Constant Field Values

Contents

• org.mulinlab.*

org.mulinlab.*

org.mulinlab.varnote.cmdline.constant.Arguments

Modifier and Type	Constant Field	Value
public static final java.lang.String	ANNO_CONFIG_LONG	"anno-config"
public static final java.lang.String	ANNO_CONFIG_SHORT	"A"
public static final java.lang.String	ANNO_FO_LONG	"force-overlap"
public static final java.lang.String	ANNO_FO_SHORT	"FO"
public static final java.lang.String	ANNO_OF_LONG	"out-format"
public static final java.lang.String	ANNO_OF_SHORT	"OF"
public static final java.lang.String	ANNO_VH_LONG	"vcf-header-for-bed"
public static final java.lang.String	ANNO_VH_SHORT	"VH"
public static final java.lang.String	DB_DOC	"\nPossible attributes: {index, mode, tag}.\nindex - The index type that should be used to retrieve data. Default value is \"VarNote\". Possible values: {VarNote, TBI}, optional \nmode - Mode of Intersection. default value is \"0\". Possible values: {0, 1, 2}, optional.\n\t 0: Intersect mode, perform common interaction operation\n\t according to query and database formats;\n\t 1: Exact match mode, force the program only to consider\n\t the chromosome position of database records that exactly match\n\t the corresponding chromosome position of query;\n\t 2: Full close mode, force the program to report database\n\t records that overlap both endpoints of query interval regardless\n\t of original query and database formats.\ntag - A label to rename the database in the output file, optional. By default, the program will use original file name as tag for the database.\n\n"
public static final java.lang.String	DB_INPUT_LONG	"d-files"
public static final java.lang.String	DB_INPUT_SHORT	"D"
public static final java.lang.String	FILE_TYPE_DOC	"VCF format is a vcf file with header, VCFLike format "
public static final java.lang.String	FORMAT_ALT_LONG	"alt"
public static final java.lang.String	FORMAT_BEGIN_LONG	"begin"
public static final java.lang.String	FORMAT_BEGIN_SHORT	"B"
public static final java.lang.String	FORMAT_CHROM_LONG	"chrom"
public static final java.lang.String	FORMAT_CHROM_SHORT	"C"
public static final java.lang.String	FORMAT_COMMENT_LONG	"comment-indicator"
public static final java.lang.String	FORMAT_COMMENT_SHORT	"CI"
public static final java.lang.String	FORMAT_END_LONG	"end"
public static final java.lang.String	FORMAT_END_SHORT	"E"
public static final java.lang.String	FORMAT_HEADER_LONG	"has-header"
public static final java.lang.String	FORMAT_HEADER_PATH_LONG	"header-path"
public static final java.lang.String	FORMAT_HEADER_PATH_SHORT	"HP"
public static final java.lang.String	FORMAT_HEADER_SHORT	"header"
public static final java.lang.String	FORMAT_LONG	"format"
public static final java.lang.String	FORMAT_REF_LONG	"ref"
public static final java.lang.String	FORMAT_SHORT	"F"
public static final java.lang.String	FORMAT_SKIP_LONG	"skip"
public static final java.lang.String	FORMAT_SKIP_SHORT	"S"
public static final java.lang.String	FORMAT_ZERO_LONG	"is-zero-based"
public static final java.lang.String	FORMAT_ZERO_SHORT	"0"
public static final java.lang.String	INDEX_DOC	"The path of the TAB-delimited genome position file compressed by bgzip program. The file must be position-sorted (first by sequence name and then by leftmost coordinate). \n\nPossible Tags: {vcf, vcfLike, bed, bedAllele, coordOnly, coordAllele, tab} \n\nPossible attributes for all tags: {ci}\nPossible attributes for \"tab\" tag: {c, b, e, ref, alt, 0}\nc: column of sequence name (1-based)\nb: column of start chromosomal position (1-based)\ne: column of end chromosomal position (1-based)\nref: column of reference allele\nalt: column of alternative allele\n0: specify the position in the data file is 0-based rather than 1-based\nci: comment indicator\n"
