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// Author: Mark Chaisson
#pragma once
#include "BlasrHeaders.h"
//-------------------------Fetch Reads----------------------------//
template <typename T_Sequence>
bool GetNextReadThroughSemaphore(ReaderAgglomerate &reader, MappingParameters ¶ms,
T_Sequence &read, std::string &readGroupId, int &associatedRandInt,
MappingSemaphores &semaphores);
//---------------------MAKE & CHECK READS-------------------------//
//FIXME: move to SMRTSequence
bool ReadHasMeaningfulQualityValues(FASTQSequence &sequence);
//FIXME: Move to SMRTSequence
// Given a SMRT sequence and a subread interval, make the subread.
// Input:
// smrtRead - a SMRT sequence
// subreadInterval - a subread interval
// params - mapping parameters
// Output:
// subreadSequence - the constructed subread
void MakeSubreadOfInterval(SMRTSequence &subreadSequence, SMRTSequence &smrtRead,
ReadInterval &subreadInterval, MappingParameters ¶ms);
//FIXME: Move to SMRTSequence
// Given a SMRT sequence and one of its subreads, make the
// reverse complement of the subread in the coordinate of the
// reverse complement sequence of the SMRT sequence.
// Input:
// smrtRead - a SMRT read
// subreadSequence - a subread of smrtRead
// Output:
// subreadSequenceRC - the reverse complement of the subread
// in the coordinate of the reverse
// complement of the SMRT read.
void MakeSubreadRC(SMRTSequence &subreadSequenceRC, SMRTSequence &subreadSequence,
SMRTSequence &smrtRead);
// Construct subreads invervals from subreads
void MakeSubreadIntervals(std::vector<SMRTSequence> &subreads,
std::vector<ReadInterval> &subreadIntervals);
// Return index of subread which will be used as concordant template.
// If Zmw has exactly one subread, return index of the subread (i.e., 0).
// If Zmw has exactly two subreads, return index of the longer subread.
// If Zmw has three or more subreads, return index of the median-length
// subread in range subreadIntervals[1:-1]. Avoid using the first and last
// subreads (which are less likely to be full-pass) if possible.
int GetIndexOfConcordantTemplate(const std::vector<ReadInterval> &subreadIntervals);
//-------------------------MISC-----------------------------------//
int CountZero(unsigned char *ptr, int length);
#include "BlasrMiscsImpl.hpp"
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