offset of 33
`String`
`getFragmentQualities(long offset)`
getFragmentQualities using ASCII offset of 33
`String`
`getFragmentQualities(long offset, long length)`
getFragmentQualities using ASCII offset of 33
`boolean`
`isAligned()`
check to see if Fragment has alignment data (requires interface 1.1)
`boolean`
`isPaired()`
isPaired

## Method Details

### getFragmentId

String getFragmentId() throws ErrorMsg
getFragmentId

Returns:
  the unique ID of the fragment
Throws:
  `ErrorMsg` - upon an error accessing data

### getFragmentBases

String getFragmentBases() throws ErrorMsg
getFragmentBases

Returns:
  sequence bases
Throws:
  `ErrorMsg` - upon an error accessing data

### getFragmentBases

String getFragmentBases(long offset) throws ErrorMsg, IndexOutOfBoundsException
getFragmentBases

Parameters:
  `offset` - is zero-based and non-negative
Returns:
  sequence bases
Throws:
  `ErrorMsg` - upon an error accessing data
  `IndexOutOfBoundsException` - upon invalid offset

### getFragmentBases

String getFragmentBases(long offset, long length) throws ErrorMsg, IndexOutOfBoundsException
getFragmentBases

Parameters:
  `offset` - is zero-based and non-negative
  `length` - must be ≥ 0
Returns:
  sequence bases
Throws:
  `ErrorMsg` - upon an error accessing data
  `IndexOutOfBoundsException` - upon invalid offset

### getFragmentQualities

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

### getFragmentQualities

String getFragmentQualities(long offset) throws ErrorMsg, 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 data
  `IndexOutOfBoundsException` - upon invalid offset

### getFragmentQualities

String getFragmentQualities(long offset, long length) throws ErrorMsg, IndexOutOfBoundsException
getFragmentQualities using ASCII offset of 33

Parameters:
  `offset` - is zero-based and non-negative
  `length` - must be ≥ 0
Returns:
  phred quality values
Throws:
  `ErrorMsg` - upon an error accessing data
  `IndexOutOfBoundsException` - upon invalid offset/length

### isPaired

boolean isPaired() throws ErrorMsg
isPaired

Returns:
  true if fragment has a mate
Throws:
  `ErrorMsg` - upon an error accessing data

### isAligned

boolean isAligned() throws ErrorMsg
check to see if Fragment has alignment data (requires interface 1.1)

Returns:
  true if Fragment is aligned
Throws:
  `ErrorMsg` - if object is invalid or implementation too old