htsjdk.samtools

Class TextCigarCodec

java.lang.Object

htsjdk.samtools.TextCigarCodec

public class TextCigarCodec
extends java.lang.Object

Convert between String and Cigar class representations of CIGAR.

Constructor Summary

Constructors

Constructor and Description
TextCigarCodec()

Method Summary

Methods

Modifier and Type	Method and Description
static Cigar	decode(java.lang.String textCigar) Convert from String CIGAR representation to Cigar class representation.
static java.lang.String	encode(Cigar cigar) Convert from Cigar class representation to String.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TextCigarCodec

public TextCigarCodec()

Method Detail

encode

public static java.lang.String encode(Cigar cigar)

Convert from Cigar class representation to String.

Parameters:

cigar - in Cigar class format

Returns:

CIGAR in String form ala SAM text file. "*" means empty CIGAR.

decode

public static Cigar decode(java.lang.String textCigar)

Convert from String CIGAR representation to Cigar class representation. Does not do validation beyond the most basic CIGAR string well-formedness, i.e. each operator is valid, and preceded by a decimal length.

Parameters:

textCigar - CIGAR in String form ala SAM text file. "*" means empty CIGAR.

Returns:

cigar in Cigar class format

Throws:

java.lang.RuntimeException - if textCigar is invalid at the most basic level.