public static final java.lang.String	INDEX_LIST_CHROM_LONG	"list-chroms"
public static final java.lang.String	INDEX_LITS_CHROM_SHORT	"LC"
public static final java.lang.String	INDEX_OUTPUT_LONG	"out-folder"
public static final java.lang.String	INDEX_OUTPUT_SHORT	"O"
public static final java.lang.String	INDEX_PRINT_FORMAT_LONG	"print-format"
public static final java.lang.String	INDEX_PRINT_FORMAT_SHORT	"PF"
public static final java.lang.String	INDEX_PRINT_HEADER_LONG	"print-header"
public static final java.lang.String	INDEX_PRINT_HEADER_SHORT	"PH"
public static final java.lang.String	INDEX_PRINT_META_LONG	"print-meta-data"
public static final java.lang.String	INDEX_PRINT_META_SHORT	"PM"
public static final java.lang.String	INDEX_REPLACE_HEADER_LONG	"reheader"
public static final java.lang.String	INDEX_REPLACE_HEADER_SHORT	"RH"
public static final java.lang.String	INPUT_LONG	"input"
public static final java.lang.String	INPUT_SHORT	"I"
public static final java.lang.String	INTERSECT_COUNT_LONG	"is-count"
public static final java.lang.String	INTERSECT_COUNT_SHORT	"C"
public static final java.lang.String	INTERSECT_INPUT_LONG	"query-file"
public static final java.lang.String	INTERSECT_INPUT_SHORT	"Q"
public static final java.lang.String	INTERSECT_LOJ_LONG	"is-loj"
public static final java.lang.String	INTERSECT_LOJ_SHORT	"loj"
public static final java.lang.String	INTERSECT_OUT_LONG	"out-file"
public static final java.lang.String	INTERSECT_OUT_MODE_LONG	"out-mode"
public static final java.lang.String	INTERSECT_OUT_MODE_SHORT	"OM"
public static final java.lang.String	INTERSECT_OUT_SHORT	"O"
public static final java.lang.String	INTERSECT_RC_LONG	"is-remove-comment"
public static final java.lang.String	INTERSECT_RC_SHORT	"RC"
public static final java.lang.String	INTERSECT_THREAD_LONG	"thread"
public static final java.lang.String	INTERSECT_THREAD_SHORT	"T"
public static final java.lang.String	INTERSECT_ZIP_LONG	"is-zip"
public static final java.lang.String	INTERSECT_ZIP_SHORT	"Z"
public static final java.lang.String	LOG_LONG	"log"
public static final java.lang.String	QUERY_DOC	"Path of query file, support plain text or gzip compressed file. For gzip, up to <hl1>4Gb original file size</hl1> is supported currently.\n\nPossible Tags: {vcf, vcfLike, bed, bedAllele, coordOnly, coordAllele, tab} \n\nPossible attributes for all tags: {sep, ci}\nPossible attributes for \"tab\" tag: {c, b, e, ref, alt, 0}\nc: column of sequence name (1-based)\nb: column of start chromosomal position (1-based)\ne: column of end chromosomal position (1-based)\nref: column of reference allele\nalt: column of alternative allele\n0: specify the position in the data file is 0-based rather than 1-based\nsep: specifies the character that separates fields in file, possible values are: {TAB, COMMA}\nci: comment indicator\n"
public static final java.lang.String	QUERY_INPUT_LONG	"q-region"
public static final java.lang.String	QUERY_INPUT_SHORT	"Q"
public static final java.lang.String	QUERY_LABEL_LONG	"is-label"
public static final java.lang.String	QUERY_LABEL_SHORT	"L"
public static final java.lang.String	USE_JDK_LONG	"use-jdk-deflater"
public static final java.lang.String	USE_JDK_SHORT	"UJD"
public static final java.lang.String	USE_JDKI_LONG	"use-jdk-inflater"
public static final java.lang.String	USE_JDKI_SHORT	"UJI"

