org.broadinstitute.hellbender.engine

Interface Shard<T>

All Superinterfaces:

java.lang.Iterable<T>, htsjdk.samtools.util.Locatable

All Known Implementing Classes:

DownsampleableSparkReadShard, ShardBoundaryShard, ShardToMultiIntervalShardAdapter

public interface Shard<T>
extends java.lang.Iterable<T>, htsjdk.samtools.util.Locatable

A Shard of records of type T covering a specific genomic interval, optionally expanded by a configurable amount of padded data, that provides the ability to iterate over its records.

Method Summary

Modifier and Type	Method and Description
static java.util.List<ShardBoundary>	divideIntervalIntoShards(SimpleInterval interval, int shardSize, int shardStep, int shardPadding, htsjdk.samtools.SAMSequenceDictionary dictionary) Divide an interval into ShardBoundaries.
static java.util.List<ShardBoundary>	divideIntervalIntoShards(SimpleInterval interval, int shardSize, int shardPadding, htsjdk.samtools.SAMSequenceDictionary dictionary) Divide an interval into ShardBoundaries.
default java.lang.String	getContig()
default int	getEnd()
SimpleInterval	getInterval()
SimpleInterval	getPaddedInterval()
default int	getStart()

Methods inherited from interface java.lang.Iterable

forEach, iterator, spliterator

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Method Detail

getInterval

SimpleInterval getInterval()

Returns:

the interval this shard spans

getPaddedInterval

SimpleInterval getPaddedInterval()

Returns:

the interval this shard spans, potentially with additional padding on each side it must be the case that for a given Shard getPaddedSpan().contains(getInterval())

getStart

default int getStart()

Specified by:

getStart in interface htsjdk.samtools.util.Locatable

Returns:

the start of the non-padded interval this shard covers

getEnd

default int getEnd()

Specified by:

getEnd in interface htsjdk.samtools.util.Locatable

Returns:

the end of the non-padded interval this shard covers

getContig

default java.lang.String getContig()

Specified by:

getContig in interface htsjdk.samtools.util.Locatable

Returns:

contig this shard belongs to

divideIntervalIntoShards

static java.util.List<ShardBoundary> divideIntervalIntoShards(SimpleInterval interval,
                                                              int shardSize,
                                                              int shardPadding,
                                                              htsjdk.samtools.SAMSequenceDictionary dictionary)

Divide an interval into ShardBoundaries. Each shard will cover up to shardSize bases, include shardPadding bases of extra padding on either side, and begin shardSize bases after the previous shard (ie., shards will not overlap except potentially in the padded regions).

Parameters:

interval - interval to shard; must be on the contig according to the provided dictionary

shardSize - desired shard size; intervals larger than this will be divided into shards of up to this size

shardPadding - desired shard padding; each shard's interval will be padded on both sides by this number of bases (may be 0)

dictionary - sequence dictionary for reads

Returns:

List of ShardBoundary objects spanning the interval

divideIntervalIntoShards

static java.util.List<ShardBoundary> divideIntervalIntoShards(SimpleInterval interval,
                                                              int shardSize,
                                                              int shardStep,
                                                              int shardPadding,
                                                              htsjdk.samtools.SAMSequenceDictionary dictionary)

Divide an interval into ShardBoundaries. Each shard will cover up to shardSize bases, include shardPadding bases of extra padding on either side, and begin shardStep bases after the previous shard.

Parameters:

interval - interval to shard; must be on the contig according to the provided dictionary

shardSize - desired shard size; intervals larger than this will be divided into shards of up to this size

shardStep - each shard will begin this many bases away from the previous shard

shardPadding - desired shard padding; each shard's interval will be padded on both sides by this number of bases (may be 0)

dictionary - sequence dictionary for reads

Returns:

List of ShardBoundary objects spanning the interval