Package htsjdk.samtools
Class Defaults
java.lang.Object
htsjdk.samtools.Defaults
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
FieldsModifier and TypeFieldDescriptionstatic final int
Buffer size, in bytes, used whenever reading/writing files or streams.static final int
Compression level to be used for writing BAM and other block-compressed outputs.static final boolean
Should BAM index files be created when writing out coordinate sorted BAM files? Default = false.static final boolean
Should MD5 files be created when writing out SAM and BAM files? Default = false.static final String
Custom reader factory able to handle URL based resources like ga4gh.static final String
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 final String
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 final boolean
Disable use of the Snappy compressor.static final String
The name of the system property that disables snappy.static final String
A mask (pattern) to use when building EBI reference service URL for a given MD5 checksum.static final int
Even if BUFFER_SIZE is 0, this is guaranteed to be non-zero.static final boolean
static final String
static final File
The reference FASTA file.static final SamFlagField
The output format of the flag field when writing SAM text.static final String
static final boolean
Boolean describing whether downloading of SRA native libraries is allowed, in case such native libraries are not found locally.static final boolean
Should asynchronous read I/O be used where supported by the samtools package (one thread per file).static final boolean
Should asynchronous write I/O be used where supported by the samtools package (one thread per file).static final boolean
Should asynchronous write I/O be used where supported by the tribble package (one thread per file).static final boolean
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 -
Method Summary
Modifier and TypeMethodDescriptionReturns a map of all default values (keys are names), lexicographically sorted by keys.
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Field Details
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CREATE_INDEX
public static final boolean CREATE_INDEXShould BAM index files be created when writing out coordinate sorted BAM files? Default = false. -
CREATE_MD5
public static final boolean CREATE_MD5Should MD5 files be created when writing out SAM and BAM files? Default = false. -
USE_ASYNC_IO_READ_FOR_SAMTOOLS
public static final boolean USE_ASYNC_IO_READ_FOR_SAMTOOLSShould asynchronous read I/O be used where supported by the samtools package (one thread per file). Default = false. -
USE_ASYNC_IO_WRITE_FOR_SAMTOOLS
public static final boolean USE_ASYNC_IO_WRITE_FOR_SAMTOOLSShould asynchronous write I/O be used where supported by the samtools package (one thread per file). Default = false. -
USE_ASYNC_IO_WRITE_FOR_TRIBBLE
public static final boolean USE_ASYNC_IO_WRITE_FOR_TRIBBLEShould asynchronous write I/O be used where supported by the tribble package (one thread per file). Default = false. -
COMPRESSION_LEVEL
public static final int COMPRESSION_LEVELCompression level to be used for writing BAM and other block-compressed outputs. Default = 5. -
BUFFER_SIZE
public static final int BUFFER_SIZEBuffer size, in bytes, used whenever reading/writing files or streams. Default = 128k. -
SAM_FLAG_FIELD_FORMAT
The output format of the flag field when writing SAM text. Ignored for reading SAM text. Default = DECIMAL -
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. -
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. -
OPTIMISTIC_VCF_4_4
public static final boolean OPTIMISTIC_VCF_4_4 -
NON_ZERO_BUFFER_SIZE
public static final int NON_ZERO_BUFFER_SIZEEven if BUFFER_SIZE is 0, this is guaranteed to be non-zero. If BUFFER_SIZE is non-zero, this == BUFFER_SIZE (Default = 128k). -
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. -
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 = "". -
USE_CRAM_REF_DOWNLOAD
public static final boolean USE_CRAM_REF_DOWNLOADBoolean 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. -
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". -
SRA_LIBRARIES_DOWNLOAD
public static final boolean SRA_LIBRARIES_DOWNLOADBoolean describing whether downloading of SRA native libraries is allowed, in case such native libraries are not found locally. Default = false. -
DISABLE_SNAPPY_PROPERTY_NAME
The name of the system property that disables snappy. Default = "snappy.disable".- See Also:
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OPTIMISTIC_VCF_4_4_PROPERTY
- See Also:
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DISABLE_SNAPPY_COMPRESSOR
public static final boolean DISABLE_SNAPPY_COMPRESSORDisable use of the Snappy compressor. Default = false. -
SAMJDK_PREFIX
- See Also:
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Constructor Details
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Defaults
public Defaults()
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Method Details
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allDefaults
Returns a map of all default values (keys are names), lexicographically sorted by keys. The returned map is unmodifiable. This function is useful for example when logging all defaults.
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