Class Defaults


  • 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.
    • 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_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.
      • 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.
      • 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.
      • COMPRESSION_LEVEL

        public static final int COMPRESSION_LEVEL
        Compression 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.
      • 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
      • 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.
      • 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.
      • 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).
      • 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.
      • 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 = "".
      • 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.
      • 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".
      • 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.
      • 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
      • DISABLE_SNAPPY_COMPRESSOR

        public static final boolean DISABLE_SNAPPY_COMPRESSOR
        Disable use of the Snappy compressor. Default = false.
    • Constructor Detail

      • Defaults

        public Defaults()
    • Method Detail

      • allDefaults

        public static SortedMap<String,​Object> 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.