org.disq_bio.disq

Class HtsjdkVariantsRddStorage

java.lang.Object

org.disq_bio.disq.HtsjdkVariantsRddStorage

public class HtsjdkVariantsRddStorage
extends Object

The entry point for reading or writing a HtsjdkVariantsRdd.

Method Summary

Modifier and Type	Method and Description
static HtsjdkVariantsRddStorage	makeDefault(org.apache.spark.api.java.JavaSparkContext sparkContext) Create a HtsjdkVariantsRddStorage from a Spark context object.
HtsjdkVariantsRdd	read(String path) Read variants from the given path.
<T extends htsjdk.samtools.util.Locatable> HtsjdkVariantsRdd	read(String path, List<T> intervals) Read variants from the given path, using the given intervals to filter the variants.
HtsjdkVariantsRddStorage	splitSize(int splitSize)
void	write(HtsjdkVariantsRdd htsjdkVariantsRdd, String path, WriteOption... writeOptions) Write variants to a file or files specified by the given path.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

makeDefault

public static HtsjdkVariantsRddStorage makeDefault(org.apache.spark.api.java.JavaSparkContext sparkContext)

Create a HtsjdkVariantsRddStorage from a Spark context object.

Parameters:

sparkContext - the Spark context to use

Returns:

a HtsjdkVariantsRddStorage

splitSize

public HtsjdkVariantsRddStorage splitSize(int splitSize)

Parameters:

splitSize - the requested size of file splits in bytes when reading

Returns:

the current HtsjdkVariantsRddStorage

read

public HtsjdkVariantsRdd read(String path)
                       throws IOException

Read variants from the given path. The input files must be VCF format, optionally compressed.

Parameters:

path - the file or directory to read from

Returns:

a HtsjdkVariantsRdd that allows access to the variants

Throws:

IOException - if an IO error occurs while reading the header

read

public <T extends htsjdk.samtools.util.Locatable> HtsjdkVariantsRdd read(String path,
                                                                         List<T> intervals)
                                                                  throws IOException

Read variants from the given path, using the given intervals to filter the variants. The input files must be VCF format, optionally compressed.

Type Parameters:

T - the type of Locatable for specifying intervals

Parameters:

path - the file or directory to read from

intervals - intervals to filter variants by

Returns:

a HtsjdkVariantsRdd that allows access to the variants

Throws:

IOException - if an IO error occurs while reading the header

write

public void write(HtsjdkVariantsRdd htsjdkVariantsRdd,
                  String path,
                  WriteOption... writeOptions)
           throws IOException

Write variants to a file or files specified by the given path. Write options may be specified to control the format and compression options to use (if not clear from the path extension), and the number of files to write (single vs. multiple).

Parameters:

htsjdkVariantsRdd - a HtsjdkVariantsRdd containing the header and the variants

path - the file or directory to write to

writeOptions - options to control aspects of how to write the variants (e.g. VariantsFormatWriteOption and FileCardinalityWriteOption

Throws:

IOException - if an IO error occurs while writing