org.mulinlab.varnote.cmdline.constant.CommandLineDefaults

Modifier and Type	Constant Field	Value
public static final int	HELP_SIMILARITY_FLOOR	7
public static final int	MINIMUM_SUBSTRING_LENGTH	5

org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader<T>

Modifier and Type	Constant Field	Value
public static final java.lang.String	COMMENT_LINE	"#"
public static final java.lang.String	END	"end"
public static final java.lang.String	OVERLAP_EQUAL	"="
public static final java.lang.String	OVERLAP_NOTE	"@"

org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader<T>

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLOW_LARGE_VARIANTS	"allowLargeVariants"
public static final java.lang.String	COMMNT_INDICATOR	"comment_indicator"
public static final java.lang.String	DB_BEGIN	"[db]"
public static final java.lang.String	DB_INDEX_TYPE	"db_index_type"
public static final java.lang.String	DB_LABEL	"db_tag"
public static final java.lang.String	DB_MODE	"db_mode"
public static final java.lang.String	DB_PATH	"db_path"
public static final java.lang.String	HAS_HEADER	"has_header"
public static final java.lang.String	HEADER	"header"
public static final java.lang.String	HEADER_PATH	"header_path"
public static final java.lang.String	ISZIP	"is_zip"
public static final java.lang.String	LOJ	"is_loj"
public static final java.lang.String	MAX_VARIANT_LENGTH	"maxVariantLength"
public static final java.lang.String	MODE	"mode"
public static final java.lang.String	OUTPUT_MODE	"out_mode"
public static final java.lang.String	OUTPUT_PATH	"out_file"
public static final java.lang.String	QUERY	"query_file"
public static final java.lang.String	QUERY_ALT	"alt"
public static final java.lang.String	QUERY_BEGIN	"begin"
public static final java.lang.String	QUERY_CHROM	"chrom"
public static final java.lang.String	QUERY_END	"end"
public static final java.lang.String	QUERY_FORMAT	"query_format"
public static final java.lang.String	QUERY_REF	"ref"
public static final java.lang.String	REMOVE_COMMENT	"remove_comment"
public static final java.lang.String	THREAD	"thread"
public static final java.lang.String	USE_JDK_INFLATER	"use_jdk_inflater"
public static final java.lang.String	VERBOSE	"is_log"
public static final java.lang.String	ZERO_BASED	"zero_based"

org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader<T>

Modifier and Type	Constant Field	Value
public static final java.lang.String	COLUMNS	"cols"
public static final java.lang.String	COMMNT_INDICATOR	"comment_indicator"
public static final java.lang.String	FIELDS	"fields"
public static final java.lang.String	HAS_HEADER	"has_header"
public static final java.lang.String	HEADER_PATH	"header_path"
public static final java.lang.String	INFO_FIELDS	"info_fields"
public static final java.lang.String	OUT_NAMES	"out_names"
public static final java.lang.String	VCFINFO	"vcf_info_path"

org.mulinlab.varnote.cmdline.txtreader.anno.FormatReader<T>

Modifier and Type	Constant Field	Value
public static final java.lang.String	BEGIN	"@"
public static final java.lang.String	COMMENT	"#"
public static final java.lang.String	FORMAT	"format"
public static final java.lang.String	OUT_FORMAT	"out_format"

org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader<T>

Modifier and Type	Constant Field	Value
public static final java.lang.String	BEGIN	"@"
public static final java.lang.String	COMMENT	"#"
public static final java.lang.String	COUNT	"count"
public static final java.lang.String	DESC	"descrition"
public static final java.lang.String	ID	"id"
public static final java.lang.String	TYPE	"type"

org.mulinlab.varnote.cmdline.txtreader.run.AnnoRunReader<T>

Modifier and Type	Constant Field	Value
public static final java.lang.String	ANNO_CONFIG	"anno_config"
public static final java.lang.String	ANNO_FORMAT	"out_format"
public static final java.lang.String	FORCE_OVERLAP	"force_overlap"
public static final java.lang.String	VCF_HEADER_PATH_FOR_BED	"vcf_header_for_bed"

