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// ==========================================================================
// bisar
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Sabrina Krakau <sabrina.krakau@fu-berlin.de>
// ==========================================================================
//#define POST_PRO_PROFILE
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/arg_parse.h>
#include <seqan/file.h>
#include <seqan/store.h>
#include <seqan/bam_io.h>
#include <seqan/score.h>
#include "bisar_score_data.h"
#include "bisar_score.h"
#include "bisar_base.h"
#include "bisar.h"
using namespace seqan2;
struct AppOptions
{
// Verbosity level. 0 -- quiet, 1 -- normal, 2 -- verbose, 3 -- very verbose.
int verbosity;
CharString readFileName;
CharString readFileName2;
CharString samFileName;
CharString refFileName;
CharString outputFileName;
int intervalOffset;
double minMapq;
double max4Error; // max. allowed real error rate
double max3Error; // max. allowed error rate in 3 letter alphabet (corresponding to mapper settings)
double maxScore;
unsigned maxBasePenalty; // limit the penalty for a single base
int minScore;
bool outputSingleMates;
double scoreMatch;
double scoreMismatch;
bool simpleScore;
bool nonSimpleSubstErrors;
bool nonSimpleInsErrors;
bool nonSimpleDelErrors;
double delErrorRate;
double lambda;
double gapOpenScore;
double gapExtendScore;
double scalingFactorDelErrors;
double scalingFactorInsErrors;
double bsConversionRate;
double globalMethRate;
double seqIdentity; // Used for substitution matrix construction [0.0-1.0]
double refNRate; // Used for substitution matrix construction
double pseudoMatchScale;
AppOptions() :
verbosity(1),
intervalOffset(3),
minMapq(1),
max4Error(4),
max3Error(3),
maxScore(1000000), // TODO: what would be reasonable?
maxBasePenalty(-3), // scaled to single penalties
minScore(0),
outputSingleMates(true), // Output also read whose mate didn't map & if no match mate pair found, output mates single
scoreMatch(10.0), // at the moment only used for pseudoWorstScore
scoreMismatch(0.01),
simpleScore(true),
nonSimpleSubstErrors(false),
nonSimpleInsErrors(false),
nonSimpleDelErrors(false),
delErrorRate(0.001),
lambda(1.0),
gapOpenScore(-4.5),
gapExtendScore(-2.0),
scalingFactorDelErrors(5.0),
scalingFactorInsErrors(5.0),
bsConversionRate(0.99),
globalMethRate(0.5),
seqIdentity(0.9),
refNRate(0.01),
pseudoMatchScale(0.9)
{}
};
// ==========================================================================
// Functions
// ==========================================================================
// --------------------------------------------------------------------------
// Function parseCommandLine()
// --------------------------------------------------------------------------
ArgumentParser::ParseResult
parseCommandLine(AppOptions & options, int argc, char const ** argv)
{
// Setup ArgumentParser.
ArgumentParser parser("bisar");
// Set short description, version, and date.
setShortDescription(parser, "Pairwise four-letter realignment computation for bisulfite reads");
setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
setDate(parser, SEQAN_DATE);
setCategory(parser, "BS-Seq Analysis");
// Define usage line and long description.
addUsageLine(parser, "[\\fIOPTIONS\\fP] <\\fIALIGNMENT FILE\\fP> <\\fIGENOME FILE\\fP> <\\fIREADS FILE\\fP>");
addUsageLine(parser, "[\\fIOPTIONS\\fP] <\\fIALIGNMENT FILE\\fP> <\\fIGENOME FILE\\fP> <\\fIPE-READS FILE1\\fP> <\\fIPE-READS FILE2\\fP>");
addDescription(parser, "This program reads three-letter mappings of bisulfite reads and computes local pairwise four-letter realignments using an advanced statistical alignment model.");
// We require ... arguments.
