bamread.cpp

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/*  $Id: bamread.cpp 100329 2023-07-20 14:34:22Z vasilche $
 * ===========================================================================
 *
 *                            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.
 *
 * ===========================================================================
 *
 * Authors:  Eugene Vasilchenko
 *
 * File Description:
 *   Access to BAM files
 *
 */
 
#include <ncbi_pch.hpp>
#include <sra/readers/bam/bamread.hpp>
#include <sra/readers/ncbi_traces_path.hpp>
#include <util/simple_buffer.hpp>
 
#include <klib/rc.h>
#include <klib/log.h>
#include <klib/text.h>
#include <klib/sra-release-version.h>
#include <kfg/config.h>
#include <vfs/path.h>
#include <vfs/manager.h>
#include <kns/manager.h>
#include <kns/http.h>
#include <kns/tls.h>
#include <align/bam.h>
#include <align/align-access.h>
 
#include <corelib/ncbifile.hpp>
#include <corelib/ncbiapp_api.hpp>
#include <corelib/request_ctx.hpp>
#include <objects/general/general__.hpp>
#include <objects/seq/seq__.hpp>
#include <objects/seqset/seqset__.hpp>
#include <objects/seqalign/seqalign__.hpp>
#include <util/sequtil/sequtil_manip.hpp>
#include <numeric>
#include <thread>
 
#ifndef NCBI_THROW2_FMT
# define NCBI_THROW2_FMT(exception_class, err_code, message, extra)     \
    throw NCBI_EXCEPTION2(exception_class, err_code, FORMAT(message), extra)
#endif
 
#if NCBI_SSE > 40
# define USE_SSE
#endif
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
class CSeq_entry;
 
static const char kBamExt[] = ".bam";
static const char kBaiExt[] = ".bai";
 
 
DEFINE_BAM_REF_TRAITS(VFSManager, );
DEFINE_BAM_REF_TRAITS(AlignAccessMgr, const);
DEFINE_BAM_REF_TRAITS(AlignAccessDB,  const);
DEFINE_BAM_REF_TRAITS(AlignAccessRefSeqEnumerator, );
DEFINE_BAM_REF_TRAITS(AlignAccessAlignmentEnumerator, );
DEFINE_BAM_REF_TRAITS(BAMFile, const);
DEFINE_BAM_REF_TRAITS(BAMAlignment, const);
SPECIALIZE_BAM_REF_TRAITS(KConfig, );
SPECIALIZE_BAM_REF_TRAITS(KNSManager, );
DEFINE_BAM_REF_TRAITS(KConfig, );
DEFINE_BAM_REF_TRAITS(KNSManager, );
 
 
CBamException::CBamException(void)
    : m_RC(0)
{
}
 
 
CBamException::CBamException(const CDiagCompileInfo& info,
                             const CException* prev_exc,
                             EErrCode err_code,
                             const string& message,
                             EDiagSev severity)
    : CException(info, prev_exc, CException::EErrCode(err_code), message),
      m_RC(0)
{
    this->x_Init(info, message, prev_exc, severity);
    this->x_InitErrCode(CException::EErrCode(err_code));
}
 
 
CBamException::CBamException(const CDiagCompileInfo& info,
                             const CException* prev_exc,
                             EErrCode err_code,
                             const string& message,
                             rc_t rc,
                             EDiagSev severity)
    : CException(info, prev_exc, CException::EErrCode(err_code), message),
      m_RC(rc)
{
    this->x_Init(info, message, prev_exc, severity);
    this->x_InitErrCode(CException::EErrCode(err_code));
}
 
 
CBamException::CBamException(const CDiagCompileInfo& info,
                             const CException* prev_exc,
                             EErrCode err_code,
                             const string& message,
                             rc_t rc,
                             const string& param,
                             EDiagSev severity)
    : CException(info, prev_exc, CException::EErrCode(err_code), message),
      m_RC(rc),
      m_Param(param)
{
    this->x_Init(info, message, prev_exc, severity);
    this->x_InitErrCode(CException::EErrCode(err_code));
}
 
 
CBamException::CBamException(const CBamException& other)
    : CException( other),
      m_RC(other.m_RC),
      m_Param(other.m_Param)
{
    x_Assign(other);
}
 
 
CBamException::~CBamException(void) throw()
{
}
 
 
const CException* CBamException::x_Clone(void) const
{
    return new CBamException(*this);
}
 
 
const char* CBamException::GetType(void) const
{
    return "CBamException";
}
 
 
CBamException::TErrCode CBamException::GetErrCode(void) const
{
    return typeid(*this) == typeid(CBamException) ?
        x_GetErrCode() : CException::GetErrCode();
}
 
 
const char* CBamException::GetErrCodeString(void) const
{
    switch (GetErrCode()) {
    case eOtherError:   return "eOtherError";
    case eNullPtr:      return "eNullPtr";
    case eAddRefFailed: return "eAddRefFailed";
    case eInvalidArg:   return "eInvalidArg";
    case eInitFailed:   return "eInitFailed";
    case eNoData:       return "eNoData";
    case eBadCIGAR:     return "eBadCIGAR";
    case eInvalidBAMFormat: return "eInvalidBAMFormat";
    case eInvalidBAIFormat: return "eInvalidBAIFormat";
    case eFileNotFound: return "eFileNotFound";
    default:            return CException::GetErrCodeString();
    }
}
 
