htsjdk.samtools

Class Defaults

java.lang.Object

htsjdk.samtools.Defaults

public class Defaults
extends java.lang.Object

Embodies defaults for global values that affect how the SAM JDK operates. Defaults are encoded in the class and are also overridable using system properties.

Field Summary

Fields

Modifier and Type	Field and Description
static int	BUFFER_SIZE Buffer size, in bytes, used whenever reading/writing files or streams.
static int	COMPRESSION_LEVEL Compresion level to be used for writing BAM and other block-compressed outputs.
static boolean	CREATE_INDEX Should BAM index files be created when writing out coordinate sorted BAM files? Default = false.
static boolean	CREATE_MD5 Should MD5 files be created when writing out SAM and BAM files? Default = false.
static java.lang.String	CUSTOM_READER_FACTORY Custom reader factory able to handle URL based resources like ga4gh.
static java.lang.String	EBI_REFERENCE_SEVICE_URL_MASK A mask (pattern) to use when building EBI reference service URL for a given MD5 checksum.
static java.lang.String	INTEL_DEFLATER_SHARED_LIBRARY_PATH Path to libIntelDeflater.so.
static int	NON_ZERO_BUFFER_SIZE Even if BUFFER_SIZE is 0, this is guaranteed to be non-zero.
static java.io.File	REFERENCE_FASTA The reference FASTA file.
static boolean	TRY_USE_INTEL_DEFLATER Should BlockCompressedOutputStream attempt to load libIntelDeflater?
static boolean	USE_ASYNC_IO Should asynchronous I/O be used when writing out SAM and BAM files (one thread per file).
static boolean	USE_CRAM_REF_DOWNLOAD Boolean describing whether downloading a reference file is allowed (for CRAM files), in case the reference file is not specified by the user Enabling this is not necessarily a good idea, since this process often fails

Constructor Summary

Constructors

Constructor and Description
Defaults()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

CREATE_INDEX

public static final boolean CREATE_INDEX

Should BAM index files be created when writing out coordinate sorted BAM files? Default = false.

CREATE_MD5

public static final boolean CREATE_MD5

Should MD5 files be created when writing out SAM and BAM files? Default = false.

USE_ASYNC_IO

public static final boolean USE_ASYNC_IO

Should asynchronous I/O be used when writing out SAM and BAM files (one thread per file). Default = false.

COMPRESSION_LEVEL

public static final int COMPRESSION_LEVEL

Compresion level to be used for writing BAM and other block-compressed outputs. Default = 5.

BUFFER_SIZE

public static final int BUFFER_SIZE

Buffer size, in bytes, used whenever reading/writing files or streams. Default = 128k.

NON_ZERO_BUFFER_SIZE

public static final int NON_ZERO_BUFFER_SIZE

Even if BUFFER_SIZE is 0, this is guaranteed to be non-zero. If BUFFER_SIZE is non-zero, this == BUFFER_SIZE

TRY_USE_INTEL_DEFLATER

public static final boolean TRY_USE_INTEL_DEFLATER

Should BlockCompressedOutputStream attempt to load libIntelDeflater?

INTEL_DEFLATER_SHARED_LIBRARY_PATH

public static final java.lang.String INTEL_DEFLATER_SHARED_LIBRARY_PATH

Path to libIntelDeflater.so. If this is not set, the library is looked for in the directory where the executable jar lives.

REFERENCE_FASTA

public static final java.io.File REFERENCE_FASTA

The reference FASTA file. If this is not set, the file is null. This file may be required for reading writing SAM files (ex. CRAM).

CUSTOM_READER_FACTORY

public static final java.lang.String CUSTOM_READER_FACTORY

Custom reader factory able to handle URL based resources like ga4gh. Expected format: ,[,] E.g. https://www.googleapis.com/genomics/v1beta/reads/,com.google.genomics.ReaderFactory OR https://www.googleapis.com/genomics/v1beta/reads/,com.google.genomics.ReaderFactory,/tmp/genomics.jar

USE_CRAM_REF_DOWNLOAD

public static final boolean USE_CRAM_REF_DOWNLOAD

Boolean describing whether downloading a reference file is allowed (for CRAM files), in case the reference file is not specified by the user Enabling this is not necessarily a good idea, since this process often fails

EBI_REFERENCE_SEVICE_URL_MASK

public static final java.lang.String EBI_REFERENCE_SEVICE_URL_MASK

A mask (pattern) to use when building EBI reference service URL for a given MD5 checksum. Must contain one and only one string placeholder.

Constructor Detail

Defaults

public Defaults()