Package org.snpeff.fileIterator
Class SamFileIterator
Reads a SAM file
Note: This is a very 'rustic' reader (we should use Picard's API instead)
- Author:
- pcingola
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Methods inherited from class org.snpeff.fileIterator.FileIterator
close, countNewLineChars, getFilePointer, getLine, getLineNum, guessNewLineChars, hasNext, hasSeek, init, isDebug, load, next, readLine, ready, remove, seek, setAutoClose, setDebug, setVerbose, toString
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, 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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debug
public static boolean debug
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Constructor Details
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SamFileIterator
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Method Details
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getHeaders
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iterator
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readNext
Read a sequence from the file- Specified by:
readNext
in classFileIterator<SamEntry>
- Returns:
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