public class BAMFileSpan extends java.lang.Object implements SAMFileSpan, java.io.Serializable
Constructor and 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(java.util.List<Chunk> chunks)
Create a new chunk list from the given list of chunks.
|
Modifier and Type | Method and Description |
---|---|
protected void |
add(BAMFileSpan span)
Merge one span into another
|
protected void |
add(Chunk chunk)
Adds a new chunk to this list.
|
BAMFileSpan |
clone()
Deep clone the given chunk list.
|
java.util.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 list
|
protected 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.
|
java.lang.String |
toString()
Creates a string representation of this chunk list.
|
public BAMFileSpan()
public BAMFileSpan(Chunk chunk)
chunk
- Chunk to use as the sole region in this span.public BAMFileSpan(java.util.List<Chunk> chunks)
chunks
- Constituent chunks.public boolean isEmpty()
isEmpty
in interface SAMFileSpan
public BAMFileSpan clone()
clone
in class java.lang.Object
public SAMFileSpan removeContentsBefore(SAMFileSpan fileSpan)
removeContentsBefore
in interface SAMFileSpan
fileSpan
- The filespan before which to eliminate.public SAMFileSpan removeContentsAfter(SAMFileSpan fileSpan)
fileSpan
- The filespan after which to eliminate.public SAMFileSpan getContentsFollowing()
getContentsFollowing
in interface SAMFileSpan
protected void add(BAMFileSpan span)
span
- - span with chunks to add to this oneprotected void add(Chunk chunk)
chunk
- Chunk to add.public long[] toCoordinateArray()
public long getFirstOffset()
public java.util.List<Chunk> getChunks()
protected Chunk getSingleChunk()
protected static SAMFileSpan toChunkList(long[] coordinateArray)
coordinateArray
- List of chunks to convert.public java.lang.String toString()
toString
in class java.lang.Object
public static BAMFileSpan merge(BAMFileSpan[] spans)