Package htsjdk.samtools.reference
Class ReferenceSequence
- java.lang.Object
-
- htsjdk.samtools.reference.ReferenceSequence
-
public class ReferenceSequence extends Object
Wrapper around a reference sequence that has been read from a reference file.
-
-
Constructor Summary
Constructors Constructor Description ReferenceSequence(String name, int index, byte[] bases)
creates a fully formed ReferenceSequence
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description byte[]
getBases()
Gets the array of bases that define this sequence.String
getBaseString()
Returns the bases represented by this ReferenceSequence as a String.int
getContigIndex()
Gets the 0-based index of this contig in the source file from which it came.String
getName()
Gets the set of names given to this sequence in the source file.int
length()
Gets the length of this reference sequence in bases.String
toString()
-
-
-
Constructor Detail
-
ReferenceSequence
public ReferenceSequence(String name, int index, byte[] bases)
creates a fully formed ReferenceSequence- Parameters:
name
- the name of the sequence from the source fileindex
- the zero based index of this contig in the source filebases
- the bases themselves stored as one-byte characters
-
-
Method Detail
-
getName
public String getName()
Gets the set of names given to this sequence in the source file.
-
getBases
public byte[] getBases()
Gets the array of bases that define this sequence. The bases can include any letter and possibly include masking information in the form of lower case letters. This array is mutable (obviously!) and it NOT a clone of the array held interally. Do not modify it!!!
-
getBaseString
public String getBaseString()
Returns the bases represented by this ReferenceSequence as a String. Since this will copy the bases and convert them to two-byte characters, this should not be used on very long reference sequences, but as a convenience when manipulating short sequences returned byReferenceSequenceFile.getSubsequenceAt(String, long, long)
- Returns:
- The set of bases represented by this ReferenceSequence, as a String
-
getContigIndex
public int getContigIndex()
Gets the 0-based index of this contig in the source file from which it came.
-
length
public int length()
Gets the length of this reference sequence in bases.
-
-