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/*
* =====================================================================================
*
* Filename: MovieAlnIndexLookupTable.h
*
* Description: For cpp/pbihdfutils/LoadPulses.cpp use only.
* Cache all the information required for loading metric from pls/bas
* to cmp file.
* mapping movieAlignmentIndex in movieIndexSets[movieIndex] to:
* alignmentIndex: index of this alignment in cmpFile.alnInfo.alignments
* refGroupIndex : index of this alignment in cmpReader.refAlignGroups
* readGroupIndex: index of this alignment in cmpReader.refAlignGroups\
* [refGroupIndex]->readGroupds[readGroupIndex]
* offsetBegin : offset begin for this alignment in cmpFile
* dataset /ref/movie/AlnArray
* offsetEnd : offset enda
* queryStart : start position of query of this alignment
* queryEnd : end position of query of this alignment
* readIndex : index of this alignment in baseFile.readStartPositions
* readStart : start position of this alignment in baseFile
* readLength : read length of this alignment in baseFile
* plsReadIndex : index of this alignment in pulseFile.pulseStartPositions
* alignedSequence
* : aligned sequence of this alignment
*
* Version: 1.0
* Created: 12/19/2012 03:50:21 PM
* Revision: none
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* =====================================================================================
*/
#ifndef _LOADPULSES_MovieAlnIndexLookupTable_HPP_
#define _LOADPULSES_MovieAlnIndexLookupTable_HPP_
#include <iostream>
#include <string>
#include <pbdata/Types.h>
class MovieAlnIndexLookupTable
{
public:
bool skip;
// as movies may split into multiple parts, skip=true if
// this alignment is not found in the movie
size_t movieAlignmentIndex;
// movieIndexSets[movieIndex][toFrom[movieAlignmentIndex]]
UInt alignmentIndex;
// cmpFile.alnInfo.alignments[alignmentIndex]
UInt holeNumber;
// holeNumber corresponding to this alignment in baseFile
size_t refGroupIndex;
// cmpReader.refAlignGroups[refGroupIndex]
size_t readGroupIndex;
// cmpReader.refAlignGroups[refGroupIndex]->readGroups[readGroupIndex]
UInt offsetBegin, offsetEnd;
// offset begin and end for this alignment in /ref/movie/AlnArray
// = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin/End()
UInt queryStart, queryEnd;
// start/end for this read = cmpFile.alnInfo.
// alignments[alignmentIndex].GetQueryStart/End()
size_t readIndex;
// index of this alignment in baseFile.readStartPositions
// = index of this hole number in BaseCalls/ZMW/HoleNumber
// baseFile.LookupReadIndexByHoleNumber(holeNumber, out=readIndex)
size_t readStart;
// start pos of this alignment in baseFile
// = baseFile.readStartPositions[readIndex]
int readLength;
// read length of this alignment in baseFile
// = baseFile.readStartPositions[readIndex+1] - readStart
size_t plsReadIndex;
// index of this alignment in pulseFile.pulseStartPositions
// = index of this hole number in PulseCalls/ZMW/HoleNumbers
// = pulseFile.LookupReadIndexByHoleNumber(holeNumber, out=plsReadIndex)
// std::vector<int> baseToAlignmentMap;
// keep all the baseToAlignmentMap in memory for now
// Note that baseToAlignmentMap is not initialized when
// BuildLookupTable is called.
std::string alignedSequence;
MovieAlnIndexLookupTable();
void SetValue(const bool& skipP, const size_t& movieAlignmentIndexP,
const UInt& alignmentIndexP, const size_t& refGroupIndexP,
const size_t& readGroupIndexP, const UInt& holeNumberP, const UInt& offsetBeginP,
const UInt& offsetEndP, const UInt& queryStartP, const UInt& queryEndP,
const size_t& readIndexP, const size_t& readStartP, const int& readLengthP,
const size_t& plsReadIndexP);
void print();
};
#endif
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