SequencedFragment (Hadoop-BAM 7.9.1 API)

java.lang.Object
- org.seqdoop.hadoop_bam.SequencedFragment

All Implemented Interfaces:: org.apache.hadoop.io.Writable

public class SequencedFragment
extends Object
implements org.apache.hadoop.io.Writable

Field Summary

Fields
Modifier and Type	Field and Description
`protected Integer`	`controlNumber`
`protected static int`	`ControlNumber_Present`
`protected Boolean`	`filterPassed`
`protected static int`	`FilterPassed_Present`
`protected String`	`flowcellId`
`protected static int`	`FlowcellId_Present`
`protected String`	`indexSequence`
`protected static int`	`IndexSequence_Present`
`protected String`	`instrument`
`protected static int`	`Instrument_Present`
`protected Integer`	`lane`
`protected static int`	`Lane_Present`
`protected org.apache.hadoop.io.Text`	`quality`
`protected Integer`	`read`
`protected static int`	`Read_Present`
`protected Integer`	`runNumber`
`protected static int`	`RunNumber_Present`
`protected org.apache.hadoop.io.Text`	`sequence`
`protected Integer`	`tile`
`protected static int`	`Tile_Present`
`protected Integer`	`xpos`
`protected static int`	`Xpos_Present`
`protected Integer`	`ypos`
`protected static int`	`Ypos_Present`

Constructor Summary

Constructors
Constructor and Description

SequencedFragment()

Constructors
Constructor and Description
`SequencedFragment()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`clear()`
`static void`	`convertQuality(org.apache.hadoop.io.Text quality, FormatConstants.BaseQualityEncoding current, FormatConstants.BaseQualityEncoding target)` Convert quality scores in-place.
`boolean`	`equals(Object other)`
`Integer`	`getControlNumber()`
`Boolean`	`getFilterPassed()`
`String`	`getFlowcellId()`
`String`	`getIndexSequence()`
`String`	`getInstrument()`
`Integer`	`getLane()`
`org.apache.hadoop.io.Text`	`getQuality()` Get quality Text object.
`Integer`	`getRead()`
`Integer`	`getRunNumber()`
`org.apache.hadoop.io.Text`	`getSequence()` Get sequence Text object.
`Integer`	`getTile()`
`Integer`	`getXpos()`
`Integer`	`getYpos()`
`int`	`hashCode()`
`void`	`readFields(DataInput in)`
`void`	`setControlNumber(Integer v)`
`void`	`setFilterPassed(Boolean v)`
`void`	`setFlowcellId(String v)`
`void`	`setIndexSequence(String v)`
`void`	`setInstrument(String v)`
`void`	`setLane(Integer v)`
`void`	`setQuality(org.apache.hadoop.io.Text qual)` Set quality.
`void`	`setRead(Integer v)`
`void`	`setRunNumber(Integer v)`
`void`	`setSequence(org.apache.hadoop.io.Text seq)`
`void`	`setTile(Integer v)`
`void`	`setXpos(Integer v)`
`void`	`setYpos(Integer v)`
`String`	`toString()` Recreates a pseudo qseq record with the fields available.
`static int`	`verifyQuality(org.apache.hadoop.io.Text quality, FormatConstants.BaseQualityEncoding encoding)` Verify that the given quality bytes are within the range allowed for the specified encoding.
`void`	`write(DataOutput out)`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

sequence

protected org.apache.hadoop.io.Text sequence

quality

protected org.apache.hadoop.io.Text quality

instrument
```
protected String instrument
```

runNumber
```
protected Integer runNumber
```

flowcellId
```
protected String flowcellId
```

lane
```
protected Integer lane
```

tile
```
protected Integer tile
```

xpos
```
protected Integer xpos
```

ypos
```
protected Integer ypos
```

read
```
protected Integer read
```

filterPassed
```
protected Boolean filterPassed
```

controlNumber
```
protected Integer controlNumber
```

indexSequence
```
protected String indexSequence
```

Instrument_Present
```
protected static final int Instrument_Present
```
See Also:

Constant Field Values

RunNumber_Present
```
protected static final int RunNumber_Present
```
See Also:

Constant Field Values

FlowcellId_Present
```
protected static final int FlowcellId_Present
```
See Also:

Constant Field Values

Lane_Present
```
protected static final int Lane_Present
```
See Also:

Constant Field Values

Tile_Present
```
protected static final int Tile_Present
```
See Also:

Constant Field Values

Xpos_Present
```
protected static final int Xpos_Present
```
See Also:

Constant Field Values

Ypos_Present
```
protected static final int Ypos_Present
```
See Also:

Constant Field Values

Read_Present
```
protected static final int Read_Present
```
See Also:

Constant Field Values

FilterPassed_Present
```
protected static final int FilterPassed_Present
```
See Also:

Constant Field Values

ControlNumber_Present
```
protected static final int ControlNumber_Present
```
See Also:

Constant Field Values

IndexSequence_Present
```
protected static final int IndexSequence_Present
```
See Also:

Constant Field Values

Constructor Detail
- SequencedFragment
```
public SequencedFragment()
```

Method Detail
- clear
```
public void clear()
```
- getSequence
```
public org.apache.hadoop.io.Text getSequence()
```
  Get sequence Text object. Trade encapsulation for efficiency. Here we expose the internal Text object so that data may be read and written diretly from/to it. Sequence should always be written using CAPITAL letters and 'N' for unknown bases.
- getQuality
```
public org.apache.hadoop.io.Text getQuality()
```
  Get quality Text object. Trade encapsulation for efficiency. Here we expose the internal Text object so that data may be read and written diretly from/to it. Quality should always be in ASCII-encoded Phred+33 format (sanger).
- setInstrument
```
public void setInstrument(String v)
```
- setRunNumber
```
public void setRunNumber(Integer v)
```
- setFlowcellId
```
public void setFlowcellId(String v)
```
- setLane
```
public void setLane(Integer v)
```
- setTile
```
public void setTile(Integer v)
```
- setXpos
```
public void setXpos(Integer v)
```
- setYpos
```
public void setYpos(Integer v)
```
- setRead
```
public void setRead(Integer v)
```
- setFilterPassed
```
public void setFilterPassed(Boolean v)
```
- setControlNumber
```
public void setControlNumber(Integer v)
```
- setIndexSequence
```
public void setIndexSequence(String v)
```
- setSequence
```
public void setSequence(org.apache.hadoop.io.Text seq)
```
- setQuality
```
public void setQuality(org.apache.hadoop.io.Text qual)
```
  Set quality. Quality should be encoded in Sanger Phred+33 format.
- getInstrument
```
public String getInstrument()
```
- getRunNumber
```
public Integer getRunNumber()
```
- getFlowcellId
```
public String getFlowcellId()
```
- getLane
```
public Integer getLane()
```
- getTile
```
public Integer getTile()
```
- getXpos
```
public Integer getXpos()
```
- getYpos
```
public Integer getYpos()
```
- getRead
```
public Integer getRead()
```
- getFilterPassed
```
public Boolean getFilterPassed()
```
- getControlNumber
```
public Integer getControlNumber()
```
- getIndexSequence
```
public String getIndexSequence()
```
- toString
```
public String toString()
```
  Recreates a pseudo qseq record with the fields available.
  
  Overrides:
  
  toString in class Object
- equals
```
public boolean equals(Object other)
```
  Overrides:
  
  equals in class Object
- hashCode
```
public int hashCode()
```
  Overrides:
  
  hashCode in class Object
- convertQuality
```
public static void convertQuality(org.apache.hadoop.io.Text quality,
                                  FormatConstants.BaseQualityEncoding current,
                                  FormatConstants.BaseQualityEncoding target)
```
  Convert quality scores in-place.
  
  Throws:
  
  FormatException - if quality scores are out of the range allowed by the current encoding.
  
  IllegalArgumentException - if current and target quality encodings are the same.
- verifyQuality
```
public static int verifyQuality(org.apache.hadoop.io.Text quality,
                                FormatConstants.BaseQualityEncoding encoding)
```
  Verify that the given quality bytes are within the range allowed for the specified encoding. In theory, the Sanger encoding uses the entire range of characters from ASCII 33 to 126, giving a value range of [0,93]. However, values over 60 are unlikely in practice, and are more likely to be caused by mistaking a file that uses Illumina encoding for Sanger. So, we'll enforce the same range supported by Illumina encoding ([0,62]) for Sanger.
  
  Returns:
  
  -1 if quality is ok.
- readFields
```
public void readFields(DataInput in)
                throws IOException
```
  Specified by:
  
  readFields in interface org.apache.hadoop.io.Writable
  
  Throws:
  
  IOException
- write
```
public void write(DataOutput out)
           throws IOException
```
  Specified by:
  
  write in interface org.apache.hadoop.io.Writable
  
  Throws:
  
  IOException

Class SequencedFragment

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

sequence

quality

instrument

runNumber

flowcellId

lane

tile

xpos

ypos

read

filterPassed

controlNumber

indexSequence

Instrument_Present

RunNumber_Present

FlowcellId_Present

Lane_Present

Tile_Present

Xpos_Present

Ypos_Present

Read_Present

FilterPassed_Present

ControlNumber_Present

IndexSequence_Present

Constructor Detail

SequencedFragment

Method Detail

clear

getSequence

getQuality

setInstrument

setRunNumber

setFlowcellId

setLane

setTile

setXpos

setYpos

setRead

setFilterPassed

setControlNumber

setIndexSequence

setSequence

setQuality

getInstrument

getRunNumber

getFlowcellId

getLane

getTile

getXpos

getYpos

getRead

getFilterPassed

getControlNumber

getIndexSequence

toString

equals

hashCode

convertQuality

verifyQuality

readFields

write