magicblast_args.cpp

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/*  $Id: magicblast_args.cpp 88808 2020-01-21 10:48:40Z boratyng $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Author: Greg Boratyn
 *
 */
 
/** @file blastmapper_args.cpp
 * Implementation of the BLASTMAPPER command line arguments
 */
 
#include <ncbi_pch.hpp>
#include <algo/blast/blastinput/magicblast_args.hpp>
#include <algo/blast/api/blast_exception.hpp>
#include <algo/blast/blastinput/blast_fasta_input.hpp>
#include <algo/blast/blastinput/blast_input_aux.hpp>
//#include <algo/blast/api/version.hpp>
#include <algo/blast/api/magicblast_options.hpp>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)
USING_SCOPE(objects);
 
 
/// StdCmdLineArgs with output stream for unaligned reads
class CMapperStdCmdLineArgs : public CStdCmdLineArgs
{
public:
    CMapperStdCmdLineArgs(void) : CStdCmdLineArgs() {}
 
    virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc) {
 
        CStdCmdLineArgs::SetArgumentDescriptions(arg_desc);
 
        arg_desc.SetCurrentGroup("General search options");
 
        arg_desc.AddOptionalKey(kArgUnalignedOutput, "output_file",
                                "Report unaligned reads to this file",
                                CArgDescriptions::eOutputFile);
 
        arg_desc.SetDependency(kArgUnalignedOutput,
                               CArgDescriptions::eExcludes,
                               kArgNoUnaligned);
 
        arg_desc.SetCurrentGroup("");        
    }
};
 
 
/// Special generic search arguments for blastmapper
class CMapperGenericSearchArgs : public CGenericSearchArgs
{
public:
    CMapperGenericSearchArgs(void) : CGenericSearchArgs(false) {}
 
    virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc) {
 
        arg_desc.SetCurrentGroup("General search options");
 
        arg_desc.AddDefaultKey(kArgWordSize, "int_value", "Minimum number of "
                               "consecutive bases matching exactly",
                               CArgDescriptions::eInteger,
                               NStr::IntToString(BLAST_WORDSIZE_MAPPER));
 
        arg_desc.SetConstraint(kArgWordSize,
                               new CArgAllowValuesGreaterThanOrEqual(12));
 
 
        // gap open penalty
        arg_desc.AddDefaultKey(kArgGapOpen, "open_penalty",
                               "Cost to open a gap",
                               CArgDescriptions::eInteger, "0");
 
        // gap extend penalty
        arg_desc.AddDefaultKey(kArgGapExtend, "extend_penalty",
                               "Cost to extend a gap",
                               CArgDescriptions::eInteger, "4");
 
        // FIXME: not sure if this one is needed
        arg_desc.SetCurrentGroup("Restrict search or results");
        arg_desc.AddDefaultKey(kArgPercentIdentity, "float_value",
                               "Percent identity cutoff for alignments",
                               CArgDescriptions::eDouble, "0.0");
        arg_desc.SetConstraint(kArgPercentIdentity,
                               new CArgAllow_Doubles(0.0, 100.0));
 
        // strand-specific flags (mutually exclusive)
        arg_desc.AddFlag(kArgFwdRev,
                         "Strand specific reads forward/reverse"
//                               ", requires -only_strand_specific for non-SAM "
//                               "output format"
                         );
        arg_desc.AddFlag(kArgRevFwd,
                               "Strand specific reads reverse/forward"
//                               ", requires -only_strand_specific for non-SAM "
//                               "output format"
                         );
        // FIXME: save for later feature enhancement
//        arg_desc.AddFlag(kArgFwdOnly,
//                "Strand specific reads forward only", true);
//        arg_desc.AddFlag(kArgRevOnly,
//                "Strand specific reads reverse only", true);
//        arg_desc.AddFlag(kArgOnlyStrandSpecific,
//                               "Only show strand specific reads, "
//                               "requires either -fr or -rf",
//                               true);
 
        arg_desc.SetDependency(kArgFwdRev,
                               CArgDescriptions::eExcludes,
                               kArgRevFwd);
        // FIXME: save for later feature enhancement
//        arg_desc.SetDependency(kArgFwdOnly,
//                               CArgDescriptions::eRequires,
//                               kArgOnlyStrandSpecific);
//        arg_desc.SetDependency(kArgRevOnly,
//                               CArgDescriptions::eRequires,
//                               kArgOnlyStrandSpecific);
    }
};
 
/// Nucleotide args with no reward score
class CMapperNuclArgs : public CNuclArgs
{
public:
    CMapperNuclArgs(void) : CNuclArgs() {}
 
    virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc) {
        arg_desc.SetCurrentGroup("General search options");
        // blastn mismatch penalty
        arg_desc.AddDefaultKey(kArgMismatch, "penalty",
                               "Penalty for a nucleotide mismatch",
                               CArgDescriptions::eInteger, "-4");
        arg_desc.SetConstraint(kArgMismatch,
                               new CArgAllowValuesLessThanOrEqual(0));
        arg_desc.SetCurrentGroup("");
    }
};
 
