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Classes | Public Member Functions | Static Public Member Functions | Private Member Functions | Static Private Member Functions | Private Attributes | Static Private Attributes

TabixReader Class Reference

Collaboration diagram for TabixReader:
Collaboration graph

List of all members.


class  Iterator
class  TIndex
class  TIntv
class  TPair64

Public Member Functions

int[] parseReg (final String reg)
Iterator query (final String reg)
Iterator query (final int tid, final int beg, final int end)
void readIndex (final File fp) throws IOException
void readIndex () throws IOException
String readLine () throws IOException
 TabixReader (final String fn) throws IOException

Static Public Member Functions

static void main (String[] args)
static int readInt (final InputStream is) throws IOException
static String readLine (final InputStream is) throws IOException
static long readLong (final InputStream is) throws IOException

Private Member Functions

int chr2tid (final String chr)
TIntv getIntv (final String s)

Static Private Member Functions

static boolean less64 (final long u, final long v)
static int reg2bins (final int beg, final int _end, final int[] list)

Private Attributes

int mBc
HashMap< String, Integer > mChr2tid
int mEc
String mFn
BlockCompressedInputStream mFp
TIndex[] mIndex
int mMeta
int mPreset
int mSc
String[] mSeq
int mSkip

Static Private Attributes

static int MAX_BIN = 37450
static int TAD_LIDX_SHIFT = 14
static int TAD_MIN_CHUNK_GAP = 32768

Detailed Description

Definition at line 37 of file TabixReader.java.

The documentation for this class was generated from the following file:

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