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configuration.json
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{
"action": [
{
"default": {
"default output compression": "unknown",
"default output compression level": "5",
"default output format": "sam",
"filter incoming qc fail": false,
"filter outgoing qc fail": false,
"input": [
"/dev/stdin"
],
"output": [
"/dev/stdout"
],
"report url": "/dev/stderr",
"sample": {
"algorithm": "passthrough"
}
},
"description": "Multiplex and Demultiplex annotated DNA sequence reads",
"epilog": [
" -i/--input defaults to /dev/stdin with inputing layout sensing.",
" -o/--output default to /dev/stdout with SAM format.",
" -I/--base-input and -O/--base-output default to the working directory.",
" -V/--validate, -C/--compile and -S/--static disable job excution and only emit information.",
" -s/--sense-input will guess input layout by examining the first few reads of each input file.",
" -S/--static emits a static configuration file with all imports resolved.",
" -C/--compile emits a compiled configuration file ready for execution with implicit attributes resolved.",
" -i/--input and -o/--output can be repeated to provide multiple paths,",
" i.e. `pheniqs mux -i in_segment_1.fastq -i in_segment_2.fastq -o out_segment_1.fastq -o out_segment_2.fastq`"
],
"implementation": "transcode",
"name": "mux",
"option": [
{
"handle": [
"-h",
"--help"
],
"help": "Show this help",
"name": "help only",
"type": "boolean"
},
{
"cardinality": "*",
"extension": [
"fq",
"fq.gz",
"fastq",
"fastq.gz",
"bam",
"cram",
"sam"
],
"handle": [
"-i",
"--input"
],
"help": "Path to an input file. May be repeated.",
"inode": "file",
"meta": "PATH",
"name": "input",
"type": "url"
},
{
"cardinality": "*",
"extension": [
"fq",
"fq.gz",
"fastq",
"fastq.gz",
"bam",
"cram",
"sam"
],
"handle": [
"-o",
"--output"
],
"help": "Path to an output file. May be repeated.",
"inode": "file",
"meta": "PATH",
"name": "output",
"type": "url"
},
{
"extension": [
"json"
],
"handle": [
"-c",
"--config"
],
"help": "Path to configuration file",
"inode": "file",
"meta": "PATH",
"name": "configuration url",
"type": "url"
},
{
"extension": [
"json"
],
"handle": [
"-R",
"--report"
],
"help": "Path to report file",
"inode": "file",
"meta": "PATH",
"name": "report url",
"type": "url"
},
{
"extension": [
"json"
],
"handle": [
"--prior"
],
"help": "Path to adjusted prior job file",
"inode": "file",
"meta": "PATH",
"name": "prior adjusted job url",
"type": "url"
},
{
"handle": [
"-I",
"--base-input"
],
"help": "Base input url",
"inode": "directory",
"name": "base input url",
"type": "url"
},
{
"handle": [
"-O",
"--base-output"
],
"help": "Base output url",
"inode": "directory",
"name": "base output url",
"type": "url"
},
{
"handle": [
"-s",
"--sense-input"
],
"help": "Sense input segment layout",
"name": "sense input layout",
"type": "boolean"
},
{
"handle": [
"-n",
"--no-output-npf"
],
"help": "Filter outgoing QC failed reads",
"name": "filter outgoing qc fail",
"type": "boolean"
},
{
"handle": [
"-N",
"--no-input-npf"
],
"help": "Filter incoming QC failed reads.",
"name": "filter incoming qc fail",
"type": "boolean"
},
{
"handle": [
"-l",
"--leading"
],
"help": "Leading read segment index",
"name": "leading segment index",
"type": "integer"
},
{
"choice": [
"fastq",
"sam",
"bam",
"cram"
],
"handle": [
"-F",
"--format"
],
"help": "Defult output format",
"name": "default output format",
"type": "string"
},
{
"choice": [
"none",
"gz",
"bgzf"
],
"handle": [
"-Z",
"--compression"
],
"help": "Defult output compression",
"name": "default output compression",
"type": "string"
},
{
"choice": [
"0",
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8",
"9"
],
"handle": [
"-L",
"--level"
],
"help": "Defult output compression level",
"name": "default output compression level",
"type": "string"
},
{
"cardinality": "*",
"handle": [
"-T",
"--token"
],
"help": "Output read token",
"meta": "SEGMENT:START:END",
"name": "template token",
"type": "string"
},
{
"choice": [
"CAPILLARY",
"LS454",
"ILLUMINA",
"SOLID",
"HELICOS",
"IONTORRENT",
"ONT",
"PACBIO"
],
"handle": [
"-P",
"--platform"
],
"help": "Sequencing platform",
"name": "platform",
"type": "string"
},
{
"handle": [
"-q",
"--quality"
],
