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Constant Field Values

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htsjdk.samtools.*

htsjdk.samtools.BamFileIoUtils
public static final java.lang.String BAM_FILE_EXTENSION ".bam"

htsjdk.samtools.BAMIndex
public static final java.lang.String BAMIndexSuffix ".bai"

htsjdk.samtools.GenomicIndexUtil
public static final int BIN_GENOMIC_SPAN 536870912
public static final int MAX_BINS 37450
public static final int UNSET_GENOMIC_LOCATION 0

htsjdk.samtools.LinearIndex
public static final int BAM_LIDX_SHIFT 14

htsjdk.samtools.ReservedTagConstants
public static final java.lang.String OC "OC"
public static final java.lang.String XF "XF"
public static final java.lang.String XN "XN"
public static final java.lang.String XQ "XQ"
public static final java.lang.String XS "XS"
public static final java.lang.String XT "XT"

htsjdk.samtools.SAMFileHeader
public static final java.lang.String CURRENT_VERSION "1.4"
public static final java.lang.String GROUP_ORDER_TAG "GO"
public static final java.lang.String SORT_ORDER_TAG "SO"
public static final java.lang.String VERSION_TAG "VN"

htsjdk.samtools.SAMProgramRecord
public static final java.lang.String COMMAND_LINE_TAG "CL"
public static final java.lang.String PREVIOUS_PROGRAM_GROUP_ID_TAG "PP"
public static final java.lang.String PROGRAM_GROUP_ID_TAG "ID"
public static final java.lang.String PROGRAM_NAME_TAG "PN"
public static final java.lang.String PROGRAM_VERSION_TAG "VN"

htsjdk.samtools.SAMReadGroupRecord
public static final java.lang.String DATE_RUN_PRODUCED_TAG "DT"
public static final java.lang.String DESCRIPTION_TAG "DS"
public static final java.lang.String FLOW_ORDER_TAG "FO"
public static final java.lang.String KEY_SEQUENCE_TAG "KS"
public static final java.lang.String LIBRARY_TAG "LB"
public static final java.lang.String PLATFORM_TAG "PL"
public static final java.lang.String PLATFORM_UNIT_TAG "PU"
public static final java.lang.String PREDICTED_MEDIAN_INSERT_SIZE_TAG "PI"
public static final java.lang.String READ_GROUP_ID_TAG "ID"
public static final java.lang.String READ_GROUP_SAMPLE_TAG "SM"
public static final java.lang.String SEQUENCING_CENTER_TAG "CN"

htsjdk.samtools.SAMRecord
public static final int MAX_INSERT_SIZE 536870912
public static final java.lang.String NO_ALIGNMENT_CIGAR "*"
public static final int NO_ALIGNMENT_REFERENCE_INDEX -1
public static final java.lang.String NO_ALIGNMENT_REFERENCE_NAME "*"
public static final int NO_ALIGNMENT_START 0
public static final int NO_MAPPING_QUALITY 0
public static final java.lang.String NULL_QUALS_STRING "*"
public static final java.lang.String NULL_SEQUENCE_STRING "*"
public static final int UNKNOWN_MAPPING_QUALITY 255

htsjdk.samtools.SAMRecordSetBuilder
public static final int DEFAULT_CHROMOSOME_LENGTH 200000000

htsjdk.samtools.SAMSequenceRecord
public static final java.lang.String ASSEMBLY_TAG "AS"
public static final java.lang.String MD5_TAG "M5"
public static final java.lang.String RESERVED_MRNM_SEQUENCE_NAME "="
public static final java.lang.String SEQUENCE_LENGTH_TAG "LN"
public static final java.lang.String SEQUENCE_NAME_TAG "SN"
public static final java.lang.String SPECIES_TAG "SP"
public static final int UNKNOWN_SEQUENCE_LENGTH 0
public static final java.lang.String URI_TAG "UR"

htsjdk.samtools.SAMUtils
public static final int MAX_PHRED_SCORE 93

htsjdk.samtools.SQTagUtil
public static final byte MAX_QUALITY 63

htsjdk.samtools.cram.build.Sam2CramRecordFactory
public static final byte ignorePositionsWithQualityScore -1
public static final byte QS_asciiOffset 33
public static final java.lang.String UNKNOWN_READ_GROUP_ID "UNKNOWN"
public static final java.lang.String UNKNOWN_READ_GROUP_SAMPLE "UNKNOWN"
public static final byte unsetQualityScore 32

