org.broadinstitute.hellbender.tools.copynumber.arguments

Class CopyNumberArgumentValidationUtils

java.lang.Object

org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils

public final class CopyNumberArgumentValidationUtils
extends java.lang.Object

Method Summary

Modifier and Type	Method and Description
static java.lang.String	addTrailingSlashIfNecessary(java.lang.String outputDir)
static java.lang.String	getCanonicalPath(java.io.File file) File paths that are passed to PythonScriptExecutor must be canonical (rather than absolute).
static java.lang.String	getCanonicalPath(java.lang.String filename) File paths that are passed to PythonScriptExecutor must be canonical (rather than absolute).
static boolean	isSameDictionary(htsjdk.samtools.SAMSequenceDictionary dictionary1, htsjdk.samtools.SAMSequenceDictionary dictionary2) Compares two non-null sequence dictionaries using sequence index, name, and length only.
static SimpleIntervalCollection	resolveIntervals(java.io.File readCountFile, IntervalArgumentCollection intervalArgumentCollection, org.apache.logging.log4j.Logger logger) Resolve intervals from an IntervalArgumentCollection and a read-count file.
static void	validateAndPrepareOutputDirectories(java.io.File... outputDirectories) Validate that output directories are writeable.
static AnnotatedIntervalCollection	validateAnnotatedIntervals(java.io.File annotatedIntervalsFile, AbstractLocatableCollection<?,?> locatableCollection, org.apache.logging.log4j.Logger logger) Checks equality of the sequence dictionary and intervals contained in an locatableCollection against those contained in an AnnotatedIntervalCollection represented by annotatedIntervalsFile.
static AnnotatedIntervalCollection	validateAnnotatedIntervalsSubset(java.io.File annotatedIntervalsFile, AbstractLocatableCollection<?,?> locatableCollection, org.apache.logging.log4j.Logger logger) Same as validateAnnotatedIntervals(java.io.File, org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractLocatableCollection<?, ?>, org.apache.logging.log4j.Logger), except we only require that annotatedIntervalsFile contains as a subset all the intervals contained in locatableCollection along with equality of the sequence dictionaries.
static void	validateInputs(java.io.File... inputs) Validate that input files and/or directories are readable if they are not null (i.e., optional inputs).
static void	validateIntervalArgumentCollection(IntervalArgumentCollection intervalArgumentCollection) Validate that the interval-argument collection parameters minimally modify the input intervals.
static <T extends htsjdk.samtools.util.Locatable> void	validateIntervals(java.util.List<T> intervals, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary) Validate that a list of locatables is valid and sorted according to a sequence dictionary and contains no duplicates or overlaps.
static void	validateOutputFiles(java.io.File... outputFiles) Validate that output files are writeable, whether or not they already exist.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

validateIntervalArgumentCollection

public static void validateIntervalArgumentCollection(IntervalArgumentCollection intervalArgumentCollection)

Validate that the interval-argument collection parameters minimally modify the input intervals.

validateIntervals

public static <T extends htsjdk.samtools.util.Locatable> void validateIntervals(java.util.List<T> intervals,
                                                                                htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)

Validate that a list of locatables is valid and sorted according to a sequence dictionary and contains no duplicates or overlaps.

isSameDictionary

public static boolean isSameDictionary(htsjdk.samtools.SAMSequenceDictionary dictionary1,
                                       htsjdk.samtools.SAMSequenceDictionary dictionary2)

Compares two non-null sequence dictionaries using sequence index, name, and length only. Less stringent than SAMSequenceDictionary.isSameDictionary(htsjdk.samtools.SAMSequenceDictionary).

resolveIntervals

public static SimpleIntervalCollection resolveIntervals(java.io.File readCountFile,
                                                        IntervalArgumentCollection intervalArgumentCollection,
                                                        org.apache.logging.log4j.Logger logger)

Resolve intervals from an IntervalArgumentCollection and a read-count file. If intervals are not specified in the IntervalArgumentCollection, they are taken from the read-count file. The sequence dictionary is taken from the read-count file. A SimpleIntervalCollection constructed using these intervals and sequence dictionary is returned and can be used for further validation.

validateAnnotatedIntervals

public static AnnotatedIntervalCollection validateAnnotatedIntervals(java.io.File annotatedIntervalsFile,
                                                                     AbstractLocatableCollection<?,?> locatableCollection,
                                                                     org.apache.logging.log4j.Logger logger)

Checks equality of the sequence dictionary and intervals contained in an locatableCollection against those contained in an AnnotatedIntervalCollection represented by annotatedIntervalsFile. If the latter is null, then null is returned; otherwise, the AnnotatedIntervalCollection represented by inputAnnotatedIntervalsFile is returned if the intervals are equal, and an exception is thrown if they are not.

validateAnnotatedIntervalsSubset

public static AnnotatedIntervalCollection validateAnnotatedIntervalsSubset(java.io.File annotatedIntervalsFile,
                                                                           AbstractLocatableCollection<?,?> locatableCollection,
                                                                           org.apache.logging.log4j.Logger logger)

Same as validateAnnotatedIntervals(java.io.File, org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractLocatableCollection<?, ?>, org.apache.logging.log4j.Logger), except we only require that annotatedIntervalsFile contains as a subset all the intervals contained in locatableCollection along with equality of the sequence dictionaries. The corresponding subset of annotated intervals is returned if appropriate.

validateInputs

public static void validateInputs(java.io.File... inputs)

Validate that input files and/or directories are readable if they are not null (i.e., optional inputs).

validateOutputFiles

public static void validateOutputFiles(java.io.File... outputFiles)

Validate that output files are writeable, whether or not they already exist.

validateAndPrepareOutputDirectories

public static void validateAndPrepareOutputDirectories(java.io.File... outputDirectories)

Validate that output directories are writeable. If a directory does not exist, create it.

getCanonicalPath

public static java.lang.String getCanonicalPath(java.io.File file)

File paths that are passed to PythonScriptExecutor must be canonical (rather than absolute). See https://github.com/broadinstitute/gatk/issues/4724.

getCanonicalPath

public static java.lang.String getCanonicalPath(java.lang.String filename)

File paths that are passed to PythonScriptExecutor must be canonical (rather than absolute). See https://github.com/broadinstitute/gatk/issues/4724.

addTrailingSlashIfNecessary

public static java.lang.String addTrailingSlashIfNecessary(java.lang.String outputDir)