"help": "Enable quality control",
"name": "enable quality control",
"type": "boolean"
},
{
"handle": [
"-V",
"--validate"
],
"help": "Validate configuration file and emit a report",
"name": "validate only",
"type": "boolean"
},
{
"handle": [
"-D",
"--distance"
],
"help": "Display pairwise barcode distance during validation",
"name": "display distance",
"type": "boolean"
},
{
"handle": [
"-C",
"--compile"
],
"help": "Compiled JSON configuration file",
"name": "compile only",
"type": "boolean"
},
{
"handle": [
"-S",
"--static"
],
"help": "Static configuration JSON file",
"name": "static only",
"type": "boolean"
},
{
"handle": [
"-j",
"--job"
],
"help": "Include a copy of the compiled job in the report",
"name": "include compiled job",
"type": "boolean"
},
{
"handle": [
"-t",
"--threads"
],
"help": "Thread pool size",
"name": "threads",
"type": "integer"
},
{
"handle": [
"--decoding-threads"
],
"help": "Number of parallel decoding threads",
"name": "decoding threads",
"type": "integer"
},
{
"handle": [
"--htslib-threads"
],
"help": "Size of htslib thread pool size",
"name": "htslib threads",
"type": "integer"
},
{
"handle": [
"-B",
"--buffer"
],
"help": "Feed buffer capacity",
"name": "buffer capacity",
"type": "integer"
},
{
"handle": [
"--precision"
],
"help": "Output floating point precision",
"name": "float precision",
"type": "integer"
}
]
}
],
"comment": "pheniqs command line configuration file",
"default": {
"buffer capacity": 2048,
"corrected quality": 30,
"float precision": 15,
"input phred offset": 33,
"leading segment index": 0,
"output phred offset": 33,
"platform": "ILLUMINA"
},
"description": "",
"license": [
"This program comes with ABSOLUTELY NO WARRANTY. This is free software,",
"and you are welcome to redistribute it under certain conditions."
],
"name": "pheniqs",
"option": [
{
"handle": [
"-h",
"--help"
],
"help": "Show this help",
"name": "help only",
"type": "boolean"
},
{
"handle": [
"--version"
],
"help": "Show program version",
"name": "version only",
"type": "boolean"
}
],
"projection": {
"action": {
"application name": null,
"application version": null,
"base input url": null,
"base output url": null,
"default": null,
"epilog": null,
"full command": null,
"implementation": "generic",
"include compiled job": null,
"license": null,
"projection": null,
"schema": null,
"working directory": null
},
"cellular:barcode": {
"algorithm": null,
"concentration": 1,
"segment cardinality": null
},
"cellular:decoder": {
"algorithm": "pamld",
"codec": null,
"confidence threshold": 0.95,
"corrected quality": null,
"distance tolerance": null,
"high quality distance threshold": 0,
"high quality threshold": 30,
"noise": 0.01,
"quality masking threshold": 0,
"segment cardinality": 0,
"undetermined": null
},
"molecular:barcode": {
"algorithm": null,
"concentration": 1,
"segment cardinality": null
},
"molecular:decoder": {
"algorithm": "naive",
"codec": null,
"confidence threshold": 0.95,
"corrected quality": null,
"distance tolerance": null,
"high quality distance threshold": 0,
"high quality threshold": 30,
"noise": 0.01,
"quality masking threshold": 0,
"segment cardinality": 0,
"undetermined": null
},
"multiplex:barcode": {
"enable quality control": null,
"filter outgoing qc fail": false,
"output": null
},
"multiplex:decoder": {
"base output url": null,
"enable quality control": null,
"filter outgoing qc fail": false,
"output": null
},
"sample:barcode": {
"CN": null,
"DT": null,
"LB": null,
"PG": null,
"PI": null,
"PL": null,
"PM": null,
"SM": null,
"algorithm": null,
"concentration": 1,
"flowcell id": null,
"flowcell lane number": null,
"segment cardinality": null
},
"sample:decoder": {
"CN": null,
"DT": null,
"LB": null,
"PG": null,
"PI": null,
"PL": null,
"PM": null,
"SM": null,
"algorithm": "pamld",
"codec": null,
"confidence threshold": 0.95,
"corrected quality": null,
"distance tolerance": null,
"flowcell id": null,
"flowcell lane number": null,
"high quality distance threshold": 0,
"high quality threshold": 30,
"noise": 0.01,
"quality masking threshold": 0,
"segment cardinality": 0,
"undetermined": null
}
},
"prolog": [
"For more information please visit http://biosails.github.io/pheniqs",
"Lior Galanti < [email protected] > NYU Center for Genomics & Systems Biology 2018."
