Constant Field Values

picard.analysis.*

• picard.analysis.CollectInsertSizeMetrics 

  Modifier and Type	Constant Field	Value
  protected static final String	Histogram_R_SCRIPT	"picard/analysis/insertSizeHistogram.R"

• picard.analysis.CollectRrbsMetrics 

  Modifier and Type	Constant Field	Value
  public static final String	DETAIL_FILE_EXTENSION	"rrbs_detail_metrics"
  public static final String	PDF_FILE_EXTENSION	"rrbs_qc.pdf"
  public static final String	SUMMARY_FILE_EXTENSION	"rrbs_summary_metrics"

• picard.analysis.artifacts.SequencingArtifactMetrics 

  Modifier and Type	Constant Field	Value
  public static final String	BAIT_BIAS_DETAILS_EXT	".bait_bias_detail_metrics"
  public static final String	BAIT_BIAS_SUMMARY_EXT	".bait_bias_summary_metrics"
  public static final String	ERROR_SUMMARY_EXT	".error_summary_metrics"
  public static final String	PRE_ADAPTER_DETAILS_EXT	".pre_adapter_detail_metrics"
  public static final String	PRE_ADAPTER_SUMMARY_EXT	".pre_adapter_summary_metrics"

• picard.analysis.directed.TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics> 

  Modifier and Type	Constant Field	Value
  public static final int	NEAR_PROBE_DISTANCE_DEFAULT	250

picard.cmdline.*

• picard.cmdline.StandardOptionDefinitions 

  Modifier and Type	Constant Field	Value
  public static final String	ASSUME_SORT_ORDER_SHORT_NAME	"ASO"
  public static final String	ASSUME_SORTED_SHORT_NAME	"AS"
  public static final String	EXPECTED_INSERT_SIZE_SHORT_NAME	"INSERT"
  public static final String	INPUT_SHORT_NAME	"I"
  public static final String	LANE_SHORT_NAME	"L"
  public static final String	LIBRARY_NAME_SHORT_NAME	"LIB"
  public static final String	METRICS_FILE_SHORT_NAME	"M"
  public static final String	MINIMUM_LOD_SHORT_NAME	"LOD"
  public static final String	MINIMUM_MAPPING_QUALITY_SHORT_NAME	"MQ"
  public static final String	OUTPUT_SHORT_NAME	"O"
  public static final String	PF_READS_ONLY_SHORT_NAME	"PF"
  public static final String	PROGRAM_RECORD_ID_SHORT_NAME	"PG"
  public static final String	READ_GROUP_ID_SHORT_NAME	"RG"
  public static final String	REFERENCE_SHORT_NAME	"R"
  public static final String	SAMPLE_ALIAS_SHORT_NAME	"ALIAS"
  public static final String	SEQUENCE_DICTIONARY_SHORT_NAME	"SD"
  public static final String	SORT_ORDER_SHORT_NAME	"SO"
  public static final String	USE_ORIGINAL_QUALITIES_SHORT_NAME	"OQ"

picard.fingerprint.*

• picard.fingerprint.CheckFingerprint 

  Modifier and Type	Constant Field	Value
  public static final String	FINGERPRINT_DETAIL_FILE_SUFFIX	"fingerprinting_detail_metrics"
  public static final String	FINGERPRINT_SUMMARY_FILE_SUFFIX	"fingerprinting_summary_metrics"

• picard.fingerprint.FingerprintChecker 

  Modifier and Type	Constant Field	Value
  public static final double	DEFAULT_GENOTYPING_ERROR_RATE	0.01
  public static final int	DEFAULT_MAXIMAL_PL_DIFFERENCE	30
  public static final int	DEFAULT_MINIMUM_BASE_QUALITY	20
  public static final int	DEFAULT_MINIMUM_MAPPING_QUALITY	10

• picard.fingerprint.HaplotypeMap 

  Modifier and Type	Constant Field	Value
  public static final String	HET_GENOTYPE_FOR_PHASING	"HetGenotypeForPhasing"
  public static final String	PHASESET_PREFIX	"PhaseSet"
  public static final String	SYNTHETIC_PHASESET_PREFIX	"Synthetic"

picard.illumina.*

• picard.illumina.ExtractIlluminaBarcodes 

  Modifier and Type	Constant Field	Value
  public static final String	BARCODE_NAME_COLUMN	"barcode_name"
  public static final String	BARCODE_SEQUENCE_1_COLUMN	"barcode_sequence_1"
  public static final String	BARCODE_SEQUENCE_COLUMN	"barcode_sequence"
  public static final String	LIBRARY_NAME_COLUMN	"library_name"

• picard.illumina.IlluminaBasecallsToSam 

  Modifier and Type	Constant Field	Value
  public static final String	USAGE	"Generate a SAM or BAM file from data in an Illumina basecalls output directory"

• picard.illumina.parser.MultiTileBclParser 

  Modifier and Type	Constant Field	Value
  public static final byte	MASKING_QUALITY	2

• picard.illumina.parser.ParameterizedFileUtil 

  Modifier and Type	Constant Field	Value
  protected static final boolean	DefaultSkipEmptyFiles	true
  public static final String	PER_TILE_PATTERN_STRING	"s_(\\d+)_(\\d{1,5})"

• picard.illumina.parser.ReadStructure 

  Modifier and Type	Constant Field	Value
  public static final String	PARAMETER_DOC	"A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the input data consists of 80 base clusters and we provide a read structure of \"28T8M8B8S28T\" then the sequence may be split up into four reads:\n* read one with 28 cycles (bases) of template\n* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)\n* read three with 8 cycles (bases) of sample barcode\n* 8 cycles (bases) skipped.\n* read four with 28 cycles (bases) of template\nThe skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein."