htsjdk.samtools.cram.encoding.read_features.BaseQualityScore
public static final byte operator 81

htsjdk.samtools.cram.encoding.read_features.Deletion
public static final byte operator 68

htsjdk.samtools.cram.encoding.read_features.HardClip
public static final byte operator 72

htsjdk.samtools.cram.encoding.read_features.InsertBase
public static final byte operator 105

htsjdk.samtools.cram.encoding.read_features.Insertion
public static final byte operator 73

htsjdk.samtools.cram.encoding.read_features.Padding
public static final byte operator 80

htsjdk.samtools.cram.encoding.read_features.ReadBase
public static final byte operator 66

htsjdk.samtools.cram.encoding.read_features.ReadFeature
public static final byte STOP_OPERATOR 36

htsjdk.samtools.cram.encoding.read_features.RefSkip
public static final byte operator 78

htsjdk.samtools.cram.encoding.read_features.SoftClip
public static final byte operator 83

htsjdk.samtools.cram.encoding.read_features.Substitution
public static final byte operator 88

htsjdk.samtools.cram.encoding.reader.AbstractFastqReader
public static final int maxReadBufferLength 1048576

htsjdk.samtools.cram.encoding.writer.Writer
public static final int TEST_MARK -1599029040

htsjdk.samtools.cram.mask.FastaByteArrayMaskFactory
public static final int DEFAULT_BUFFER_SIZE 1024
public static final byte DEFAULT_MASK_BYTE 120
public static final byte DEFAULT_NON_MASK_BYTE 95

htsjdk.samtools.cram.mask.IntegerListMaskFactory
public static final int DEFAULT_BUFFER_SIZE 1024
public static final java.lang.String DEFAULT_DEMLIITER " "

htsjdk.samtools.cram.structure.CramCompressionRecord
public static final int DETACHED_FLAG 2
public static final int DUPLICATE_FLAG 1024
public static final int FIRST_SEGMENT_FLAG 64
public static final int FORCE_PRESERVE_QS_FLAG 1
public static final int HAS_MATE_DOWNSTREAM_FLAG 4
public static final int LAST_SEGMENT_FLAG 128
public static final int MATE_NEG_STRAND_FLAG 1
public static final int MATE_UNMAPPED_FLAG 2
public static final int MULTIFRAGMENT_FLAG 1
public static final int NEGATIVE_STRAND_FLAG 16
public static final int PROPER_PAIR_FLAG 2
public static final int SECONDARY_ALIGNMENT_FLAG 256
public static final int SEGMENT_UNMAPPED_FLAG 4
public static final int VENDOR_FILTERED_FLAG 512

htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
public static final int DUPLICATE_READ_FLAG 1024
public static final int FIRST_OF_PAIR_FLAG 64
public static final int MATE_STRAND_FLAG 32
public static final int MATE_UNMAPPED_FLAG 8
public static final int NOT_PRIMARY_ALIGNMENT_FLAG 256
public static final int PROPER_PAIR_FLAG 2
public static final int READ_FAILS_VENDOR_QUALITY_CHECK_FLAG 512
public static final int READ_PAIRED_FLAG 1
public static final int READ_STRAND_FLAG 16
public static final int READ_UNMAPPED_FLAG 4
public static final int SECOND_OF_PAIR_FLAG 128

htsjdk.samtools.cram.structure.ReadTag
public static final int BQZ 4346202
public static final int OQZ 5198170

htsjdk.samtools.cram.structure.Slice
public static final int MUTLIREF -2
public static final int UNMAPPED_OR_NOREF -1

htsjdk.samtools.fastq.FastqConstants
public static final java.lang.String QUALITY_HEADER "+"
public static final java.lang.String SEQUENCE_HEADER "@"

htsjdk.samtools.liftover.LiftOver
public static final double DEFAULT_LIFTOVER_MINMATCH 0.95

htsjdk.samtools.metrics.MetricsFile<BEAN extends MetricBase,HKEY extends java.lang.Comparable>
public static final java.lang.String HISTO_HEADER "## HISTOGRAM\t"
public static final java.lang.String MAJOR_HEADER_PREFIX "## "
public static final java.lang.String METRIC_HEADER "## METRICS CLASS\t"
public static final java.lang.String MINOR_HEADER_PREFIX "# "
public static final java.lang.String SEPARATOR "\t"

