Package | Description |
---|---|
htsjdk.variant.variantcontext.writer |
Modifier and Type | Method and Description |
---|---|
VariantContextWriterBuilder |
VariantContextWriterBuilder.clearIndexCreator()
Do not pass an
IndexCreator to the next VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.clearOptions()
Remove all options from the set of
Options for the VariantContextWriterBuilder . |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setBuffer(int bufferSize)
Set a buffer size for the file output stream passed to the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setCreateMD5()
Create an MD5 digest file for the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setCreateMD5(boolean createMD5)
Choose whether to also create an MD5 digest file for the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setIndexCreator(IndexCreator idxCreator)
Set an IndexCreator for the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setOption(Options option)
Add one option to the set of
Options for the VariantContextWriterBuilder , if it's not already present. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setOptions(EnumSet<Options> options)
Replace the set of
Options for the VariantContextWriterBuilder with a new set. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setOutputBCFStream(OutputStream outStream)
Set the output BCF stream for the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setOutputFile(File outFile)
Set the output file for the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setOutputFile(String outFile)
Set the output file for the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setOutputFileType(VariantContextWriterBuilder.OutputType outType)
Set the output file type for the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setOutputStream(OutputStream outStream)
Set the output stream (VCF, by default) for the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setOutputVCFStream(OutputStream outStream)
Set the output VCF stream for the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.setReferenceDictionary(SAMSequenceDictionary refDict)
Set the reference dictionary to be used by
VariantContextWriter s created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.unsetBuffering()
Do not use buffering in the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.unsetCreateMD5()
Don't create an MD5 digest file for the next
VariantContextWriter created by this builder. |
VariantContextWriterBuilder |
VariantContextWriterBuilder.unsetOption(Options option)
Remove one option from the set of
Options for the VariantContextWriterBuilder , if it's present. |