• picard.illumina.parser.readers.AbstractIlluminaPositionFileReader 

  Modifier and Type	Constant Field	Value
  public static final float	MAX_POS	1.0E7f
  public static final float	MIN_POS	-10.0f
  public static final String	S_LOCS_FILE	"s.locs"

• picard.illumina.parser.readers.BclQualityEvaluationStrategy 

  Modifier and Type	Constant Field	Value
  public static final int	ILLUMINA_ALLEGED_MINIMUM_QUALITY	2

• picard.illumina.parser.readers.FilterFileReader 

  Modifier and Type	Constant Field	Value
  public static final int	EXPECTED_VERSION	3

• picard.illumina.quality.CollectHiSeqXPfFailMetrics 

  Modifier and Type	Constant Field	Value
  public static final String	detailedMetricsExtension	".pffail_detailed_metrics"
  public static final String	summaryMetricsExtension	".pffail_summary_metrics"

picard.metrics.*

• picard.metrics.MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,Histogram_KEY extends Comparable,ARGTYPE> 

  Modifier and Type	Constant Field	Value
  public static final String	UNKNOWN	"unknown"

picard.sam.*

• picard.sam.AbstractAlignmentMerger 

  Modifier and Type	Constant Field	Value
  public static final int	MAX_RECORDS_IN_RAM	500000

• picard.sam.AddOrReplaceReadGroups 

  Modifier and Type	Constant Field	Value
  public static final String	READGROUP_ID_REGEX	"^[ -~]+$"

• picard.sam.SplitSamByLibrary 

  Modifier and Type	Constant Field	Value
  public static final int	NO_LIBRARIES_SPECIFIED_IN_HEADER	2

• picard.sam.markduplicates.MarkDuplicates 

  Modifier and Type	Constant Field	Value
  public static final String	DUPLICATE_SET_INDEX_TAG	"DI"
  public static final String	DUPLICATE_SET_SIZE_TAG	"DS"
  public static final String	DUPLICATE_TYPE_LIBRARY	"LB"
  public static final String	DUPLICATE_TYPE_SEQUENCING	"SQ"
  public static final String	DUPLICATE_TYPE_TAG	"DT"

• picard.sam.markduplicates.util.OpticalDuplicateFinder 

  Modifier and Type	Constant Field	Value
  public static final int	DEFAULT_BIG_DUPLICATE_SET_SIZE	1000
  public static final int	DEFAULT_MAX_DUPLICATE_SET_SIZE	300000
  public static final int	DEFAULT_OPTICAL_DUPLICATE_DISTANCE	100

• picard.sam.markduplicates.util.ReadEnds 

  Modifier and Type	Constant Field	Value
  public static final byte	F	0
  public static final byte	FF	2
  public static final byte	FR	3
  public static final byte	R	1
  public static final byte	RF	5
  public static final byte	RR	4

• picard.sam.markduplicates.util.ReadEndsForMarkDuplicates 

  Modifier and Type	Constant Field	Value
  protected static final int	SIZE_OF	69

• picard.sam.util.PhysicalLocation 

  Modifier and Type	Constant Field	Value
  public static final int	NO_VALUE	-1

picard.util.*

• picard.util.AdapterMarker 

  Modifier and Type	Constant Field	Value
  public static final int	DEFAULT_ADAPTER_LENGTH	30
  public static final int	DEFAULT_NUM_ADAPTERS_TO_KEEP	1
  public static final int	DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN	100

• picard.util.AsyncIterator<T> 

  Modifier and Type	Constant Field	Value
  public static final int	DEFAULT_QUEUE_SIZE	2000

• picard.util.ClippingUtility 

  Modifier and Type	Constant Field	Value
  public static final double	MAX_ERROR_RATE	0.1
  public static final double	MAX_PE_ERROR_RATE	0.1
  public static final int	MIN_MATCH_BASES	12
  public static final int	MIN_MATCH_PE_BASES	6
  public static final int	NO_MATCH	-1

• picard.util.IlluminaUtil 

  Modifier and Type	Constant Field	Value
  public static final String	BARCODE_DELIMITER	"-"

• picard.util.LiftoverUtils 

  Modifier and Type	Constant Field	Value
  public static final String	REV_COMPED_ALLELES	"ReverseComplementedAlleles"
  public static final String	SWAPPED_ALLELES	"SwappedAlleles"

