Constant Field Values

Contents

• main.*
• util.*

main.*

main.Musial

Modifier and Type	Constant Field	Value
public static final String	OUTPUT_EXTENSION	".json.gz"

util.*

util.Constants

Modifier and Type	Constant Field	Value
public static final String	ANY_NUCLEOTIDE	"N"
public static final String	BASE_SYMBOLS	"ARNDCQEGHILKMFPSTWYVBJZX*"
public static final String	COLON	":"
public static final String	COMMA	","
public static final String	DOT	"."
public static final String	EMPTY	""
public static final String	EQUAL	"="
public static final String	GAP	"-"
public static final char	GAP_CHAR	'-'
public static final String	GENOMIC_COORDINATES_PREFIX	"g."
public static final String	GREATER_THAN	">"
public static final String	PIPE	"\\|"
public static final String	REFERENCE	"reference"
public static final String	SEMICOLON	";"
public static final String	SIGN	"#"
public static final String	SNP_EFF_PREFIX	"snpeff_"
public static final String	SYNONYMOUS	"SYNONYMOUS"
public static final String	TAB	"\t"
public static final String	TERMINAL_AA	"*"
public static final String	UNDER_SCORE	"_"
public static final String	UNDERSCORE	"_"

util.Constants.AttributesKeys

Modifier and Type	Constant Field	Value
public static final String	ALLELIC_FREQUENCY	"allelic_frequency"
public static final String	DIVERSITY_ALLELE	"diversity_allele"
public static final String	DIVERSITY_PROTEOFORM	"diversity_proteoform"
public static final String	FREQUENCY_DISRUPTED	"frequency_disrupted_proteoform"
public static final String	FREQUENCY_FILTERED_CALLS	"frequency_calls_filtered"
public static final String	FREQUENCY_REFERENCE	"frequency_reference_allele"
public static final String	MEAN_COVERAGE	"mean_coverage"
public static final String	MEAN_ENTROPY	"mean_entropy"
public static final String	NUMBER_OF_ALLELES	"count_allele"
public static final String	NUMBER_OF_INDELS	"no_variant_indel"
public static final String	NUMBER_OF_PROTEOFORMS	"count_proteoform"
public static final String	NUMBER_OF_SNVS	"no_variant_snv"
public static final String	SEQUENCE_LENGTH_DEVIATION	"length_delta"
public static final String	SO_EFFECTS	"so_effects"
public static final String	VARIANT_FREQUENCY	"variant_frequency"