],
"schema": {
"instruction:lax": {
"$ref": "#/definitions/instruction",
"$schema": "http://json-schema.org/draft-04/schema#",
"definitions": {
"barcode_length": {
"examples": [
[
8,
8
]
],
"items": {
"description": "Number of IUPAC encoded nucleotides in the technical sequence.",
"examples": [
16
],
"minimum": 0,
"title": "Barcode segment length",
"type": "integer"
},
"minItems": 1,
"title": "Barcode length array",
"type": "array"
},
"barcode_sequence": {
"examples": [
[
"CGAGGCTG",
"AGAGGATA"
]
],
"items": {
"description": "IUPAC encoded DNA sequence. Degenerate nucleotides are not allowed.",
"examples": [
"CGAGGCTG"
],
"format": "regex",
"pattern": "^[ATCG=]+$",
"title": "Barcode segment sequence",
"type": "string"
},
"minItems": 1,
"title": "Barcode sequence array",
"type": "array"
},
"buffer_capacity": {
"description": "Number of buffered records in an input or output feed.",
"examples": [
2048
],
"minimum": 16,
"title": "Feed buffer capacity",
"type": "integer"
},
"buffer_resolution": {
"description": "Number of segments of each read interleaved into the feed.",
"examples": [
4
],
"minimum": 1,
"title": "Feed buffer resolution",
"type": "integer"
},
"classifier_type": {
"description": "The type of tag the classifier is decoding: sample, cellular or molecular. ",
"enum": [
"sample",
"cellular",
"molecular"
],
"title": "Classifier type",
"type": "string"
},
"compile_only": {
"description": "Compile instructions and emit as JSON without executing.",
"title": "Compile instruction",
"type": "boolean"
},
"concentration": {
"description": "Prior probability that a read will match the barcode.",
"minimum": 0,
"title": "Barcode concentration",
"type": "number"
},
"confidence_threshold": {
"description": "Non inclusive lower bound on the accepted decoding probability to be considered sucessful.",
"examples": [
0.95
],
"exclusiveMaximum": true,
"exclusiveMinimum": true,
"maximum": 1,
"minimum": 0,
"title": "Confidence threshold",
"type": "number"
},
"corrected_quality": {
"description": "Phred quality to assign to error corrected nucletides when interating them into the output read sequnce.",
"examples": [
30
],
"maximum": 104,
"minimum": 2,
"title": "Corrected quality",
"type": "integer"
},
"decoder": {
"properties": {
"CN": {
"$ref": "#/definitions/rg_cn"
},
"DS": {
"$ref": "#/definitions/rg_ds"
},
"DT": {
"$ref": "#/definitions/rg_dt"
},
"FO": {
"$ref": "#/definitions/rg_fo"
},
"KS": {
"$ref": "#/definitions/rg_ks"
},
"LB": {
"$ref": "#/definitions/rg_lb"
},
"PG": {
"$ref": "#/definitions/rg_pg"
},
"PI": {
"$ref": "#/definitions/rg_pi"
},
"PL": {
"$ref": "#/definitions/rg_pl"
},
"PM": {
"$ref": "#/definitions/rg_pm"
},
"SM": {
"$ref": "#/definitions/rg_sm"
},
"algorithm": {
"$ref": "#/definitions/decoding_algorithm"
},
"barcode length": {
"$ref": "#/definitions/barcode_length"
},
"base": {
"$ref": "#/definitions/decoder_base"
},
"base output url": {
"$ref": "#/definitions/url"
},
"classifier type": {
"$ref": "#/definitions/classifier_type"
},
"codec": {
"additionalProperties": {
"$ref": "#/definitions/decoder_class"
},
"type": "object"
},
"confidence threshold": {
"$ref": "#/definitions/confidence_threshold"
},
"corrected quality": {
"$ref": "#/definitions/corrected_quality"
},
"distance tolerance": {
"$ref": "#/definitions/distance_tolerance"
},
"flowcell id": {
"$ref": "#/definitions/flowcell_id"
},
"flowcell lane number": {