• picard.util.MathUtil 

  Modifier and Type	Constant Field	Value
  public static final double	MAX_PROB_BELOW_ONE	0.9999999999999999

• picard.util.help.HelpConstants 

  Modifier and Type	Constant Field	Value
  public static final String	DOC_CAT_BASE_CALLING	"Base Calling"
  public static final String	DOC_CAT_BASE_CALLING_SUMMARY	"Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters"
  public static final String	DOC_CAT_DIAGNOSTICS_AND_QC	"Diagnostics and Quality Control"
  public static final String	DOC_CAT_DIAGNOSTICS_AND_QC_SUMMARY	"Tools that collect sequencing quality related and comparative metrics"
  public static final String	DOC_CAT_INTERVALS_MANIPULATION	"Intervals Manipulation"
  public static final String	DOC_CAT_INTERVALS_MANIPULATION_SUMMARY	"Tools that process genomic intervals in various formats"
  public static final String	DOC_CAT_OTHER	"Other"
  public static final String	DOC_CAT_OTHER_SUMMARY	"Miscellaneous tools, e.g. those that aid in data streaming"
  public static final String	DOC_CAT_READ_DATA_MANIPULATION	"Read Data Manipulation"
  public static final String	DOC_CAT_READ_DATA_MANIPULATION_SUMMARY	"Tools that manipulate read data in SAM, BAM or CRAM format"
  public static final String	DOC_CAT_REFERENCE	"Reference"
  public static final String	DOC_CAT_REFERENCE_SUMMARY	"Tools that analyze and manipulate FASTA format references"
  public static final String	DOC_CAT_TEST	"Test Tools"
  public static final String	DOC_CAT_TEST_SUMMARY	"Tools for internal test purposes"
  public static final String	DOC_CAT_VARIANT_EVALUATION	"Variant Evaluation and Refinement"
  public static final String	DOC_CAT_VARIANT_EVALUATION_SUMMARY	"Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine"
  public static final String	DOC_CAT_VARIANT_FILTERING	"Variant Filtering"
  public static final String	DOC_CAT_VARIANT_FILTERING_SUMMARY	"Tools that filter variants by annotating the FILTER column"
  public static final String	DOC_CAT_VARIANT_MANIPULATION	"Variant Manipulation"
  public static final String	DOC_CAT_VARIANT_MANIPULATION_SUMMARY	"Tools that manipulate variant call format (VCF) data"
  public static final String	DOC_SUPERCAT_EXCLUDE	"exclude"
  public static final String	DOC_SUPERCAT_TOOLS	"tools"
  public static final String	DOC_SUPERCAT_UTILITIES	"utilities"

picard.vcf.*

• picard.vcf.GenotypeConcordance 

  Modifier and Type	Constant Field	Value
  public static final String	CONTINGENCY_METRICS_FILE_EXTENSION	".genotype_concordance_contingency_metrics"
  public static final String	CONTINGENCY_STATE_TAG	"CONC_ST"
  public static final String	DETAILED_METRICS_FILE_EXTENSION	".genotype_concordance_detail_metrics"
  public static final String	OUTPUT_VCF_CALL_SAMPLE_NAME	"call"
  public static final String	OUTPUT_VCF_FILE_EXTENSION	".genotype_concordance.vcf.gz"
  public static final String	OUTPUT_VCF_TRUTH_SAMPLE_NAME	"truth"
  public static final String	SUMMARY_METRICS_FILE_EXTENSION	".genotype_concordance_summary_metrics"

• picard.vcf.LiftoverVcf 

  Modifier and Type	Constant Field	Value
  public static final String	ATTEMPTED_LOCUS	"AttemptedLocus"
  public static final String	FILTER_CANNOT_LIFTOVER_INDEL	"ReverseComplementedIndel"
  public static final String	FILTER_INDEL_STRADDLES_TWO_INTERVALS	"IndelStraddlesMultipleIntevals"
  public static final String	FILTER_MISMATCHING_REF_ALLELE	"MismatchedRefAllele"
  public static final String	FILTER_NO_TARGET	"NoTarget"
  public static final String	ORIGINAL_CONTIG	"OriginalContig"
  public static final String	ORIGINAL_START	"OriginalStart"

• picard.vcf.VcfToIntervalList 

  Modifier and Type	Constant Field	Value
  public static final String	INCLUDE_FILTERED_SHORT_NAME	"IF"

• picard.vcf.filter.AlleleBalanceFilter 

  Modifier and Type	Constant Field	Value
  public static final String	AB_FILTER	"AlleleBalance"

• picard.vcf.filter.FilterApplyingVariantIterator 

  Modifier and Type	Constant Field	Value
  public static final String	ALL_GTS_FILTERED	"AllGtsFiltered"
  public static final String	PASS_FILTER	"PASS"

• picard.vcf.filter.QdFilter 

  Modifier and Type	Constant Field	Value
  public static final String	FILTER_NAME	"LowQD"