java.lang.Object
- htsjdk.samtools.reference.FastaReferenceWriterBuilder

```
public class FastaReferenceWriterBuilder
extends Object
```
Buider for a FastaReferenceWriter
You can set each of the four outputs (fasta, dictionary and index, both gzi and fai) to a file or a stream. by default if you provide a file to the fasta an accompanying set of indexes and dictionary will be created. This behaviour can be controlled by setMakeDictOutput(boolean) and setMakeFaiOutput(boolean) and setMakeGziOutput(boolean)
The default bases-per-line is 60.
Setting a file or an output stream for any of the four outputs (fasta, fai, gzi or dict) will invalidate the other output type (i.e. setting a file output will invalidate a previous stream and vice-versa).

Constructor Summary

Constructors
Constructor Description

FastaReferenceWriterBuilder()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`FastaReferenceWriter`	`build()`	Create the `FastaReferenceWriter`.
`protected static int`	`checkBasesPerLine(int value)`
`boolean`	`getEmitMd5()`
`FastaReferenceWriterBuilder`	`setBasesPerLine(int basesPerLine)`	Sets the number of bases each line of the fasta file will have.
`FastaReferenceWriterBuilder`	`setDictFile(Path dictFile)`	Set the output dictionary file to write to.
`FastaReferenceWriterBuilder`	`setDictOutput(OutputStream dictOutput)`	Set the output stream for writing the dictionary.
`FastaReferenceWriterBuilder`	`setEmitMd5(boolean emitMd5)`
`FastaReferenceWriterBuilder`	`setFastaFile(Path fastaFile)`	Set the output fasta file to write to.
`FastaReferenceWriterBuilder`	`setFastaOutput(OutputStream fastaOutput)`	Set the output stream for writing the reference.
`FastaReferenceWriterBuilder`	`setGziIndexFile(Path gziIndexFile)`	Set the output gzi index file to write to.
`FastaReferenceWriterBuilder`	`setGziIndexOutput(OutputStream gziIndexOutput)`	Set the output stream for writing the index.
`FastaReferenceWriterBuilder`	`setIndexFile(Path faiIndexFile)`	Set the output fai index file to write to.
`FastaReferenceWriterBuilder`	`setIndexOutput(OutputStream faiIndexOutput)`	Set the output stream for writing the index.
`FastaReferenceWriterBuilder`	`setMakeDictOutput(boolean makeDictOutput)`	Sets whether to automatically generate an dictionary file from the name of the fasta-file (assuming it is given as a file).
`FastaReferenceWriterBuilder`	`setMakeFaiOutput(boolean makeFaiOutput)`	Sets whether to automatically generate an index file from the name of the fasta-file (assuming it is given as a file).
`FastaReferenceWriterBuilder`	`setMakeGziOutput(boolean makeGziOutput)`	Sets whether to automatically generate a gzi index file using an index file name derived from the name of the fasta-file (assuming the fasta file is a valid bgzipped file).

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

- Constructor Detail
  - FastaReferenceWriterBuilder
```
public FastaReferenceWriterBuilder()
```
- Method Detail
  - checkBasesPerLine
```
protected static int checkBasesPerLine(int value)
```
  - setFastaFile
```
public FastaReferenceWriterBuilder setFastaFile(Path fastaFile)
```
    Set the output fasta file to write to. Will automatically write a blockCompressed output for files ending with ".gz" extension. If the index file and output stream are both null and makeFaiOutput is true (default), a default index file will be created as well. If the gzi index file and output stream are both null and makeGziOutput is true (default), a default gzi index file will be created if the output is block compressed. If the dictionary file and output stream are both null and makeDictOutput is true (default), a default dictionary file will be created as well. You can only provide a compressed stream to the fastaOutput, and only in the case that an index isn't written.
    
    Parameters:
    
    fastaFile - a Path to the output fasta file.
    
    Returns:
    
    this builder
  - setMakeFaiOutput
```
public FastaReferenceWriterBuilder setMakeFaiOutput(boolean makeFaiOutput)
```
    Sets whether to automatically generate an index file from the name of the fasta-file (assuming it is given as a file). This can only happen if both the index file and output stream have not been provided.
    
