//
// Copyright 2009 Illumina, Inc.
//
// This software is covered by the "Illumina Genome Analyzer Software
// License Agreement" and the "Illumina Source Code License Agreement",
// and certain third party copyright/licenses, and any user of this
// source file is bound by the terms therein (see accompanying files
// Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
// Illumina_Source_Code_License_Agreement.pdf and third party
// copyright/license notices).
//
//

/// \file

/// \author Ivan Mikoulitch
///

#include "SamMD/samMDlib.h"
#include "SamMD/samReader.h"
#include "SamMD/fastaReader.h"
#include "SamMD/log.h"
#include "SamMD/utils.h"

//////////////////////////////////////////////////////////////////////
SamMD::SamMD(const string& samFile, const string& fastaFiles)
{
	samFile_=samFile;
	fastaFiles_=fastaFiles;
}

//////////////////////////////////////////////////////////////////////
SamMD::~SamMD(void)
{
}

//////////////////////////////////////////////////////////////////////
vector<string> SamMD::ReadFastFileList()
{
	vector<string> files;

	ifstream fs(fastaFiles_.c_str());

	if (!fs.is_open()) return files;

	try
	{
		string line;

		while(getline(fs, line))
		{
			if (line.empty()) continue;
			files.push_back(line);
		}
	}
	catch(...)
	{
		files.clear();
	}

	if (fs.is_open()) fs.close();

	return files;
}

//////////////////////////////////////////////////////////////////////
bool SamMD::CreateMatchDescriptors()
{
	// reading list of fasta files
	vector<string> fasta_files = ReadFastFileList();

	if(fasta_files.empty())
	{
		Log::Error("Cannot read list of fasta files from '" + fastaFiles_ + "'.");
		return false;
	}

	// reading sam file
	SamReader sr(samFile_);

	if(!sr.ReadSamFile())
	{
		sr.Close();
		Log::Error("Cannot read sam file: '" + samFile_ + "'");
		return false;
	}

	// making match descriptors in memory
	try
	{
		vector<string>::const_iterator ff_it = fasta_files.begin();

		while(ff_it!=fasta_files.end())
		{
			FastaReader fr(*ff_it);

			if(!fr.Open())
			{
				Log::Warning("Cannot open fasta file: "+*ff_it);
				Log::Warning("Continuing processing.");
				++ff_it;
				continue;
			}

			while(fr.ReadNextReference())
			{
				sr.ProcessReferenceData(fr);
			}

			fr.Close();

			++ff_it;
		}
	}
	catch(...)
	{
		sr.Close();
		Log::Exception("Exception occured during processing match descriptors.");
		return false;
	}

	// making modified sam file
	sr.CreateModifiedSamFile();

	sr.Close();

	return true;
}