org.mulinlab.varnote.config.anno.FieldFormat

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALLELE	"allele"
public static final int	ALLELE_INDENTIFIER	-1
public static final int	ALLELE_LENGTH	6
public static final java.lang.String	EXCEPTION	"Can not recognize variable in "
public static final java.lang.String	LOOP	"..$n"
public static final int	LOOP_INDENTIFIER	-2
public static final java.lang.String	N	"n"
public static final char	N_CHAR	110
public static final int	N_INDENTIFIER	-3
public static final java.lang.String	VARIABLE_BEGIN	"$"

org.mulinlab.varnote.config.anno.NormalField

Modifier and Type	Constant Field	Value
public final java.lang.String	COMMA	","
public static final int	FORCE_OVERLAP	-2
public static final java.lang.String	NO_VAL	"No-val"
public static final int	NOT_MATCH	-1

org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

Modifier and Type	Constant Field	Value
public static final java.lang.String	NULLVALUE	"."
public static final java.lang.String	UNDERLINE	"_"
public static final java.lang.String	VCF_INFO_EQUAL	"="

org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

Modifier and Type	Constant Field	Value
public static final char	EXCLUDE	45
public static final java.lang.String	INFO_EXT	".vcfinfo"

org.mulinlab.varnote.config.anno.query.AbstractQueryParser

Modifier and Type	Constant Field	Value
public static final int	INFO_COL	8
public static final java.lang.String	INFO_FIELD_SEPARATOR	";"
public static final java.lang.String	NULLVALUE	"."
public static final java.lang.String	TAB	"\t"
public static final java.lang.String	VCF_HEADER_INDICATOR	"#"
public static final java.lang.String	VCF_INFO_EQUAL	"="

org.mulinlab.varnote.config.io.temp.ThreadPrintter

Modifier and Type	Constant Field	Value
protected static final char	newline	10

org.mulinlab.varnote.config.parser.AnnoParser

Modifier and Type	Constant Field	Value
public static final java.lang.String	INFO_FIELD_SEPARATOR	";"
public static final java.lang.String	NULLVALUE	"."
public static final java.lang.String	TAB	"\t"

org.mulinlab.varnote.config.run.OverlapRunConfig

Modifier and Type	Constant Field	Value
protected static final java.lang.String	OVERLAP_EQUAL	"="
protected static final java.lang.String	OVERLAP_NOTE	"@"

org.mulinlab.varnote.config.run.RunConfig

Modifier and Type	Constant Field	Value
protected static final java.lang.String	TAB	"\t"