addArgument(parser, ArgParseArgument(ArgParseArgument::INPUT_FILE, "ALIGNMENTS"));
setHelpText(parser, 0, "SAM input file containing three-letter read alignments (must be sorted by query names).");
setValidValues(parser, 0, BamFileIn::getFileExtensions());
addArgument(parser, ArgParseArgument(ArgParseArgument::INPUT_FILE, "GENOME"));
setHelpText(parser, 1, "A reference genome file.");
setValidValues(parser, 1, SeqFileIn::getFileExtensions());
addArgument(parser, ArgParseArgument(ArgParseArgument::INPUT_FILE, "READS", true));
setHelpText(parser, 2, "Either one (single-end) or two (paired-end) read files.");
setValidValues(parser, 2, SeqFileIn::getFileExtensions());
addSection(parser, "Options");
addOption(parser, ArgParseOption("o", "output-file", "Mapping output file.", ArgParseArgument::OUTPUT_FILE));
setValidValues(parser, "output-file", BamFileOut::getFileExtensions());
setRequired(parser, "output-file", true);
addOption(parser, ArgParseOption("e3", "max3-error", "Max. error rate in 3-letter alphabet.", ArgParseArgument::DOUBLE));
setMinValue(parser, "max3-error", "0");
setMaxValue(parser, "max3-error", "100");
setDefaultValue(parser, "max3-error", options.max3Error);
addOption(parser, ArgParseOption("e4", "max4-error", "Max. error rate in 4-letter alphabet.", ArgParseArgument::DOUBLE));
setMinValue(parser, "max4-error", "0");
setMaxValue(parser, "max4-error", "100");
setDefaultValue(parser, "max4-error", options.max4Error);
addOption(parser, ArgParseOption("mq", "min-mapq", "Min required mapping quality.", ArgParseArgument::DOUBLE));
setMinValue(parser, "min-mapq", "0");
setDefaultValue(parser, "min-mapq", options.minMapq);
addOption(parser, ArgParseOption("ns", "non-simple", "Use non-uniform SNP distributions."));
hideOption(parser, "ns");
addOption(parser, ArgParseOption("nse", "ns-subst-errors", "Use empirical substitution error frequencies of Illumina sequencing data for alignment scoring scheme (corresponding to Dohm et al. 2008)."));
addOption(parser, ArgParseOption("nsi", "ns-ins-errors", "Use empirical insertion error frequencies of Illumina sequencing data for alignment scoring scheme (corresponding to Minoche et al. 2011)."));
addOption(parser, ArgParseOption("nsd", "ns-del-errors", "Use empirical deletion error frequencies of Illumina sequencing data for alignment scoring scheme (corresponding to Minoche et al. 2011)."));
addOption(parser, ArgParseOption("der", "del-error-rate", "Deletion error rate.", ArgParseArgument::DOUBLE));
setMinValue(parser, "del-error-rate", "0");
setMaxValue(parser, "del-error-rate", "1");
setDefaultValue(parser, "del-error-rate", options.delErrorRate);
addOption(parser, ArgParseOption("gas", "gap-open-score", "Gap open score (original, must be proportional to mismatch scores).", ArgParseArgument::DOUBLE));
setDefaultValue(parser, "gap-open-score", options.gapOpenScore);
addOption(parser, ArgParseOption("ges", "gap-extend-score", "Gap extend score.", ArgParseArgument::DOUBLE));
setDefaultValue(parser, "gap-extend-score", options.gapExtendScore);
addOption(parser, ArgParseOption("bsc", "bs-conversion-rate", "Bisulfite conversion rate.", ArgParseArgument::DOUBLE));
setMinValue(parser, "bs-conversion-rate", "0");
setMaxValue(parser, "bs-conversion-rate", "1");
setDefaultValue(parser, "bs-conversion-rate", options.bsConversionRate);
addOption(parser, ArgParseOption("gmr", "global-meth-rate", "Global methylation rate.", ArgParseArgument::DOUBLE));
setMinValue(parser, "global-meth-rate", "0");
setMaxValue(parser, "global-meth-rate", "1");
setDefaultValue(parser, "global-meth-rate", options.globalMethRate);
addOption(parser, ArgParseOption("i", "seq-identity", "Sequence identity used for substitution matrix.", ArgParseArgument::DOUBLE));
setMinValue(parser, "seq-identity", "0");
setMaxValue(parser, "seq-identity", "1");
setDefaultValue(parser, "seq-identity", options.seqIdentity);
addOption(parser, ArgParseOption("rn", "ref-n", "Rate of Ns in reference sequence.", ArgParseArgument::DOUBLE));
setMinValue(parser, "ref-n", "0");
setMaxValue(parser, "ref-n", "1");
setDefaultValue(parser, "ref-n", options.refNRate);
addOption(parser, ArgParseOption("pms", "pseudo-match-scale", "Scaling for pseudo match score. ", ArgParseArgument::DOUBLE));
setMinValue(parser, "pseudo-match-scale", "0");
setDefaultValue(parser, "pseudo-match-scale", options.pseudoMatchScale);
hideOption(parser, "pms");
addOption(parser, ArgParseOption("q", "quiet", "Set verbosity to a minimum."));
addOption(parser, ArgParseOption("v", "verbose", "Enable verbose output."));
addOption(parser, ArgParseOption("vv", "very-verbose", "Enable very verbose output."));
// Add Examples Section.
