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#ifndef _BLASR_REGION_UTILS_HPP_
#define _BLASR_REGION_UTILS_HPP_
#include <algorithm>
#include <cmath>
#include <alignment/statistics/StatUtils.hpp>
#include <pbdata/SMRTSequence.hpp>
#include <pbdata/reads/ReadInterval.hpp>
#include <pbdata/reads/RegionTable.hpp>
bool LookupHQRegion(int holeNumber, RegionTable ®ionTable, int &start, int &end, int &score);
template <typename T_Sequence>
bool MaskRead(T_Sequence &fastaRead, ZMWGroupEntry &zmwData, RegionTable ®ionTable);
template <typename T_Sequence>
bool GetReadTrimCoordinates(T_Sequence &fastaRead, ZMWGroupEntry &zmwData, RegionTable ®ionTable,
DNALength &readStart, DNALength &readEnd, int &score);
// Given a vecotr of ReadInterval objects and their corresponding
// directions, intersect each object with an interval
// [hqStart, hqEnd), if there is no intersection or the intersected
// interval is less than minIntervalLength, remove this object and
// their corresponding directions; otherwise, replace this object
// with the intersected interval and keep their directions.
// Return index of the (left-most) longest subread interval in the
// updated vector.
int GetHighQualitySubreadsIntervals(std::vector<ReadInterval> &subreadIntervals,
std::vector<int> &subreadDirections, int hqStart, int hqEnd,
int minIntervalLength = 0);
// Given a vector of subreads and a vector of adapters, return
// indices of all full-pass subreads.
std::vector<int> GetFullPassSubreadIndices(std::vector<ReadInterval> &subreadIntervals,
std::vector<ReadInterval> &adapterIntervals);
// Given a vector of subreads and a vector of adapters, return
// index of the (left-most) longest subread which has both
// adapters before & after itself. If no full-pass subreads are
// available, return -1.
int GetLongestFullSubreadIndex(std::vector<ReadInterval> &subreadIntervals,
std::vector<ReadInterval> &adapterIntervals);
// Given a vector of subreads and a vector of adapters, return
// index of the median length subread which has both
// adapters before & after itself. If no full-pass subreads are
// available, return -1.
int GetMedianLengthFullSubreadIndex(std::vector<ReadInterval> &subreadIntervals,
std::vector<ReadInterval> &adapterIntervals);
// Given a vector of subreads and a vector of adapters, return
// index of the typical fullpass subread which can represent subreads
// of this zmw.
// * if there is no fullpass subread, return -1;
// * if number of fullpass subreads is less than 4, return index of the
// left-most longest subread
// * if number of fullpass subreads is greater than or equal 4,
// * if length of the longest read does not exceed
// meanLength + 1.96 * deviationLength
// then, return index of the longest left-most subread
// * otherwise, return index of the second longest left-most subread
int GetTypicalFullSubreadIndex(std::vector<ReadInterval> &subreadIntervals,
std::vector<ReadInterval> &adapterIntervals);
// Create a vector of n directions consisting of interleaved 0 and 1s.
void CreateDirections(std::vector<int> &directions, const int &n);
// Flop all directions in the given vector, if flop is true.
void UpdateDirections(std::vector<int> &directions, bool flop = false);
#include "RegionUtilsImpl.hpp"
#endif
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