/// Longest intron size with non-zero defalut value
class CMapperLargestIntronSizeArgs : public CLargestIntronSizeArgs
{
public:
    virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc) {
        arg_desc.SetCurrentGroup("General search options");
        // largest intron length
        arg_desc.AddDefaultKey(kArgMaxIntronLength, "length",
                    "Maximum allowed intron length",
                    CArgDescriptions::eInteger,
                    NStr::IntToString(500000));
        arg_desc.SetConstraint(kArgMaxIntronLength,
                               new CArgAllowValuesGreaterThanOrEqual(0));
        arg_desc.SetCurrentGroup("");
    }
};
 
/// RemoteArgs with no option for remote
class CMapperRemoteArgs : public CRemoteArgs
{
public:
    virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc) {}
};
 
 
/// Program description without BLAST+ version
class CMapperProgramDescriptionArgs : public CProgramDescriptionArgs
{
public:
    CMapperProgramDescriptionArgs(const string& program_name,
                                  const string& program_desc)
        : CProgramDescriptionArgs(program_name, program_desc) {}
 
    virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc) {
        arg_desc.SetUsageContext(m_ProgName, m_ProgDesc);
    }
};
 
 
/// MT args that allow multiple threads with a FASTA subject
class CMapperMTArgs : public CMTArgs
{
public:
    virtual void ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& /* opts */) {
        const int kMaxValue = static_cast<int>(GetCpuCount());
 
        if (args.Exist(kArgNumThreads) &&
            args[kArgNumThreads].HasValue()) {
 
            // use the minimum of the two: user requested number of threads and
            // number of available CPUs for number of threads
            int num_threads = args[kArgNumThreads].AsInteger();
            if (num_threads > kMaxValue) {
                m_NumThreads = kMaxValue;
                
                ERR_POST(Warning << (string)"Number of threads was reduced to "
                         + NStr::IntToString((unsigned int)m_NumThreads) +
                         " to match the number of available CPUs");
            }
            else {
                m_NumThreads = num_threads;
            }
        }
    }
};
 
CMagicBlastAppArgs::CMagicBlastAppArgs()
{
    // remove search strategy args added in parent class constructor
    m_Args.clear();
 
    CRef<IBlastCmdLineArgs> arg;
    static const char kProgram[] = "magicblast";
    arg.Reset(new CMapperProgramDescriptionArgs(kProgram, "Short read mapper"));
    m_Args.push_back(arg);
 
    m_BlastDbArgs.Reset(new CBlastDatabaseArgs(false, false, false, true));
    m_BlastDbArgs->SetDatabaseMaskingSupport(true);
    arg.Reset(m_BlastDbArgs);
    m_Args.push_back(arg);
 
    m_StdCmdLineArgs.Reset(new CMapperStdCmdLineArgs);
    m_StdCmdLineArgs->SetGzipEnabled(true);
    arg.Reset(m_StdCmdLineArgs);
    m_Args.push_back(arg);
 
    arg.Reset(new CMapperGenericSearchArgs);
    m_Args.push_back(arg);
 
    arg.Reset(new CMapperNuclArgs);
    m_Args.push_back(arg);
 
    m_QueryOptsArgs.Reset(new CMapperQueryOptionsArgs);
    arg.Reset(m_QueryOptsArgs);
    m_Args.push_back(arg);
 
    arg.Reset(new CMapperFormattingArgs);
    m_FormattingArgs.Reset(
            dynamic_cast<CFormattingArgs*>(arg.GetNonNullPointer())
    );
    m_Args.push_back(arg);
 
    m_MTArgs.Reset(new CMapperMTArgs);
    arg.Reset(m_MTArgs);
    m_Args.push_back(arg);
 
    m_RemoteArgs.Reset(new CMapperRemoteArgs);
    arg.Reset(m_RemoteArgs);
    m_Args.push_back(arg);
 
    m_DebugArgs.Reset(new CDebugArgs);
    arg.Reset(m_DebugArgs);
    m_Args.push_back(arg);
 
    arg.Reset(new CMapperLargestIntronSizeArgs);
    m_Args.push_back(arg);
 
    arg.Reset(new CMappingArgs);
    m_Args.push_back(arg);
}
 
CRef<CBlastOptionsHandle>
CMagicBlastAppArgs::x_CreateOptionsHandle(
                                         CBlastOptions::EAPILocality locality,
                                         const CArgs& args)
{
    return CRef<CBlastOptionsHandle>(new CMagicBlastOptionsHandle(locality));
}
 
int
CMagicBlastAppArgs::GetQueryBatchSize() const
{
    bool is_remote = (m_RemoteArgs.NotEmpty() && m_RemoteArgs->ExecuteRemotely());
    return blast::GetQueryBatchSize(eMapper, false, is_remote, true);
}
 
END_SCOPE(blast)
END_NCBI_SCOPE