include.h

/*
    Pheniqs : PHilology ENcoder wIth Quality Statistics
    Copyright (C) 2018  Lior Galanti
    NYU Center for Genetics and System Biology

    Author: Lior Galanti <lior.galanti@nyu.edu>

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU Affero General Public License as
    published by the Free Software Foundation, either version 3 of the
    License, or (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU Affero General Public License for more details.

    You should have received a copy of the GNU Affero General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/

#ifndef PHENIQS_INCLUDE_H
#define PHENIQS_INCLUDE_H

/*  Support for accouting for the illumina control number in FASTQ comment field
    Currently disabled by default
    #define PHENIQS_ILLUMINA_CONTROL_NUMBER
*/

/*  Support for propegating SAM tags pheniqs does not directly interact with
    Incomplete experimental code pending further reasearch into rules for transforming tags
    #define PHENIQS_EXTENDED_SAM_TAG
*/

/*  Support for propegating SAM alignment fields
    Incomplete experimental code pending further reasearch into rules for transformtion
    #define PHENIQS_SAM_ALIGNMENT
*/

/* STL dependencies */
#include <algorithm>
#include <cmath>
#include <condition_variable>
#include <cstddef>
#include <cstdint>
#include <cstdlib>
#include <errno.h>
#include <exception>
#include <fstream>
#include <iomanip>
#include <iostream>
#include <limits>
#include <list>
#include <map>
#include <math.h>
#include <mutex>
#include <set>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <thread>
#include <unistd.h>
#include <unordered_map>
#include <vector>
#include <stddef.h>
#include <regex>

using std::cerr;
using std::condition_variable;
using std::cin;
using std::cout;
using std::endl;
using std::exception;
using std::fixed;
using std::hash;
using std::hex;
using std::istream;
using std::ifstream;
using std::int16_t;
using std::int32_t;
using std::int64_t;
using std::int8_t;
using std::invalid_argument;
using std::ios_base;
using std::istreambuf_iterator;
using std::list;
using std::lock_guard;
using std::log10;
using std::make_pair;
using std::map;
using std::max;
using std::min;
using std::move;
using std::mutex;
using std::numeric_limits;
using std::ostream;
using std::out_of_range;
using std::pair;
using std::recursive_mutex;
using std::set;
using std::setprecision;
using std::setw;
using std::left;
using std::right;
using std::size_t;
using std::string;
using std::thread;
using std::to_string;
using std::uint16_t;
using std::uint32_t;
using std::uint64_t;
using std::uint8_t;
using std::unique_lock;
using std::unordered_map;
using std::vector;
using std::regex;
using std::smatch;
using std::regex_match;

/*  zlib dependencies
    Used for probing gzip compressed files */
#include <zlib.h>

/* RapidJSON dependencies */
#define RAPIDJSON_NO_SIZETYPEDEFINE
#define RAPIDJSON_SCHEMA_USE_INTERNALREGEX 0
namespace rapidjson { typedef ::std::size_t SizeType; }

#include <rapidjson/document.h>
#include <rapidjson/error/en.h>
#include <rapidjson/pointer.h>
#include <rapidjson/prettywriter.h>
#include <rapidjson/schema.h>
#include <rapidjson/stringbuffer.h>
#include <rapidjson/filewritestream.h>

using rapidjson::Document;
using rapidjson::Pointer;
using rapidjson::PrettyWriter;
using rapidjson::SizeType;
using rapidjson::StringBuffer;
using rapidjson::StringRef;
using rapidjson::Type;
using rapidjson::Value;
using rapidjson::SchemaDocument;
using rapidjson::SchemaValidator;
using rapidjson::kArrayType;
using rapidjson::kNullType;
using rapidjson::kObjectType;
using rapidjson::kStringType;

/*  HTSLib dependencies
    We disable warnings from HTSLib to not litter the output until type comparisson warnings are resolved */
#ifdef __GNUC__
#pragma GCC system_header
#endif

#include <htslib/bgzf.h>
#include <htslib/hts_endian.h>
#include <htslib/hfile.h>
#include <htslib/hts.h>
#include <htslib/kseq.h>
#include <htslib/kstring.h>
#include <htslib/sam.h>
#include <htslib/thread_pool.h>

/*  Float precision
    The number of significant decimal digits when writing to output
    see https://en.wikipedia.org/wiki/Double-precision_floating-point_format#IEEE_754_double-precision_binary_floating-point_format:_binary64 */

#define PHENIQS_FLOAT_PRECISION 15

/* this should allow pheniqs to build against earlier htslib */
typedef bam_hdr_t sam_hdr_t;

#endif /* PHENIQS_INCLUDE_H */