"$ref": "#/definitions/flowcell_lane_number"
},
"high quality distance threshold": {
"$ref": "#/definitions/high_quality_distance_threshold"
},
"high quality threshold": {
"$ref": "#/definitions/high_quality_threshold"
},
"index": {
"$ref": "#/definitions/index"
},
"noise": {
"$ref": "#/definitions/noise"
},
"nucleotide cardinality": {
"$ref": "#/definitions/nucleotide_cardinality"
},
"quality masking threshold": {
"$ref": "#/definitions/quality_masking_threshold"
},
"random barcode probability": {
"$ref": "#/definitions/random_barcode_probability"
},
"segment cardinality": {
"$ref": "#/definitions/segment_cardinality"
},
"shannon bound": {
"$ref": "#/definitions/shannon_bound"
},
"transform": {
"$ref": "#/definitions/transform"
},
"undetermined": {
"$ref": "#/definitions/undetermined_decoder_class"
}
},
"type": "object"
},
"decoder_base": {
"description": "Reference to the name of a base decoder to inherit from in the decoder directive",
"minLength": 1,
"title": "Base",
"type": "string"
},
"decoder_class": {
"properties": {
"BC": {
"$ref": "#/definitions/rg_bc"
},
"CN": {
"$ref": "#/definitions/rg_cn"
},
"DS": {
"$ref": "#/definitions/rg_ds"
},
"DT": {
"$ref": "#/definitions/rg_dt"
},
"FO": {
"$ref": "#/definitions/rg_fo"
},
"ID": {
"$ref": "#/definitions/rg_id"
},
"KS": {
"$ref": "#/definitions/rg_ks"
},
"LB": {
"$ref": "#/definitions/rg_lb"
},
"PG": {
"$ref": "#/definitions/rg_pg"
},
"PI": {
"$ref": "#/definitions/rg_pi"
},
"PL": {
"$ref": "#/definitions/rg_pl"
},
"PM": {
"$ref": "#/definitions/rg_pm"
},
"PU": {
"$ref": "#/definitions/rg_pu"
},
"SM": {
"$ref": "#/definitions/rg_sm"
},
"algorithm": {
"$ref": "#/definitions/decoding_algorithm"
},
"barcode": {
"$ref": "#/definitions/barcode_sequence"
},
"concentration": {
"$ref": "#/definitions/concentration"
},
"enable quality control": {
"$ref": "#/definitions/enable_quality_control"
},
"filter outgoing qc fail": {
"$ref": "#/definitions/filter_outgoing_qc_fail"
},
"flowcell id": {
"$ref": "#/definitions/flowcell_id"
},
"flowcell lane number": {
"$ref": "#/definitions/flowcell_lane_number"
},
"index": {
"$ref": "#/definitions/index"
},
"output": {
"$ref": "#/definitions/url_array"
},
"output feed by segment": {
"$ref": "#/definitions/feed_array"
},
"segment cardinality": {
"$ref": "#/definitions/segment_cardinality"
}
},
"type": "object"
},
"decoding_algorithm": {
"description": "The decoding algorithm used by the decoder. MDD is the miniumum distance decoder, PAMLD is the Phred-Adjusted Maximum Likelihood decoder. The Naive decoder will populate SAM auxiliary tags without attempting error correction and the passthrough simply route all read to the default output.",
"enum": [
"mdd",
"pamld",
"naive",
"passthrough"
],
"title": "Decoding algorithm",
"type": "string"
},
"decoding_topic": {
"items": {
"$ref": "#/definitions/decoder"
},
"minItems": 1,
"type": "array"
},
"distance_tolerance": {
"description": "The maximum Hammig distance a minimum distance decoder will tolerate on each barcode segment",
"examples": [
[
2,
1
]
],
"items": {
"description": "The maximum Hammig distance a minimum distance decoder will tolerate on the barcode segment",
"examples": [
1
],
"minimum": 0,
"title": "Segment distance tolerance",
"type": "integer"
},
"minItems": 1,
"title": "Distance tolerance array",
"type": "array"
},
"enable_quality_control": {
"description": "Do not update Quality Control accumulators for a minor speed gain.",