htsjdk.samtools.seekablestream.SeekableBufferedStream
public static final int DEFAULT_BUFFER_SIZE 512000

htsjdk.samtools.util.AbstractAsyncWriter<T>
public static final int DEFAULT_QUEUE_SIZE 2000

htsjdk.samtools.util.BlockCompressedFilePointerUtil
public static final long MAX_BLOCK_ADDRESS 281474976710655L
public static final int MAX_OFFSET 65535

htsjdk.samtools.util.BlockCompressedStreamConstants
public static final byte BGZF_ID1 66
public static final byte BGZF_ID2 67
public static final byte BGZF_LEN 2
public static final int BLOCK_FOOTER_LENGTH 8
public static final int BLOCK_HEADER_LENGTH 18
public static final int BLOCK_LENGTH_OFFSET 16
public static final int DEFAULT_UNCOMPRESSED_BLOCK_SIZE 65498
public static final byte GZIP_CM_DEFLATE 8
public static final int GZIP_FLG 4
public static final byte GZIP_ID1 31
public static final int GZIP_ID2 139
public static final int GZIP_OS_UNKNOWN 255
public static final int GZIP_OVERHEAD 28
public static final int GZIP_XFL 0
public static final short GZIP_XLEN 6
public static final int MAX_COMPRESSED_BLOCK_SIZE 65536
public static final int NO_COMPRESSION_OVERHEAD 10

htsjdk.samtools.util.IntervalList
public static final java.lang.String INTERVAL_LIST_FILE_EXTENSION ".interval_list"

htsjdk.samtools.util.IntervalTree.Node<V1>
public static final int HAS_GREATER_PART 4
public static final int HAS_LESSER_PART 1
public static final int HAS_OVERLAPPING_PART 2
public static final int IS_ADJACENT_AND_EMPTY 0
public static final int IS_LEFT_OVERHANGING_OVERLAPPER 3
public static final int IS_RIGHT_OVERHANGING_OVERLAPPER 6
public static final int IS_STRICTLY_GREATER 4
public static final int IS_STRICTLY_LESS 1
public static final int IS_SUBSET 2
public static final int IS_SUPERSET 7

htsjdk.samtools.util.IOUtil
public static final java.lang.String DICT_FILE_EXTENSION ".dict"
public static final long FIVE_GBS 5368709120L
public static final java.lang.String INTERVAL_LIST_FILE_EXTENSION ".interval_list"
public static final long ONE_GB 1073741824L
public static final java.lang.String SAM_FILE_EXTENSION ".sam"
public static final long TWO_GBS 2147483648L

htsjdk.samtools.util.QualityEncodingDetector
public static final long DEFAULT_MAX_RECORDS_TO_ITERATE 10000L

htsjdk.samtools.util.RelativeIso8601Date
public static final java.lang.String LAZY_NOW_LABEL "NOW"

htsjdk.samtools.util.SequenceUtil
public static final byte a 97
public static final byte A 65
public static final byte c 99
public static final byte C 67
public static final byte g 103
public static final byte G 71
public static final byte n 110
public static final byte N 78
public static final byte t 116
public static final byte T 84

htsjdk.samtools.util.SolexaQualityConverter
public static final int ILLUMINA_TO_PHRED_SUBTRAHEND 31
public static final int PHRED_ADDEND 33
public static final int SOLEXA_ADDEND 64

htsjdk.samtools.util.SortingLongCollection
public static final int SIZEOF 8

htsjdk.samtools.util.StringUtil
public static final java.lang.String EMPTY_STRING ""

htsjdk.samtools.util.zip.IntelDeflater
public static final int FULL_FLUSH 3
public static final int NO_FLUSH 0
public static final int SYNC_FLUSH 2

htsjdk.tribble.*

htsjdk.tribble.FeatureCodecHeader
public static final long NO_HEADER_END 0L

htsjdk.tribble.Tribble
public static final java.lang.String STANDARD_INDEX_EXTENSION ".idx"

htsjdk.tribble.example.ExampleBinaryCodec
public static final java.lang.String HEADER_LINE "# BinaryTestFeature"