    Parameters:
    
    makeFaiOutput - a boolean flag
    
    Returns:
    
    this builder
  - setMakeDictOutput
```
public FastaReferenceWriterBuilder setMakeDictOutput(boolean makeDictOutput)
```
    Sets whether to automatically generate an dictionary file from the name of the fasta-file (assuming it is given as a file). This can only happen if both the dictionary file and output stream have not been provided.
    
    Parameters:
    
    makeDictOutput - a boolean flag
    
    Returns:
    
    this builder
  - setMakeGziOutput
```
public FastaReferenceWriterBuilder setMakeGziOutput(boolean makeGziOutput)
```
    Sets whether to automatically generate a gzi index file using an index file name derived from the name of the fasta-file (assuming the fasta file is a valid bgzipped file). This can only happen if neither an index file nor an index output stream are provided.
    
    Parameters:
    
    makeGziOutput - a boolean flag
    
    Returns:
    
    this builder
  - setBasesPerLine
```
public FastaReferenceWriterBuilder setBasesPerLine(int basesPerLine)
```
    Sets the number of bases each line of the fasta file will have. the default is 60
    
    Parameters:
    
    basesPerLine - integer (must be positive, validated on build()) indicating the number of bases per line in the output
    
    Returns:
    
    this builder
  - setIndexFile
```
public FastaReferenceWriterBuilder setIndexFile(Path faiIndexFile)
```
    Set the output fai index file to write to.
  - setGziIndexFile
```
public FastaReferenceWriterBuilder setGziIndexFile(Path gziIndexFile)
```
    Set the output gzi index file to write to.
  - setDictFile
```
public FastaReferenceWriterBuilder setDictFile(Path dictFile)
```
    Set the output dictionary file to write to.
  - setFastaOutput
```
public FastaReferenceWriterBuilder setFastaOutput(OutputStream fastaOutput)
```
    Set the output stream for writing the reference. Doesn't support compressed streams.
    NOTE: If you would like to output a BlockCompressed fasta file it is recommended you use setFastaFile(Path) as that codepath will handle generation of a gzi index automatically.
    
    Parameters:
    
    fastaOutput - a OutputStream for the output fasta file.
    
    Returns:
    
    this builder
  - setIndexOutput
```
public FastaReferenceWriterBuilder setIndexOutput(OutputStream faiIndexOutput)
```
    Set the output stream for writing the index.
    
    Parameters:
    
    faiIndexOutput - a OutputStream for the output index. Doesn't support compressed streams.
    
    Returns:
    
    this builder
  - setGziIndexOutput
```
public FastaReferenceWriterBuilder setGziIndexOutput(OutputStream gziIndexOutput)
```
    Set the output stream for writing the index.
    
    Parameters:
    
    gziIndexOutput - a OutputStream for the gzi output index. Doesn't support compressed streams.
    
    Returns:
    
    this builder
  - setDictOutput
```
public FastaReferenceWriterBuilder setDictOutput(OutputStream dictOutput)
```
    Set the output stream for writing the dictionary.
    
    Parameters:
    
    dictOutput - a OutputStream for the output dictionary. Doesn't support compressed streams.
    
    Returns:
    
    this builder
  - build
```
public FastaReferenceWriter build()
                           throws IOException
```
    Create the FastaReferenceWriter. This is were all the validations happen:
  - -One of fastaFile and fastaOutput must be non-null.
  - -the number of bases-per-line must be positive

Returns:: a FastaReferenceWriter
Throws:: IOException - if trouble opening files

getEmitMd5
```
public boolean getEmitMd5()
```
Returns:

whether the reference builder will emit M5 tag in the header lines

setEmitMd5
```
public FastaReferenceWriterBuilder setEmitMd5(boolean emitMd5)
```
Parameters:

emitMd5 - whether the reference builder will emit the M5 tag in the header line * (and populate it with the md5 digest of the sequence)

Returns:

this builder

Class FastaReferenceWriterBuilder

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FastaReferenceWriterBuilder

Method Detail

checkBasesPerLine

setFastaFile

setMakeFaiOutput

setMakeDictOutput

setMakeGziOutput

setBasesPerLine

setIndexFile

setGziIndexFile

setDictFile

setFastaOutput

setIndexOutput

setGziIndexOutput

setDictOutput

build

getEmitMd5

setEmitMd5