org.broadinstitute.hellbender.utils

Class IndexUtils

java.lang.Object

org.broadinstitute.hellbender.utils.IndexUtils

public final class IndexUtils
extends java.lang.Object

Method Summary

Modifier and Type	Method and Description
static void	checkIndexVersionAndModificationTime(java.nio.file.Path featureFile, java.nio.file.Path indexFile, htsjdk.tribble.index.Index index)
static htsjdk.samtools.SAMSequenceDictionary	createSequenceDictionaryFromFeatureIndex(java.nio.file.Path featureFile) get the sequence dictionary contig list that is in the index or null if there is no index or no contigs Note: the dictionary returned will not have the contig lengths filled in SAMSequenceRecord.UNKNOWN_SEQUENCE_LENGTH is used.
static boolean	isSequenceDictionaryFromIndex(htsjdk.samtools.SAMSequenceDictionary sequenceDictionary) Determine if sequenceDictionary has the form of a dictionary created from an index file by createSequenceDictionaryFromFeatureIndex(java.nio.file.Path)).
static htsjdk.tribble.index.Index	loadIndex(java.nio.file.Path featureFile) Loads and returns the index of the feature file or null if there is no index.
static htsjdk.tribble.index.Index	loadTabixIndex(java.nio.file.Path featureFile) Try to load the tabix index from disk, checking for out of date indexes and old versions
static htsjdk.tribble.index.Index	loadTribbleIndex(java.nio.file.Path featureFile) Load a Tribble .idx index from disk, checking for out of date indexes and old versions

Methods inherited from class java.lang.Object

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

Method Detail

loadTribbleIndex

public static htsjdk.tribble.index.Index loadTribbleIndex(java.nio.file.Path featureFile)

Load a Tribble .idx index from disk, checking for out of date indexes and old versions

Returns:

an Index, or null if we're unable to load

loadTabixIndex

public static htsjdk.tribble.index.Index loadTabixIndex(java.nio.file.Path featureFile)

Try to load the tabix index from disk, checking for out of date indexes and old versions

Returns:

an Index, or null if we're unable to load

checkIndexVersionAndModificationTime

public static void checkIndexVersionAndModificationTime(java.nio.file.Path featureFile,
                                                        java.nio.file.Path indexFile,
                                                        htsjdk.tribble.index.Index index)

Throws:

UserException - the index is not the current version. Prints a warning if the index is not up-to date (ie older than the feature file)

createSequenceDictionaryFromFeatureIndex

public static htsjdk.samtools.SAMSequenceDictionary createSequenceDictionaryFromFeatureIndex(java.nio.file.Path featureFile)

get the sequence dictionary contig list that is in the index or null if there is no index or no contigs Note: the dictionary returned will not have the contig lengths filled in SAMSequenceRecord.UNKNOWN_SEQUENCE_LENGTH is used. Note: this method is specifically designed for getting sequence dictionaries from indices on Feature files (tribble or tabix indices)

Returns:

a SAMSequenceDictionary or null if the index cannot be loaded or there are no contigs in the index

isSequenceDictionaryFromIndex

public static boolean isSequenceDictionaryFromIndex(htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)

Determine if sequenceDictionary has the form of a dictionary created from an index file by createSequenceDictionaryFromFeatureIndex(java.nio.file.Path)).

Parameters:

sequenceDictionary -

Returns:

loadIndex

public static htsjdk.tribble.index.Index loadIndex(java.nio.file.Path featureFile)

Loads and returns the index of the feature file or null if there is no index. First it tries to load the tribble index and then to load the tabix index.