Package org.snpeff.fileIterator
Class SamFileIterator
- java.lang.Object
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- org.snpeff.fileIterator.FileIterator<SamEntry>
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- org.snpeff.fileIterator.SamFileIterator
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public class SamFileIterator extends FileIterator<SamEntry>
Reads a SAM file Note: This is a very 'rustic' reader (we should use Picard's API instead)- Author:
- pcingola
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Constructor Summary
Constructors Constructor Description SamFileIterator(java.lang.String samFileName)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SamHeader
getHeaders()
java.util.Iterator<SamEntry>
iterator()
protected SamEntry
readNext()
Read a sequence from the file-
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
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Method Detail
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getHeaders
public SamHeader getHeaders()
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iterator
public java.util.Iterator<SamEntry> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<SamEntry>
- Overrides:
iterator
in classFileIterator<SamEntry>
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readNext
protected SamEntry readNext()
Read a sequence from the file- Specified by:
readNext
in classFileIterator<SamEntry>
- Returns:
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