Package htsjdk.samtools
Class BAMFileSpan
- java.lang.Object
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- htsjdk.samtools.BAMFileSpan
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- All Implemented Interfaces:
SAMFileSpan
,Serializable
,Cloneable
public class BAMFileSpan extends Object implements SAMFileSpan, Serializable
An ordered list of chunks, capable of representing a set of discontiguous regions in the BAM file. FileSpans are mutable within the package, but perceived as immutable outside the package. Some operations on FileSpans assume that the spans are sorted. In these cases, sort order will be validated.- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description BAMFileSpan()
Create a new empty list of chunks.BAMFileSpan(Chunk chunk)
Convenience constructor to construct a BAM file span from a single chunk.BAMFileSpan(List<Chunk> chunks)
Create a new chunk list from the given list of chunks.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
add(BAMFileSpan span)
Merge one span into anotherprotected void
add(Chunk chunk)
Adds a new chunk to this list.BAMFileSpan
clone()
Deep clone the given chunk list.List<Chunk>
getChunks()
Gets the constituent chunks stored in this span.SAMFileSpan
getContentsFollowing()
Gets a file span over the data immediately following this span.long
getFirstOffset()
Find the first offset in the chunk listprotected Chunk
getSingleChunk()
Checks that there is only a single chunk for this span and returns it.boolean
isEmpty()
Does this chunk list map to any position within the BAM file?static BAMFileSpan
merge(BAMFileSpan[] spans)
SAMFileSpan
removeContentsAfter(SAMFileSpan fileSpan)
Creates a new file span by removing all chunks after the given file span ends.SAMFileSpan
removeContentsBefore(SAMFileSpan fileSpan)
Creates a new file span by removing all chunks before the given file span starts.protected static SAMFileSpan
toChunkList(long[] coordinateArray)
The list of chunks is often represented as an array of longs where every even-numbered index is a start coordinate and every odd-numbered index is a stop coordinate.long[]
toCoordinateArray()
Convert the chunk list to an array of offsets, paired in [start,end) format.String
toString()
Creates a string representation of this chunk list.
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Constructor Detail
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BAMFileSpan
public BAMFileSpan()
Create a new empty list of chunks.
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BAMFileSpan
public BAMFileSpan(Chunk chunk)
Convenience constructor to construct a BAM file span from a single chunk.- Parameters:
chunk
- Chunk to use as the sole region in this span.
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Method Detail
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isEmpty
public boolean isEmpty()
Does this chunk list map to any position within the BAM file?- Specified by:
isEmpty
in interfaceSAMFileSpan
- Returns:
- True iff the ChunkList points to any data within the BAM.
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clone
public BAMFileSpan clone()
Deep clone the given chunk list.
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removeContentsBefore
public SAMFileSpan removeContentsBefore(SAMFileSpan fileSpan)
Creates a new file span by removing all chunks before the given file span starts. If a chunk in the chunk list starts before and ends after the given chunk, the first portion of the chunk will be deleted.- Specified by:
removeContentsBefore
in interfaceSAMFileSpan
- Parameters:
fileSpan
- The filespan before which to eliminate.- Returns:
- A new BAMFileSpan which contains the portion of the chunk list after the given chunk.
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removeContentsAfter
public SAMFileSpan removeContentsAfter(SAMFileSpan fileSpan)
Creates a new file span by removing all chunks after the given file span ends. If a chunk in the chunk list starts before and ends after the given chunk, the second portion of the chunk will be deleted.- Parameters:
fileSpan
- The filespan after which to eliminate.- Returns:
- A new BAMFileSpan which contains the portion of the chunk list before the given chunk.
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getContentsFollowing
public SAMFileSpan getContentsFollowing()
Gets a file span over the data immediately following this span.- Specified by:
getContentsFollowing
in interfaceSAMFileSpan
- Returns:
- The a pointer to data immediately following this span.
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add
protected void add(BAMFileSpan span)
Merge one span into another- Parameters:
span
- - span with chunks to add to this one
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add
protected void add(Chunk chunk)
Adds a new chunk to this list. Visible only within the BAm.- Parameters:
chunk
- Chunk to add.
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toCoordinateArray
public long[] toCoordinateArray()
Convert the chunk list to an array of offsets, paired in [start,end) format.- Returns:
- Array of offsets.
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getFirstOffset
public long getFirstOffset()
Find the first offset in the chunk list- Returns:
- The first offset in the span
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getChunks
public List<Chunk> getChunks()
Gets the constituent chunks stored in this span.- Returns:
- An unmodifiable list of chunks.
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getSingleChunk
protected Chunk getSingleChunk()
Checks that there is only a single chunk for this span and returns it.- Returns:
- The single chunk stored in this span
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toChunkList
protected static SAMFileSpan toChunkList(long[] coordinateArray)
The list of chunks is often represented as an array of longs where every even-numbered index is a start coordinate and every odd-numbered index is a stop coordinate. Convert from that format back to a list of chunks.- Parameters:
coordinateArray
- List of chunks to convert.- Returns:
- A list of chunks.
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toString
public String toString()
Creates a string representation of this chunk list.
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merge
public static BAMFileSpan merge(BAMFileSpan[] spans)
- Returns:
- A single BAMFileSpan that is an intelligent merge of the input spans, i.e. contiguous, overlapping and contained chunks are intelligently merged, and the chunks are sorted.
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