"title": "Disable quality control",
"type": "boolean"
},
"feed": {
"properties": {
"capacity": {
"$ref": "#/definitions/buffer_capacity"
},
"direction": {
"$ref": "#/definitions/io_direction"
},
"index": {
"$ref": "#/definitions/index"
},
"phred offset": {
"$ref": "#/definitions/phred_offset"
},
"platform": {
"$ref": "#/definitions/rg_pl"
},
"resolution": {
"$ref": "#/definitions/buffer_resolution"
},
"url": {
"$ref": "#/definitions/url"
}
},
"type": "object"
},
"feed_array": {
"items": {
"$ref": "#/definitions/feed"
},
"minItems": 1,
"type": "array"
},
"filter_incoming_qc_fail": {
"description": "Filter incoming QC failed reads.",
"title": "Filter incoming QC failed reads",
"type": "boolean"
},
"filter_outgoing_qc_fail": {
"description": "Filter outgoing QC failed reads.",
"title": "Filter outgoing QC failed reads",
"type": "boolean"
},
"flowcell_id": {
"description": "A unique identifier of the flowcel used to deduce read group identifiers.",
"examples": [
"H7LT2DSXX"
],
"minLength": 1,
"title": "Flowcell ID",
"type": "string"
},
"flowcell_lane_number": {
"description": "The flowcel lane number used to deduce read group identifiers.",
"examples": [
3
],
"minimum": 0,
"title": "Flowcell lane number",
"type": "integer"
},
"hd": {
"GO": {
"$ref": "#/definitions/hd_go"
},
"SO": {
"$ref": "#/definitions/hd_so"
},
"VN": {
"$ref": "#/definitions/hd_vn"
}
},
"hd_go": {
"description": "Grouping of alignments, indicating that similar alignment records are grouped together but the file is not necessarily sorted overall.",
"enum": [
"none",
"query",
"reference"
],
"title": "Grouping order",
"type": "string"
},
"hd_so": {
"description": "Sorting order of alignments. For coordinate sort, the major sort key is the RNAME field, with order defined by the order of @SQ lines in the header. The minor sort key is the POS field. For alignments with equal RNAME and POS, order is arbitrary. All alignments with * in RNAME field follow alignments with some other value but otherwise are in arbitrary order.",
"enum": [
"unknown",
"unsorted",
"queryname",
"coordinate"
],
"title": "Sorting order",
"type": "string"
},
"hd_vn": {
"description": "HTS format version",
"format": "regex",
"pattern": "^[0-9]+\\.[0-9]+$",
"title": "Format version",
"type": "string"
},
"high_quality_distance_threshold": {
"description": "High quality mismatch threshold above which classification fails. Match must have a number of mismatches greater or equal the threshold for classification to fail.",
"examples": [
3
],
"minimum": 0,
"title": "High quality distance threshold",
"type": "integer"
},
"high_quality_threshold": {
"description": "Phred quality threshold obove which a mismatch is considered a high quality mismatch. The quality of the sequenced nucloetide must be greater or equal the threshold to be considered a high quality mismatch.",
"examples": [
30
],
"maximum": 104,
"minimum": 2,
"title": "High quality threshold",
"type": "integer"
},
"index": {
"minimum": 0,
"type": "integer"
},
"instruction": {
"properties": {
"CN": {
"$ref": "#/definitions/rg_cn"
},
"DS": {
"$ref": "#/definitions/rg_ds"
},
"DT": {
"$ref": "#/definitions/rg_dt"
},
"FO": {
"$ref": "#/definitions/rg_fo"
},
"KS": {
"$ref": "#/definitions/rg_ks"
},
"LB": {
"$ref": "#/definitions/rg_lb"
},
"PG": {
"$ref": "#/definitions/rg_pg"
},
"PI": {
"$ref": "#/definitions/rg_pi"
},
"PL": {
"$ref": "#/definitions/rg_pl"
},
"PM": {