SamHeaderRecordSq (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.sam.SamHeaderRecord
- - org.snpeff.sam.SamHeaderRecordSq

```
public class SamHeaderRecordSq
extends SamHeaderRecord
```
SQ header: Reference sequence dictionary. The order of @SQ lines defines the alignment sorting order.

Author:

pcingola

Constructor Summary

Constructors
Constructor Description

SamHeaderRecordSq(java.lang.String line)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.lang.String`	`getAssembly()`
`int`	`getLength()`
`java.lang.String`	`getMd5()`
`java.lang.String`	`getSequenceName()`
`java.lang.String`	`getSpecies()`
`java.lang.String`	`getUri()`
`protected void`	`init()`	Initialize records before parsing
`protected void`	`parseField(java.lang.String tag, java.lang.String value)`	Parse a field for this record
`java.lang.String`	`toString()`

Methods inherited from class org.snpeff.sam.SamHeaderRecord
getRecordTypeCode, parse

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

Constructor Detail

SamHeaderRecordSq

public SamHeaderRecordSq(java.lang.String line)

Method Detail

getAssembly
```
public java.lang.String getAssembly()
```

getLength
```
public int getLength()
```

getMd5
```
public java.lang.String getMd5()
```

getSequenceName

public java.lang.String getSequenceName()

getSpecies
```
public java.lang.String getSpecies()
```

getUri
```
public java.lang.String getUri()
```

init
```
protected void init()
```
Description copied from class: SamHeaderRecord

Initialize records before parsing

Overrides:

init in class SamHeaderRecord

parseField
```
protected void parseField(java.lang.String tag,
                          java.lang.String value)
```
Description copied from class: SamHeaderRecord

Parse a field for this record

Specified by:

parseField in class SamHeaderRecord

toString
```
public java.lang.String toString()
```
Overrides:

toString in class java.lang.Object