public class ReferenceDictionary extends Object implements Serializable
contigID
. Possibly, more than one name is
assigned the same numeric id. Usually, numeric ids are assigned starting with 1 (as to correspond to the chromosome
names for human/mouse genomes, for example), but arbitrary numeric ids can be assigned (even non-continous sequence).
contigName
.contigLength
. This is used for coordinate transformation from
forward to reverse strand. This means that the genome position and interval types keep a reference to a central
ReferenceDictionary
object.ReferenceDictionaryBuilder
.Modifier and Type | Method and Description |
---|---|
com.google.common.collect.ImmutableMap<Integer,Integer> |
getContigIDToLength() |
com.google.common.collect.ImmutableMap<Integer,String> |
getContigIDToName() |
com.google.common.collect.ImmutableMap<String,Integer> |
getContigNameToID() |
void |
print(PrintStream out)
Print dictionary to
System.err for debugging purposes. |
public com.google.common.collect.ImmutableMap<String,Integer> getContigNameToID()
public com.google.common.collect.ImmutableMap<Integer,String> getContigIDToName()
public com.google.common.collect.ImmutableMap<Integer,Integer> getContigIDToLength()
public void print(PrintStream out)
System.err
for debugging purposes.out
- PrintStream
to write toCopyright © 2016. All rights reserved.