htsjdk.tribble.index.AbstractIndex
public static final int MAGIC_NUMBER 1480870228
public static final int VERSION 3

htsjdk.tribble.index.tabix.TabixFormat
public static final int GENERIC_FLAGS 0
public static final int SAM_FLAGS 1
public static final int UCSC_FLAGS 65536
public static final int VCF_FLAGS 2
public static final int ZERO_BASED 65536

htsjdk.tribble.readers.AsynchronousLineReader
public static final int DEFAULT_NUMBER_LINES_BUFFER 100

htsjdk.tribble.util.TabixUtils
public static final java.lang.String STANDARD_INDEX_EXTENSION ".tbi"

htsjdk.variant.*

htsjdk.variant.bcf2.BCF2Utils
public static final int MAX_ALLELES_IN_GENOTYPES 127
public static final int MAX_INLINE_ELEMENTS 14
public static final int OVERFLOW_ELEMENT_MARKER 15

htsjdk.variant.utils.GeneralUtils
public static final boolean DEBUG_MODE_ENABLED false
public static final double LOG10_P_OF_ZERO -1000000.0

htsjdk.variant.variantcontext.Allele
public static final java.lang.String NO_CALL_STRING "."

htsjdk.variant.variantcontext.CommonInfo
public static final double NO_LOG10_PERROR 1.0

htsjdk.variant.variantcontext.Genotype
public static final java.lang.String PHASED_ALLELE_SEPARATOR "|"
public static final java.lang.String UNPHASED_ALLELE_SEPARATOR "/"

htsjdk.variant.variantcontext.GenotypeLikelihoods
public static final int MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED 50
public static final int MAX_PL 2147483647

htsjdk.variant.variantcontext.VariantContext
public static final double NO_LOG10_PERROR 1.0

htsjdk.variant.variantcontext.writer.BCF2Encoder
public static final int WRITE_BUFFER_INITIAL_SIZE 16384

htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
protected static final int BEFORE_MOST_UPSTREAM_LOC 0

htsjdk.variant.vcf.AbstractVCFCodec
protected static final int NUM_STANDARD_FIELDS 8

htsjdk.variant.vcf.VCF3Codec
public static final java.lang.String VCF3_MAGIC_HEADER "##fileformat=VCFv3"

htsjdk.variant.vcf.VCFCodec
public static final java.lang.String VCF4_MAGIC_HEADER "##fileformat=VCFv4"

