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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2017, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2017, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
// This file is part of Lambda.
//
// Lambda is Free Software: you can redistribute it and/or modify it
// under the terms found in the LICENSE[.md|.rst] file distributed
// together with this file.
//
// Lambda 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.
//
// ==========================================================================
// lambda.cpp: Main File for Lambda
// ==========================================================================
#include <iostream>
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/arg_parse.h>
#include <seqan/seq_io.h>
#include <seqan/reduced_aminoacid.h>
#include <seqan/misc/terminal.h>
#include "output.hpp"
#include "options.hpp"
#include "holders.hpp"
#include "lambda.hpp"
using namespace seqan;
// inline BlastFormatFile
// _fileType(LambdaOptions const & options)
// {
// if (endsWith(options.output, ".m0"))
// return BlastFormatFile::PAIRWISE;
// else if (endsWith(options.output, ".m8"))
// return BlastFormatFile::TABULAR;
// else if (endsWith(options.output, ".m9"))
// return BlastFormatFile::TABULAR_WITH_COMMENTS;
// else
// return BlastFormatFile::UNKNOWN;
// }
// forwards
inline int
argConv0(LambdaOptions const & options);
//-
template <typename TOutFormat,
BlastTabularSpec h>
inline int
argConv1(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &);
//-
template <typename TOutFormat,
BlastTabularSpec h,
BlastProgram p>
inline int
argConv2(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &);
//-
template <typename TOutFormat,
typename TRedAlph,
BlastTabularSpec h,
BlastProgram p>
inline int
argConv3(LambdaOptions const & options,
TOutFormat const &,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
TRedAlph const &);
//-
template <typename TOutFormat,
typename TRedAlph,
typename TScoreExtension,
BlastTabularSpec h,
BlastProgram p>
inline int
argConv4(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
TRedAlph const & /**/,
TScoreExtension const & /**/);
//-
template <typename TIndexSpec,
typename TRedAlph,
typename TScoreExtension,
typename TOutFormat,
BlastProgram p,
BlastTabularSpec h>
inline int
realMain(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
TRedAlph const & /**/,
TScoreExtension const & /**/);
// --------------------------------------------------------------------------
// Function main()
// --------------------------------------------------------------------------
// Program entry point.
int main(int argc, char const ** argv)
{
// Parse the command line.
seqan::ArgumentParser parser;
LambdaOptions options;
seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
// If there was an error parsing or built-in argument parser functionality
// was triggered then we exit the program. The return code is 1 if there
// were errors and 0 if there were none.
if (res != seqan::ArgumentParser::PARSE_OK)
return res == seqan::ArgumentParser::PARSE_ERROR;
if (std::string(CMAKE_BUILD_TYPE) != "Release")
std::cerr << "WARNING: This binary is not built in release mode and will be much slower than it should be!\n";
return argConv0(options);
}
// CONVERT Run-time options to compile-time Format-Type
inline int
argConv0(LambdaOptions const & options)
{
CharString output = options.output;
if (endsWith(output, ".gz"))
output = prefix(output, length(output) - 3);
else if (endsWith(output, ".bz2"))
output = prefix(output, length(output) - 4);
if (endsWith(output, ".m0"))
return argConv1(options, BlastReport(), BlastTabularSpecSelector<BlastTabularSpec::NO_COMMENTS>());
else if (endsWith(output, ".m8"))
return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::NO_COMMENTS>());
else if (endsWith(output, ".m9"))
return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::COMMENTS>());
