Package org.snpeff.util
Class IubString
java.lang.Object
org.snpeff.util.IubString
Find all bases combinations from a string containing IUB codes
- Author:
- pcingola
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic int
How many IUB bases are in this string?static boolean
Does the string have ANY IUB base?static boolean
Does the string have at most 'MAX_IUB_BASES' IUB bases?boolean
hasNext()
static boolean
isUIB
(char base) iterator()
static char[]
iub2bases
(char alt) Convert a single IUB code to the corresponding bases IUB codes: M=A/C, R=A/G, W=A/T, S=C/G, Y=C/T, K=G/T and N=A/C/G/Tnext()
void
remove()
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
Methods inherited from interface java.util.Iterator
forEachRemaining
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Field Details
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MAX_IUB_BASES
public static final int MAX_IUB_BASES- See Also:
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Constructor Details
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IubString
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Method Details
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countIUB
How many IUB bases are in this string? -
hasIUB
Does the string have ANY IUB base? -
hasIUBMax
Does the string have at most 'MAX_IUB_BASES' IUB bases? -
isUIB
public static boolean isUIB(char base) -
iub2bases
public static char[] iub2bases(char alt) Convert a single IUB code to the corresponding bases IUB codes: M=A/C, R=A/G, W=A/T, S=C/G, Y=C/T, K=G/T and N=A/C/G/T -
hasNext
public boolean hasNext() -
iterator
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next
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remove
public void remove()
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