org.mulinlab.varnote.constants.GlobalParameter

Modifier and Type	Constant Field	Value
public static final java.lang.String	ANNO_CONFIG_SUFFIX	".annoc"
public static final int	BIN_GENOMIC_SPAN	536870912
public static final byte	BLOCK_ADDRESS	-6
public static final byte	BLOCK_START_WITH_END_BTYE	-2
public static final byte	BLOCK_START_WITH_END_INT	-4
public static final byte	BLOCK_START_WITH_END_SHORT	-3
public static final byte	BLOCK_START_WO_END	-1
public static final int	BUFFER_SIZE	131072
public static final byte	CHR_START	-8
public static final java.lang.String	COL	"col"
public static final java.lang.String	COMMA	","
public static final java.lang.String	COMMENT_LINE	"#"
public static final int	DEFALT_OUT_MODE_VAL	2
public static final boolean	DEFAULT_ALLOW_MAX_VIRANTS	false
public static final int	DEFAULT_COL	-1
public static final java.lang.String	DEFAULT_COMMENT_INDICATOR	"##"
public static final boolean	DEFAULT_DISPLAY_LABEL	true
public static final boolean	DEFAULT_FORCE_OVERLAP	false
public static final boolean	DEFAULT_GZIP	true
public static final boolean	DEFAULT_HAS_HEADER	false
public static final boolean	DEFAULT_IS_COUNT	false
public static final boolean	DEFAULT_IS_GZIP	true
public static final boolean	DEFAULT_LOG	true
public static final boolean	DEFAULT_LOJ	false
public static final int	DEFAULT_MAX_LENGTH	50
public static final boolean	DEFAULT_REMOVE_COMMENT	false
public static final int	DEFAULT_SKIP	0
public static final int	DEFAULT_THREAD	1
public static final boolean	DEFAULT_USE_JDK	false
public static final boolean	DEFAULT_ZERO_BASED	false
public static final java.lang.String	DOUBLE_HYPHEN	"--"
public static final int	GT_BIN_INTERVAL	1000
public static final int	GT_CHR_END	-8
public static final java.lang.String	GT_COMPRESS_FILE	".bit"
public static final java.lang.String	GT_COMPRESS_FILE_IDX	".bit.idx"
public static final int	GT_FILE_END	-9
public static final java.lang.String	GT_IDX	".idx"
public static final java.lang.String	HELP_OPTION	"--help"
public static final java.lang.String	HELP_OPTION_ABBR	"-h"
public static final char	HYPHEN_CHAR	45
public static final int	INFO_COL	8
public static final java.lang.String	INFO_FIELD_SEPARATOR	";"
public static final byte	INT_START	-7
public static final int	MAX_BINS	37450
public static final byte	MAX_BYTE	127
public static final short	MAX_BYTE_UNSIGNED	255
public static final int	MAX_HEADER_COMPARE_LENGTH	50
public static final int	MAX_SHORT	32767
public static final int	MAX_SHORT_UNSIGNED	65535
public static final java.lang.String	MERGE_LABEL	"merge"
public static final java.lang.String	NEWLINE	"\n"
public static final int	NO_CALL_IDX	-1
public static final java.lang.String	NULLVALUE	"."
public static final java.lang.String	OVERLAP_EQUAL	"="
public static final java.lang.String	OVERLAP_NOTE	"@"
public static final java.lang.String	POS_RSID_LABEL	"pos2snp"
public static final java.lang.String	PRO_CMD	"java -jar /path/to/VarNote.jar"
public static final java.lang.String	PRO_NAME	"VarNote"
public static final java.lang.String	QUERY_START	"#query"
public static final int	REF_IDX	0
public static final java.lang.String	RSID_POS_LABEL	"snp2pos"
public static final int	START_COMPARE_LENGTH	7
public static final java.lang.String	TAB	"\t"
public static final java.lang.String	TEMP	".temp"
public static final java.lang.String	UNDERLINE	"_"
public static final int	UNSET_GENOMIC_LOCATION	0
public static final byte	VANNO_FILE_END	-9
public static final java.lang.String	VCF_FIELD	"CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"
public static final java.lang.String	VCF_HEADER_INDICATOR	"#"
public static final java.lang.String	VCF_INFO_EQUAL	"="
public static final int	version	1

org.mulinlab.varnote.operations.readers.db.VannoReader

Modifier and Type	Constant Field	Value
protected static final int	END	0
protected static final int	FIND	2
protected static final int	STOP	1

org.mulinlab.varnote.utils.RunFactory

Modifier and Type	Constant Field	Value
public static final java.lang.String	OVERLAP_NOTE	"@"
public static final java.lang.String	QUERY_START	"#query"
public static final java.lang.String	TAB	"\t"

org.mulinlab.varnote.utils.VannoUtils

Modifier and Type	Constant Field	Value
public static final int	DELETION	2
public static final int	INSERTION	1
public static final int	MAX_LEN	1000
public static final int	NOT_INDEL	0
public static final int	OUT_LEN	3

org.mulinlab.varnote.utils.format.Format

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_COMMENT_INDICATOR	"##"
public static final int	DEFAULT_RSID_COL	2
public static final int	MAX_HEADER_COMPARE_LENGTH	128
public static final int	NO_COL	-1
public static final int	START_COMPARE_LENGTH	7

org.mulinlab.varnote.utils.gz.BlockCompressedFilePointerUtil

Modifier and Type	Constant Field	Value
public static final long	MAX_BLOCK_ADDRESS	281474976710655L
public static final int	MAX_OFFSET	65535