//---------------------------------------------------------
// Copyright 2017 Ontario Institute for Cancer Research
// Written by Jared Simpson (jared.simpson@oicr.on.ca)
//---------------------------------------------------------
//
// nanopolish_raw_loader - utilities and helpers for loading
// data directly from raw nanopore files without events
//
#ifndef NANOPOLISH_RAW_LOADER_H
#define NANOPOLISH_RAW_LOADER_H

#include "nanopolish_squiggle_read.h"
#include "nanopolish_anchor.h"
#include "scrappie_structures.h"

SquiggleScalings estimate_scalings_using_mom(const std::string& sequence,
                                             const PoreModel& pore_model,
                                             const event_table& et);

// Align events to k-mers of a sequence using Suzuki's adaptive banded algorithm
// see: https://www.biorxiv.org/content/early/2017/09/07/130633
std::vector<AlignedPair> adaptive_banded_simple_event_align(SquiggleRead& read,
                                                            const PoreModel& pore_model,
                                                            const std::string& sequence);

// Simple banded alignmend algorithm
// Deprecated, use the above
std::vector<AlignedPair> banded_simple_event_align(SquiggleRead& read,
                                                   const PoreModel& pore_model,
                                                   const std::string& sequence);

#endif