Package net.sf.samtools.tabix
Class TabixReader
- java.lang.Object
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- net.sf.samtools.tabix.TabixReader
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- All Implemented Interfaces:
java.lang.Iterable<java.lang.String>
public class TabixReader extends java.lang.Object implements java.lang.Iterable<java.lang.String>
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Field Summary
Fields Modifier and Type Field Description protected boolean
showHeader
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Constructor Summary
Constructors Constructor Description TabixReader(java.lang.String fileName)
TabixReader(java.lang.String fileName, boolean debug)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
chr2tid(java.lang.String chr)
void
close()
long
getFilePointer()
int
getmBc()
int
getmEc()
int
getmMeta()
int
getmPreset()
int
getmSc()
TabixIterator
iterator()
static void
main(java.lang.String[] args)
int[]
parseReg(java.lang.String reg)
Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"TabixIterator
query(java.lang.String reg)
Return an iterator for the interval in this query Format: "chr:star-end"TabixIterator
query(Variant variant)
void
readIndex()
Read the Tabix index from the default file.void
readIndex(java.io.File fp)
Read the Tabix index from a filestatic int
readInt(java.io.InputStream is)
java.lang.String
readLine()
Read one line from the data file.static long
readLong(java.io.InputStream is)
void
setDebug(boolean debug)
void
setShowHeader(boolean showHeader)
java.lang.String
toString()
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Method Detail
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main
public static void main(java.lang.String[] args)
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readInt
public static int readInt(java.io.InputStream is) throws java.io.IOException
- Throws:
java.io.IOException
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readLong
public static long readLong(java.io.InputStream is) throws java.io.IOException
- Throws:
java.io.IOException
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chr2tid
protected int chr2tid(java.lang.String chr)
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close
public void close()
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getFilePointer
public long getFilePointer()
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getmBc
public int getmBc()
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getmEc
public int getmEc()
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getmMeta
public int getmMeta()
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getmPreset
public int getmPreset()
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getmSc
public int getmSc()
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iterator
public TabixIterator iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<java.lang.String>
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parseReg
public int[] parseReg(java.lang.String reg)
Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"- Parameters:
reg
- Region string- Returns:
- An array where the three elements are [ sequence_id, region_begin, region_end] On failure, sequence_id==-1.
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query
public TabixIterator query(java.lang.String reg)
Return an iterator for the interval in this query Format: "chr:star-end"
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query
public TabixIterator query(Variant variant)
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readIndex
public void readIndex() throws java.io.IOException
Read the Tabix index from the default file.- Throws:
java.io.IOException
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readIndex
public void readIndex(java.io.File fp) throws java.io.IOException
Read the Tabix index from a file- Parameters:
fp
- File pointer- Throws:
java.io.IOException
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readLine
public java.lang.String readLine() throws java.io.IOException
Read one line from the data file.- Throws:
java.io.IOException
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setDebug
public void setDebug(boolean debug)
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setShowHeader
public void setShowHeader(boolean showHeader)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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