public class IntervalListTools extends CommandLineProgram
Modifier and Type | Class and Description |
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static class |
IntervalListTools.Action |
Modifier and Type | Field and Description |
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IntervalListTools.Action |
ACTION |
int |
BREAK_BANDS_AT_MULTIPLES_OF |
java.util.List<java.lang.String> |
COMMENT |
boolean |
INCLUDE_FILTERED |
java.util.List<java.io.File> |
INPUT |
boolean |
INVERT |
java.io.File |
OUTPUT |
int |
PADDING |
int |
SCATTER_COUNT |
java.util.List<java.io.File> |
SECOND_INPUT |
boolean |
SORT |
IntervalListScatterer.Mode |
SUBDIVISION_MODE |
boolean |
UNIQUE |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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IntervalListTools() |
Modifier and Type | Method and Description |
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protected java.lang.String[] |
customCommandLineValidation()
Put any custom command-line validation in an override of this method.
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protected int |
doWork()
Do the work after command line has been parsed.
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static java.io.File |
getScatteredFileName(java.io.File scatterDirectory,
long scatterTotal,
java.lang.String formattedIndex) |
static void |
main(java.lang.String[] args) |
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="I", doc="One or more interval lists. If multiple interval lists are provided the output is theresult of merging the inputs. Supported formats are interval_list and VCF.", minElements=1) public java.util.List<java.io.File> INPUT
@Option(doc="The output interval list file to write (if SCATTER_COUNT is 1) or the directory into which to write the scattered interval sub-directories (if SCATTER_COUNT > 1)", shortName="O", optional=true) public java.io.File OUTPUT
@Option(doc="The amount to pad each end of the intervals by before other operations are undertaken. Negative numbers are allowed and indicate intervals should be shrunk. Resulting intervals < 0 bases long will be removed. Padding is applied to the interval lists <b> before </b> the ACTION is performed.", optional=true) public int PADDING
@Option(doc="If true, merge overlapping and adjacent intervals to create a list of unique intervals. Implies SORT=true") public boolean UNIQUE
@Option(doc="Action to take on inputs.") public IntervalListTools.Action ACTION
@Option(shortName="SI", doc="Second set of intervals for SUBTRACT and DIFFERENCE operations.", optional=true) public java.util.List<java.io.File> SECOND_INPUT
@Option(doc="One or more lines of comment to add to the header of the output file.", optional=true) public java.util.List<java.lang.String> COMMENT
@Option(doc="The number of files into which to scatter the resulting list by locus; in some situations, fewer intervals may be emitted. Note - if > 1, the resultant scattered intervals will be sorted and uniqued. The sort will be inverted if the INVERT flag is set.") public int SCATTER_COUNT
@Option(doc="Whether to include filtered variants in the vcf when generating an interval list from vcf", optional=true) public boolean INCLUDE_FILTERED
@Option(shortName="BRK", doc="If set to a positive value will create a new interval list with the original intervals broken up at integer multiples of this value. Set to 0 to NOT break up intervals", optional=true) public int BREAK_BANDS_AT_MULTIPLES_OF
@Option(shortName="M", doc="Do not subdivide ") public IntervalListScatterer.Mode SUBDIVISION_MODE
public static void main(java.lang.String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
protected java.lang.String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram
public static java.io.File getScatteredFileName(java.io.File scatterDirectory, long scatterTotal, java.lang.String formattedIndex)