htsjdk.samtools.reference

Class FastaReferenceWriterBuilder

java.lang.Object

htsjdk.samtools.reference.FastaReferenceWriterBuilder

public class FastaReferenceWriterBuilder
extends java.lang.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 .

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 and Description
FastaReferenceWriterBuilder()

Method Summary

Modifier and Type	Method and 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(java.nio.file.Path dictFile) Set the output dictionary file to write to.
FastaReferenceWriterBuilder	setDictOutput(java.io.OutputStream dictOutput) Set the output stream for writing the dictionary.
FastaReferenceWriterBuilder	setEmitMd5(boolean emitMd5)
FastaReferenceWriterBuilder	setFastaFile(java.nio.file.Path fastaFile) Set the output fasta file to write to.
FastaReferenceWriterBuilder	setFastaOutput(java.io.OutputStream fastaOutput) Set the output stream for writing the reference.
FastaReferenceWriterBuilder	setGziIndexFile(java.nio.file.Path gziIndexFile) Set the output gzi index file to write to.
FastaReferenceWriterBuilder	setGziIndexOutput(java.io.OutputStream gziIndexOutput) Set the output stream for writing the index.
FastaReferenceWriterBuilder	setIndexFile(java.nio.file.Path faiIndexFile) Set the output fai index file to write to.
FastaReferenceWriterBuilder	setIndexOutput(java.io.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(java.nio.file.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

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(java.nio.file.Path faiIndexFile)

Set the output fai index file to write to.

setGziIndexFile

public FastaReferenceWriterBuilder setGziIndexFile(java.nio.file.Path gziIndexFile)

Set the output gzi index file to write to.

setDictFile

public FastaReferenceWriterBuilder setDictFile(java.nio.file.Path dictFile)

Set the output dictionary file to write to.

setFastaOutput

public FastaReferenceWriterBuilder setFastaOutput(java.io.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(java.io.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(java.io.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(java.io.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 java.io.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:

java.io.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