htsjdk.variant.vcf.VCFConstants
public static final java.lang.String ALLELE_COUNT_KEY "AC"
public static final java.lang.String ALLELE_FREQUENCY_KEY "AF"
public static final java.lang.String ALLELE_NUMBER_KEY "AN"
public static final java.lang.String ALT_HEADER_START "##ALT"
public static final java.lang.String ANCESTRAL_ALLELE_KEY "AA"
public static final java.lang.String CIGAR_KEY "CIGAR"
public static final java.lang.String CONTIG_HEADER_KEY "contig"
public static final java.lang.String CONTIG_HEADER_START "##contig"
public static final java.lang.String DBSNP_KEY "DB"
public static final char DELETION_ALLELE_v3 68
public static final java.lang.String DEPTH_KEY "DP"
public static final java.lang.String EMPTY_ALLELE "."
public static final java.lang.String EMPTY_ALTERNATE_ALLELE_FIELD "."
public static final java.lang.String EMPTY_GENOTYPE "./."
public static final java.lang.String EMPTY_ID_FIELD "."
public static final java.lang.String EMPTY_INFO_FIELD "."
public static final java.lang.String END_KEY "END"
public static final java.lang.String EXPECTED_ALLELE_COUNT_KEY "EC"
public static final java.lang.String FIELD_SEPARATOR "\t"
public static final char FIELD_SEPARATOR_CHAR 9
public static final java.lang.String FILTER_CODE_SEPARATOR ";"
public static final java.lang.String FILTER_HEADER_START "##FILTER"
public static final java.lang.String FORMAT_FIELD_SEPARATOR ":"
public static final java.lang.String FORMAT_HEADER_START "##FORMAT"
public static final java.lang.String GENOTYPE_ALLELE_DEPTHS "AD"
public static final java.lang.String GENOTYPE_FIELD_SEPARATOR ":"
public static final char GENOTYPE_FIELD_SEPARATOR_CHAR 58
public static final java.lang.String GENOTYPE_FILTER_KEY "FT"
public static final java.lang.String GENOTYPE_KEY "GT"
public static final java.lang.String GENOTYPE_LIKELIHOODS_KEY "GL"
public static final java.lang.String GENOTYPE_PL_KEY "PL"
public static final java.lang.String GENOTYPE_POSTERIORS_KEY "GP"
public static final java.lang.String GENOTYPE_QUALITY_KEY "GQ"
public static final java.lang.String HAPLOTYPE_QUALITY_KEY "HQ"
public static final java.lang.String HAPMAP2_KEY "H2"
public static final java.lang.String HAPMAP3_KEY "H3"
public static final java.lang.String ID_FIELD_SEPARATOR ";"
public static final java.lang.String INFO_FIELD_ARRAY_SEPARATOR ","
public static final char INFO_FIELD_ARRAY_SEPARATOR_CHAR 44
public static final java.lang.String INFO_FIELD_SEPARATOR ";"
public static final char INFO_FIELD_SEPARATOR_CHAR 59
public static final java.lang.String INFO_HEADER_START "##INFO"
public static final char INSERTION_ALLELE_v3 73
public static final java.lang.String MAPPING_QUALITY_ZERO_KEY "MQ0"
public static final int MAX_GENOTYPE_QUAL 99
public static final java.lang.String MISSING_DEPTH_v3 "-1"
public static final java.lang.String MISSING_GENOTYPE_QUALITY_v3 "-1"
public static final java.lang.String MISSING_HAPLOTYPE_QUALITY_v3 "-1"
public static final java.lang.String MISSING_QUALITY_v3 "-1"
public static final java.lang.String MISSING_VALUE_v4 "."
public static final java.lang.String OLD_DEPTH_KEY "RD"
public static final java.lang.String PASSES_FILTERS_v3 "0"
public static final java.lang.String PASSES_FILTERS_v4 "PASS"
public static final java.lang.String PER_ALLELE_COUNT "R"
public static final java.lang.String PER_ALTERNATE_COUNT "A"
public static final java.lang.String PER_GENOTYPE_COUNT "G"
public static final java.lang.String PHASE_QUALITY_KEY "PQ"
public static final java.lang.String PHASE_SET_KEY "PS"
public static final java.lang.String PHASED "|"
public static final java.lang.String PHASED_SWITCH_PROB_v3 "\\"
public static final java.lang.String PHASING_TOKENS "/|\\"
public static final java.lang.String RMS_BASE_QUALITY_KEY "BQ"
public static final java.lang.String RMS_MAPPING_QUALITY_KEY "MQ"
public static final java.lang.String SAMPLE_NUMBER_KEY "NS"
public static final java.lang.String SOMATIC_KEY "SOMATIC"
public static final java.lang.String STRAND_BIAS_KEY "SB"
public static final java.lang.String THOUSAND_GENOMES_KEY "1000G"
public static final java.lang.String UNBOUNDED_ENCODING_v3 "-1"
public static final java.lang.String UNBOUNDED_ENCODING_v4 "."
public static final java.lang.String UNFILTERED "."
public static final java.lang.String UNPHASED "/"
public static final java.lang.String VALIDATED_KEY "VALIDATED"

htsjdk.variant.vcf.VCFHeader
public static final java.lang.String CONTIG_KEY "contig"
public static final java.lang.String EXCLUDE_INTERVALS_KEY "excludeIntervals"
public static final java.lang.String HEADER_INDICATOR "#"
public static final java.lang.String INTERVAL_MERGING_KEY "interval_merging"
public static final java.lang.String INTERVAL_PADDING_KEY "interval_padding"
public static final java.lang.String INTERVAL_SET_RULE_KEY "interval_set_rule"
public static final java.lang.String INTERVALS_KEY "intervals"
public static final java.lang.String METADATA_INDICATOR "##"
public static final java.lang.String REFERENCE_KEY "reference"
public static final java.lang.String SOURCE_KEY "source"

htsjdk.variant.vcf.VCFHeaderLine
protected static final boolean ALLOW_UNBOUND_DESCRIPTIONS true
protected static final java.lang.String UNBOUND_DESCRIPTION "Not provided in original VCF header"

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