org.disq_bio.disq

Class HtsjdkReadsRddStorage

java.lang.Object

org.disq_bio.disq.HtsjdkReadsRddStorage

public class HtsjdkReadsRddStorage
extends Object

The entry point for reading or writing a HtsjdkReadsRdd.

Method Summary

Modifier and Type	Method and Description
static HtsjdkReadsRddStorage	makeDefault(org.apache.spark.api.java.JavaSparkContext sparkContext) Create a HtsjdkReadsRddStorage from a Spark context object.
HtsjdkReadsRdd	read(String path) Read reads from the given path.
<T extends htsjdk.samtools.util.Locatable> HtsjdkReadsRdd	read(String path, HtsjdkReadsTraversalParameters<T> traversalParameters) Read reads from the given path, using the given traversal parameters to filter the reads.
HtsjdkReadsRddStorage	referenceSourcePath(String referenceSourcePath)
HtsjdkReadsRddStorage	sbiIndexGranularity(long sbiIndexGranularity)
HtsjdkReadsRddStorage	splitSize(int splitSize)
HtsjdkReadsRddStorage	useNio(boolean useNio)
HtsjdkReadsRddStorage	validationStringency(htsjdk.samtools.ValidationStringency validationStringency)
void	write(HtsjdkReadsRdd htsjdkReadsRdd, String path, WriteOption... writeOptions) Write reads 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 HtsjdkReadsRddStorage makeDefault(org.apache.spark.api.java.JavaSparkContext sparkContext)

Create a HtsjdkReadsRddStorage from a Spark context object.

Parameters:

sparkContext - the Spark context to use

Returns:

a HtsjdkReadsRddStorage

splitSize

public HtsjdkReadsRddStorage splitSize(int splitSize)

Parameters:

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

Returns:

the current HtsjdkReadsRddStorage

validationStringency

public HtsjdkReadsRddStorage validationStringency(htsjdk.samtools.ValidationStringency validationStringency)

Parameters:

validationStringency - the validation stringency for reading

Returns:

the current HtsjdkReadsRddStorage

useNio

public HtsjdkReadsRddStorage useNio(boolean useNio)

Parameters:

useNio - whether to use NIO or the Hadoop filesystem (default) for file operations

Returns:

the current HtsjdkReadsRddStorage

referenceSourcePath

public HtsjdkReadsRddStorage referenceSourcePath(String referenceSourcePath)

Parameters:

referenceSourcePath - path to the reference; only required when reading CRAM.

Returns:

the current HtsjdkReadsRddStorage

sbiIndexGranularity

public HtsjdkReadsRddStorage sbiIndexGranularity(long sbiIndexGranularity)

Parameters:

sbiIndexGranularity - the granularity to use when writing SBI index files; only used when writing single BAM files.

Returns:

the current HtsjdkReadsRddStorage

read

public HtsjdkReadsRdd read(String path)
                    throws IOException

Read reads from the given path. The input files may be in any format (BAM/CRAM/SAM).

Parameters:

path - the file or directory to read from

Returns:

a HtsjdkReadsRdd that allows access to the reads

Throws:

IOException - if an IO error occurs while determining the format of the files and reading the header

read

public <T extends htsjdk.samtools.util.Locatable> HtsjdkReadsRdd read(String path,
                                                                      HtsjdkReadsTraversalParameters<T> traversalParameters)
                                                               throws IOException

Read reads from the given path, using the given traversal parameters to filter the reads. The input files may be in any format (BAM/CRAM/SAM).

Type Parameters:

T - the type of Locatable for specifying intervals

Parameters:

path - the file or directory to read from

traversalParameters - parameters that determine which reads should be returned, allows filtering by interval

Returns:

a HtsjdkReadsRdd that allows access to the reads

Throws:

IOException - if an IO error occurs while determining the format of the files

write

public void write(HtsjdkReadsRdd htsjdkReadsRdd,
                  String path,
                  WriteOption... writeOptions)
           throws IOException

Write reads to a file or files specified by the given path. Write options may be specified to control the format to write in (BAM/CRAM/SAM, if not clear from the path extension), and the number of files to write (single vs. multiple).

Parameters:

htsjdkReadsRdd - a HtsjdkReadsRdd containing the header and the reads

path - the file or directory to write to

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

Throws:

IOException - if an IO error occurs while writing