Package picard.illumina.parser.readers
Class FilterFileReader
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- picard.illumina.parser.readers.FilterFileReader
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public class FilterFileReader extends Object implements Iterator<Boolean>
Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not. These values are written as sequential bytes to Filter Files. The structure of a filter file is as follows: Bytes 0-3 : 0 Bytes 4-7 : unsigned int version Bytes 8-11 : unsigned int numClusters
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Field Summary
Fields Modifier and Type Field Description static int
EXPECTED_VERSION
Expected Versionlong
numClusters
The number of cluster's pf values stored in this fileint
version
Version number found in the FilterFile, this should equal 3
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Constructor Summary
Constructors Constructor Description FilterFileReader(File file)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
hasNext()
Boolean
next()
void
remove()
void
skipRecords(int numToSkip)
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface java.util.Iterator
forEachRemaining
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Field Detail
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EXPECTED_VERSION
public static final int EXPECTED_VERSION
Expected Version- See Also:
- Constant Field Values
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version
public final int version
Version number found in the FilterFile, this should equal 3
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numClusters
public final long numClusters
The number of cluster's pf values stored in this file
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Constructor Detail
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FilterFileReader
public FilterFileReader(File file)
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