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/* Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved */
#ifndef SPLICEVARIANTHYPOTHESES_H
#define SPLICEVARIANTHYPOTHESES_H
#include <iostream>
#include <string>
#include <sstream>
#include <vector>
#include <math.h>
#include <assert.h>
#include "stdlib.h"
#include "ctype.h"
#include "ClassifyVariant.h"
#include "ExtendedReadInfo.h"
#include "MiscUtil.h"
using namespace std;
using namespace ion;
class EnsembleEval;
bool SpliceVariantHypotheses(const Alignment ¤t_read, const EnsembleEval &my_ensemble,
const LocalReferenceContext &local_context, PersistingThreadObjects &thread_objects,
int &splice_start_flow, int &splice_end_flow, vector<string> &my_hypotheses,
vector<bool> & same_as_null_hypothesis, bool & changed_alignment, const InputStructures &global_context,
const ReferenceReader &ref_reader, int chr_idx);
bool SpliceAddVariantAlleles(const Alignment ¤t_read, const string& pretty_alignment,
const EnsembleEval &my_ensemble,
const LocalReferenceContext &local_context, vector<string> &my_hypotheses,
unsigned int pretty_idx, int DEBUG);
void IncrementAlignmentIndices(const char aln_symbol, int &ref_idx, int &read_idx);
void DecrementAlignmentIndices(const char aln_symbol, int &ref_idx, int &read_idx);
void IncrementFlow(const ion::FlowOrder &flow_order, const char &nuc, int &flow);
void IncrementFlows(const ion::FlowOrder &flow_order, const char &nuc, vector<int> &flows);
int GetSpliceFlows(const Alignment ¤t_read, const InputStructures &global_context,
vector<string> &my_hypotheses, vector<bool> & same_as_null_hypothesis,
int splice_start_idx, vector<int> splice_end_idx, int &splice_start_flow);
string SpliceDoRealignement (PersistingThreadObjects &thread_objects, const Alignment ¤t_read, long variant_position,
bool &changed_alignment, int DEBUG, const ReferenceReader &ref_reader, int chr_idx);
#endif // SPLICEVARIANTHYPOTHESES_H
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