else if (endsWith(output, ".sam") || endsWith(output, ".bam")) // handled elsewhere
return argConv1(options, BlastTabular(), BlastTabularSpecSelector<BlastTabularSpec::COMMENTS>());
std::cerr << "ERROR: Cannot handle output extension.\n";
return -1;
}
template <typename TOutFormat,
BlastTabularSpec h>
inline int
argConv1(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &)
{
switch(options.blastProgram)
{
#ifndef FASTBUILD
case BlastProgram::BLASTN:
return argConv3(options,
TOutFormat(),
BlastTabularSpecSelector<h>(),
BlastProgramSelector<BlastProgram::BLASTN>(),
Dna5());
#endif
case BlastProgram::BLASTP:
return argConv2(options,
TOutFormat(),
BlastTabularSpecSelector<h>(),
BlastProgramSelector<BlastProgram::BLASTP>());
case BlastProgram::BLASTX:
return argConv2(options,
TOutFormat(),
BlastTabularSpecSelector<h>(),
BlastProgramSelector<BlastProgram::BLASTX>());
#ifndef FASTBUILD
case BlastProgram::TBLASTN:
return argConv2(options,
TOutFormat(),
BlastTabularSpecSelector<h>(),
BlastProgramSelector<BlastProgram::TBLASTN>());
case BlastProgram::TBLASTX:
return argConv2(options,
TOutFormat(),
BlastTabularSpecSelector<h>(),
BlastProgramSelector<BlastProgram::TBLASTX>());
#endif
default:
break;
}
std::cerr << "ERROR: Cannot handle program mode (perhaps you are building in FASTMODE?).\n";
return -1;
}
/// Alphabet reduction
template <typename TOutFormat,
BlastTabularSpec h,
BlastProgram p>
inline int
argConv2(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &)
{
using Th = BlastTabularSpecSelector<h>;
using Tp = BlastProgramSelector<p>;
switch (options.alphReduction)
{
case 0:
return argConv3(options, TOutFormat(), Th(), Tp(), AminoAcid());
case 2:
return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>());
#if 0
case 10:
return argConv2(options, TOutFormat(), ReducedAminoAcid<ClusterReduction<10>>());
case 1:
return argConv2(options, TOutFormat(), AminoAcid10());
case 8:
return argConv2(options, TOutFormat(), ReducedAminoAcid<ClusterReduction<8>>());
case 12:
return argConv2(options, TOutFormat(), ReducedAminoAcid<ClusterReduction<12>>());
#endif
default:
break;
}
std::cerr << "ERROR: Cannot handle the specified alphabet reduction.\n";
return -1;
}
// extension model
template <typename TOutFormat,
typename TRedAlph,
BlastTabularSpec h,
BlastProgram p>
inline int
argConv3(LambdaOptions const & options,
TOutFormat const &,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
TRedAlph const &)
{
if (options.gapOpen == 0)
#ifndef LAMBDA_LINGAPS_OPT
std::cerr << "ATTENTION: You have set the additional gap open cost to 0. If you run LAMBDA "
"in this configuration regularly, you might want to rebuild it with "
"LAMBDA_LINGAPS_OPT=1 to profit from additional optimizations.\n";
#else
return argConv4(options,
TOutFormat(),
BlastTabularSpecSelector<h>(),
BlastProgramSelector<p>(),
TRedAlph(),
LinearGaps());
else
#endif
return argConv4(options,
TOutFormat(),
BlastTabularSpecSelector<h>(),
BlastProgramSelector<p>(),
TRedAlph(),
AffineGaps());
}
template <typename TOutFormat,
typename TRedAlph,
typename TScoreExtension,
BlastTabularSpec h,
BlastProgram p>
inline int
argConv4(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
TRedAlph const & /**/,
TScoreExtension const & /**/)
{
int indexType = options.dbIndexType;
// if (indexType == -1) // autodetect
// {
// //TODO FIX THIS WITH NEW EXTENSIONS
// CharString file = options.dbFile;
// append(file, ".sa");
// struct stat buffer;
// if (stat(toCString(file), &buffer) == 0)
// {
// indexType = 0;
// } else
// {
// file = options.dbFile;
// append(file, ".sa.val"); // FM Index
// struct stat buffer;
// if (stat(toCString(file), &buffer) == 0)
// {
// indexType = 1;
// } else
// {
// std::cerr << "No Index file could be found, please make sure paths "
// << "are correct and the files are readable.\n" << std::flush;
//
// return -1;
// }
// }
// }
if (indexType == 0)
