Package htsjdk.samtools
Class Defaults
- java.lang.Object
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- htsjdk.samtools.Defaults
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public class Defaults extends 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.
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Field Summary
Fields Modifier and Type Field Description static int
BUFFER_SIZE
Buffer size, in bytes, used whenever reading/writing files or streams.static int
COMPRESSION_LEVEL
Compression 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 String
CUSTOM_READER_FACTORY
Custom reader factory able to handle URL based resources like ga4gh.static String
DEFAULT_SAM_EXTENSION
The extension to assume a sam file has when the actual file doesn't have an extension, useful for when outputing to /dev/stdout, for example.static String
DEFAULT_VCF_EXTENSION
The extension to assume a vcf has when the actual file doesn't have an extension, useful for when outputing to /dev/stdout, for example.static boolean
DISABLE_SNAPPY_COMPRESSOR
Disable use of the Snappy compressor.static String
DISABLE_SNAPPY_PROPERTY_NAME
The name of the system property that disables snappy.static String
EBI_REFERENCE_SERVICE_URL_MASK
A mask (pattern) to use when building EBI reference service URL for a given MD5 checksum.static int
NON_ZERO_BUFFER_SIZE
Even if BUFFER_SIZE is 0, this is guaranteed to be non-zero.static File
REFERENCE_FASTA
The reference FASTA file.static SamFlagField
SAM_FLAG_FIELD_FORMAT
The output format of the flag field when writing SAM text.static String
SAMJDK_PREFIX
static boolean
SRA_LIBRARIES_DOWNLOAD
Boolean describing whether downloading of SRA native libraries is allowed, in case such native libraries are not found locally.static boolean
USE_ASYNC_IO_READ_FOR_SAMTOOLS
Should asynchronous read I/O be used where supported by the samtools package (one thread per file).static boolean
USE_ASYNC_IO_WRITE_FOR_SAMTOOLS
Should asynchronous write I/O be used where supported by the samtools package (one thread per file).static boolean
USE_ASYNC_IO_WRITE_FOR_TRIBBLE
Should asynchronous write I/O be used where supported by the tribble package (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.
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Constructor Summary
Constructors Constructor Description Defaults()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static SortedMap<String,Object>
allDefaults()
Returns a map of all default values (keys are names), lexicographically sorted by keys.
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Field Detail
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CREATE_INDEX
public static final boolean CREATE_INDEX
Should BAM index files be created when writing out coordinate sorted BAM files? Default = false.
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CREATE_MD5
public static final boolean CREATE_MD5
Should MD5 files be created when writing out SAM and BAM files? Default = false.
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USE_ASYNC_IO_READ_FOR_SAMTOOLS
public static final boolean USE_ASYNC_IO_READ_FOR_SAMTOOLS
Should asynchronous read I/O be used where supported by the samtools package (one thread per file). Default = false.
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USE_ASYNC_IO_WRITE_FOR_SAMTOOLS
public static final boolean USE_ASYNC_IO_WRITE_FOR_SAMTOOLS
Should asynchronous write I/O be used where supported by the samtools package (one thread per file). Default = false.
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USE_ASYNC_IO_WRITE_FOR_TRIBBLE
public static final boolean USE_ASYNC_IO_WRITE_FOR_TRIBBLE
Should asynchronous write I/O be used where supported by the tribble package (one thread per file). Default = false.
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COMPRESSION_LEVEL
public static final int COMPRESSION_LEVEL
Compression level to be used for writing BAM and other block-compressed outputs. Default = 5.
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BUFFER_SIZE
public static final int BUFFER_SIZE
Buffer size, in bytes, used whenever reading/writing files or streams. Default = 128k.
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SAM_FLAG_FIELD_FORMAT
public static final SamFlagField SAM_FLAG_FIELD_FORMAT
The output format of the flag field when writing SAM text. Ignored for reading SAM text. Default = DECIMAL
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DEFAULT_SAM_EXTENSION
public static final String DEFAULT_SAM_EXTENSION
The extension to assume a sam file has when the actual file doesn't have an extension, useful for when outputing to /dev/stdout, for example.
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DEFAULT_VCF_EXTENSION
public static final String DEFAULT_VCF_EXTENSION
The extension to assume a vcf has when the actual file doesn't have an extension, useful for when outputing to /dev/stdout, for example.
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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 (Default = 128k).
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REFERENCE_FASTA
public static final 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). Default = null.
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CUSTOM_READER_FACTORY
public static final 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 Default = "".
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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. Default = false.
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EBI_REFERENCE_SERVICE_URL_MASK
public static final String EBI_REFERENCE_SERVICE_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. Default = "https://www.ebi.ac.uk/ena/cram/md5/%s".
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SRA_LIBRARIES_DOWNLOAD
public static final boolean SRA_LIBRARIES_DOWNLOAD
Boolean describing whether downloading of SRA native libraries is allowed, in case such native libraries are not found locally. Default = false.
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DISABLE_SNAPPY_PROPERTY_NAME
public static final String DISABLE_SNAPPY_PROPERTY_NAME
The name of the system property that disables snappy. Default = "snappy.disable".- See Also:
- Constant Field Values
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DISABLE_SNAPPY_COMPRESSOR
public static final boolean DISABLE_SNAPPY_COMPRESSOR
Disable use of the Snappy compressor. Default = false.
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SAMJDK_PREFIX
public static final String SAMJDK_PREFIX
- See Also:
- Constant Field Values
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