Package picard.util
Class BedToIntervalList
java.lang.Object
picard.cmdline.CommandLineProgram
picard.util.BedToIntervalList
-
Field Summary
FieldsModifier and TypeFieldDescriptionboolean
boolean
boolean
boolean
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
doWork()
Do the work after command line has been parsed.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
-
Field Details
-
INPUT
-
SEQUENCE_DICTIONARY
@Argument(shortName="SD", doc="The sequence dictionary, or BAM/VCF/IntervalList from which a dictionary can be extracted.") public File SEQUENCE_DICTIONARY -
OUTPUT
-
SORT
@Argument(doc="If true, sort the output interval list before writing it.") public boolean SORT -
UNIQUE
@Argument(doc="If true, unique the output interval list by merging overlapping regions, before writing it (implies sort=true).") public boolean UNIQUE -
DROP_MISSING_CONTIGS
@Hidden @Argument(doc="If true, entries that are on contig-names that are missing from the provided dictionary will be dropped.") public boolean DROP_MISSING_CONTIGS -
KEEP_LENGTH_ZERO_INTERVALS
@Argument(doc="If true, write length zero intervals in input bed file to resulting interval list file.") public boolean KEEP_LENGTH_ZERO_INTERVALS
-
-
Constructor Details
-
BedToIntervalList
public BedToIntervalList()
-
-
Method Details
-
doWork
protected int doWork()Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
-