Package htsjdk.samtools.reference

Class FastaReferenceWriterBuilder

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 Details

    • FastaReferenceWriterBuilder

      public FastaReferenceWriterBuilder()

  • Method Details

    • 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