addTextSection(parser, "Examples");
addListItem(parser, "\\fBbisar\\fP \\fB-e3\\fP \\fB4\\fP \\fB-e4\\fP \\fB5\\fP \\fB-o\\fP \\fBmapped_reads_verified.sam\\fP \\fBmapped_reads.sam\\fP \\fBgenome.fa\\fP \\fBreads.fastq\\fP",
"Compute realignments for all reads with up to 4% errors in their three-letter alignment, while allowing up to 5% errors in four-letter alignments.");
addListItem(parser, "\\fBbisar\\fP \\fB-e3\\fP \\fB4\\fP \\fB-e4\\fP \\fB5\\fP \\fB-o\\fP \\fBmapped_reads_verified.sam\\fP \\fBmapped_reads.sam\\fP \\fBgenome.fa\\fP \\fBreads_L.fastq\\fP \\fBreads_R.fastq \\fP",
"Compute realignments for paired-end reads.");
// Parse command line.
ArgumentParser::ParseResult res = parse(parser, argc, argv);
// Only extract options if the program will continue after parseCommandLine()
if (res != ArgumentParser::PARSE_OK)
return res;
getArgumentValue(options.samFileName, parser, 0);
getArgumentValue(options.refFileName, parser, 1);
if (1 == getArgumentValueCount(parser, 2))
getArgumentValue(options.readFileName, parser, 2, 0);
else if (2 == getArgumentValueCount(parser, 2))
{
getArgumentValue(options.readFileName, parser, 2, 0);
getArgumentValue(options.readFileName2, parser, 2, 1);
}
else
{
std::cerr << "ERROR: " << getArgumentValueCount(parser, 2) << " read files specified (must be one or two)." << std::endl;
return ArgumentParser::PARSE_ERROR;
}
getOptionValue(options.outputFileName, parser, "output-file");
getOptionValue(options.max3Error, parser, "max3-error");
getOptionValue(options.max4Error, parser, "max4-error");
getOptionValue(options.minMapq, parser, "min-mapq");
options.nonSimpleSubstErrors = isSet(parser, "ns-subst-errors");
options.nonSimpleInsErrors = isSet(parser, "ns-ins-errors");
options.nonSimpleDelErrors = isSet(parser, "ns-del-errors");
getOptionValue(options.delErrorRate, parser, "del-error-rate");
getOptionValue(options.gapOpenScore, parser, "gap-open-score");
getOptionValue(options.gapExtendScore, parser, "gap-extend-score");
getOptionValue(options.bsConversionRate, parser, "bs-conversion-rate");
getOptionValue(options.globalMethRate, parser, "global-meth-rate");
getOptionValue(options.seqIdentity, parser, "seq-identity");
getOptionValue(options.refNRate, parser, "ref-n");
getOptionValue(options.pseudoMatchScale, parser, "pseudo-match-scale");
// Extract option values.
if (isSet(parser, "quiet"))
options.verbosity = 0;
if (isSet(parser, "verbose"))
options.verbosity = 2;
if (isSet(parser, "very-verbose"))
options.verbosity = 3;
return ArgumentParser::PARSE_OK;
}
// --------------------------------------------------------------------------
// Function main()
// --------------------------------------------------------------------------
// Program entry point.
int main(int argc, char const ** argv)
{
// Parse the command line.
ArgumentParser parser;
AppOptions options;
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 != ArgumentParser::PARSE_OK)
return res == ArgumentParser::PARSE_ERROR;
#ifdef POST_PRO_PROFILE
double timeStamp = sysTime();
#endif
if (!options.simpleScore)
postProcessMain(options, BsNonSimple());
else
postProcessMain(options, BsSimple());
#ifdef POST_PRO_PROFILE
Times::instance().time_all = sysTime() - timeStamp;
std::cout << " Time needed for all: " << Times::instance().time_all/60.0 << "min" << std::endl;
std::cout << " Time needed for globalAlignment: " << Times::instance().time_globalAlignment/60.0 << "min" << std::endl;
std::cout << " Time needed for writeBsAlignment: " << Times::instance().time_writeBsAlignment/60.0 << "min" << std::endl;
#endif
return 0;
}
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