htsjdk.samtools.cram.build

Class Utils

java.lang.Object

htsjdk.samtools.cram.build.Utils

public final class Utils
extends java.lang.Object

Method Summary

Modifier and Type	Method and Description
static byte	normalizeBase(byte base) CRAM operates with upper case bases, so both read and ref bases should be upper-cased and vocab controlled.

Methods inherited from class java.lang.Object

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

Method Detail

normalizeBase

public static byte normalizeBase(byte base)

CRAM operates with upper case bases, so both read and ref bases should be upper-cased and vocab controlled. This method does exactly this: upper case acgt and replace everything else with N.

Parameters:

base - a base to normalize

Returns:

a normalized base