return realMain<IndexSa<>>(options,
TOutFormat(),
BlastTabularSpecSelector<h>(),
BlastProgramSelector<p>(),
TRedAlph(),
TScoreExtension());
else
return realMain<TFMIndex<>>(options,
TOutFormat(),
BlastTabularSpecSelector<h>(),
BlastProgramSelector<p>(),
TRedAlph(),
TScoreExtension());
}
/// REAL MAIN
#ifdef _OPENMP
#define TID omp_get_thread_num()
#else
#define TID 0
#endif
template <typename TIndexSpec,
typename TRedAlph,
typename TScoreExtension,
typename TOutFormat,
BlastProgram p,
BlastTabularSpec h>
inline int
realMain(LambdaOptions const & options,
TOutFormat const & /**/,
BlastTabularSpecSelector<h> const &,
BlastProgramSelector<p> const &,
TRedAlph const & /**/,
TScoreExtension const & /**/)
{
using TGlobalHolder = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
using TLocalHolder = LocalDataHolder<TGlobalHolder, TScoreExtension>;
myPrint(options, 1, "LAMBDA - the Local Aligner for Massive Biological DatA"
"\n======================================================"
"\nVersion ", SEQAN_APP_VERSION, "\n\n");
if (options.verbosity >= 2)
printOptions<TLocalHolder>(options);
TGlobalHolder globalHolder;
// context(globalHolder.outfile).scoringScheme._internalScheme = matr;
int ret = prepareScoring(globalHolder, options);
if (ret)
return ret;
ret = loadSubjects(globalHolder, options);
if (ret)
return ret;
ret = loadDbIndexFromDisk(globalHolder, options);
if (ret)
return ret;
ret = loadSegintervals(globalHolder, options);
if (ret)
return ret;
ret = loadQuery(globalHolder, options);
if (ret)
return ret;
// std::cout << "1st Query:\n"
// << front(globalHolder.qrySeqs) << "\n"
// << front(globalHolder.redQrySeqs) << "\n";
//
// std::cout << "last Query:\n"
// << back(globalHolder.qrySeqs) << "\n"
// << back(globalHolder.redQrySeqs) << "\n";
//
// std::cout << "1st Subject:\n"
// << front(globalHolder.subjSeqs) << "\n"
// << front(globalHolder.redSubjSeqs) << "\n";
//
// std::cout << "last Subject:\n"
// << back(globalHolder.subjSeqs) << "\n"
// << back(globalHolder.redSubjSeqs) << "\n";
myWriteHeader(globalHolder, options);
if (options.doubleIndexing)
{
myPrint(options, 1,
"Searching ",
options.queryPart,
" blocks of query with ",
options.threads,
" threads...\n");
if ((options.isTerm) && (options.verbosity >= 1))
{
for (unsigned char i=0; i< options.threads+3; ++i)
std::cout << std::endl;
std::cout << "\033[" << options.threads+2 << "A";
}
} else
{
myPrint(options, 1, "Searching and extending hits on-line...progress:\n"
"0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%\n|");
}
double start = sysTime();
// at least a block for each thread on double-indexing,
// otherwise a block for each original query (contains 6 queries if
// translation is used)
uint64_t nBlocks = (options.doubleIndexing
? options.queryPart
: length(globalHolder.qryIds));
uint64_t lastPercent = 0;
SEQAN_OMP_PRAGMA(parallel)
{
TLocalHolder localHolder(options, globalHolder);
SEQAN_OMP_PRAGMA(for schedule(dynamic))
for (uint64_t t = 0; t < nBlocks; ++t)
{
int res = 0;
localHolder.init(t);
// seed
res = generateSeeds(localHolder);
if (res)
continue;
if (options.doubleIndexing)
{
res = generateTrieOverSeeds(localHolder);
if (res)
continue;
}
// search
search(localHolder);
// sort
sortMatches(localHolder);
// extend
res = iterateMatches(localHolder);
if (res)
continue;
if ((!options.doubleIndexing) && (TID == 0) &&
(options.verbosity >= 1))
{
unsigned curPercent = ((t * 50) / nBlocks) * 2; // round to even
printProgressBar(lastPercent, curPercent);
}
} // implicit thread sync here
if ((!options.doubleIndexing) && (TID == 0) && (options.verbosity >= 1))
printProgressBar(lastPercent, 100);
SEQAN_OMP_PRAGMA(critical(statsAdd))
{
globalHolder.stats += localHolder.stats;
}
}
if (ret)
return ret;
myWriteFooter(globalHolder, options);
if (!options.doubleIndexing)
{
myPrint(options, 2, "Runtime: ", sysTime() - start, "s.\n\n");
}
printStats(globalHolder.stats, options);
return 0;
}