 
ostream& operator<<(ostream& out, const CBamRcFormatter& rc)
{
    char buffer[1024];
    size_t error_len;
    RCExplain(rc.GetRC(), buffer, sizeof(buffer), &error_len);
    out << "0x" << hex << rc.GetRC() << dec << ": " << buffer;
    return out;
}
 
 
void CBamException::ReportExtra(ostream& out) const
{
    if ( m_RC ) {
        out << CBamRcFormatter(m_RC);
    }
    if ( !m_Param.empty() ) {
        if ( m_RC ) {
            out << ": ";
        }
        out << m_Param;
    }
}
 
 
void CBamException::ReportError(const char* msg, rc_t rc)
{
    ERR_POST(msg<<": "<<CBamRcFormatter(rc));
}
 
 
void CBamString::x_reserve(size_t min_capacity)
{
    size_t capacity = m_Capacity;
    if ( capacity == 0 ) {
        capacity = min_capacity;
    }
    else {
        while ( capacity < min_capacity ) {
            capacity <<= 1;
        }
    }
    m_Buffer.reset(new char[capacity]);
    m_Capacity = capacity;
}
 
 
const char* CSrzException::GetErrCodeString(void) const
{
    switch ( GetErrCode() ) {
    case eBadFormat:        return "eBadFormat";
    case eNotFound:         return "eNotFound";
    case eOtherError:       return "eOtherError";
    default:                return CException::GetErrCodeString();
    }
}
 
 
CSrzPath::CSrzPath(void)
{
    x_Init();
    AddRepPath(GetDefaultRepPath());
    AddVolPath(GetDefaultVolPath());
}
 
 
CSrzPath::CSrzPath(const string& rep_path, const string& vol_path)
{
    x_Init();
    AddRepPath(rep_path.empty()? GetDefaultRepPath(): rep_path);
    AddVolPath(vol_path.empty()? GetDefaultVolPath(): vol_path);
}
 
 
void CSrzPath::x_Init(void)
{
}
 
 
void CSrzPath::AddRepPath(const string& rep_path)
{
    NStr::Split(rep_path, ":", m_RepPath);
}
 
 
void CSrzPath::AddVolPath(const string& vol_path)
{
    NStr::Split(vol_path, ":", m_VolPath);
}
 
 
NCBI_PARAM_DECL(string, SRZ, REP_PATH);
NCBI_PARAM_DEF_EX(string, SRZ, REP_PATH, NCBI_SRZ_REP_PATH,
                  eParam_NoThread, SRZ_REP_PATH);
 
 
NCBI_PARAM_DECL(string, SRZ, VOL_PATH);
NCBI_PARAM_DEF_EX(string, SRZ, VOL_PATH, NCBI_SRZ_VOL_PATH,
                  eParam_NoThread, SRZ_VOL_PATH);
 
 
string CSrzPath::GetDefaultRepPath(void)
{
    return NCBI_PARAM_TYPE(SRZ, REP_PATH)::GetDefault();
}
 
 
string CSrzPath::GetDefaultVolPath(void)
{
    return NCBI_PARAM_TYPE(SRZ, VOL_PATH)::GetDefault();
}
 
 
string CSrzPath::FindAccPath(const string& acc, EMissing missing)
{
    if ( acc.size() != 9 && acc.size() != 12 ) {
        // bad length
        if ( missing == eMissing_Throw ) {
            NCBI_THROW(CSrzException, eBadFormat,
                       "SRZ accession must be 9 or 12 chars long: "+acc);
        }
        return kEmptyStr;
    }
 
    string prefix = acc.substr(0, 3);
    NStr::ToUpper(prefix);
    if ( prefix != "SRZ" && prefix != "DRZ" && prefix != "ERZ" ) {
        // bad prefix
        if ( missing == eMissing_Throw ) {
            NCBI_THROW(CSrzException, eBadFormat,
                       "SRZ accession must start with SRZ, DRZ, or ERZ: "+acc);
        }
        return kEmptyStr;
    }
 
    unsigned num;
    try {
        num = NStr::StringToUInt(CTempString(acc).substr(3));
    }
    catch( CException& /*ignored*/ ) {
        // bad number
        if ( missing == eMissing_Throw ) {
            NCBI_THROW(CSrzException, eBadFormat,
                       "SRZ accesion is improperly formatted: "+acc);
        }
        return kEmptyStr;
    }
 
    unsigned level1 = num/1000;
    char sub_dir[128];
    snprintf(sub_dir, sizeof(sub_dir), "%s/%06u/%s%s/provisional",
            prefix.c_str(), level1, prefix.c_str(), acc.c_str()+3);
    sub_dir[sizeof(sub_dir)-1] = '\0';
 
    ITERATE ( vector<string>, rep_it, m_RepPath ) {
        ITERATE ( vector<string>, vol_it, m_VolPath ) {
            string dir =
                CFile::MakePath(CFile::MakePath(*rep_it, *vol_it), sub_dir);
            if ( CFile(CFile::MakePath(dir, SRZ_CONFIG_NAME)).Exists() ) {
                return dir;
            }
        }
    }
    if ( missing == eMissing_Throw ) {
        NCBI_THROW(CSrzException, eNotFound,
                   "SRZ accession not found: "+acc);
    }
    return kEmptyStr;
}
 
 
NCBI_PARAM_DECL(bool, BAM, CIGAR_IN_ALIGN_EXT);
NCBI_PARAM_DEF(bool, BAM, CIGAR_IN_ALIGN_EXT, true);
 
 
static bool s_GetCigarInAlignExt(void)
{
    static bool value = NCBI_PARAM_TYPE(BAM, CIGAR_IN_ALIGN_EXT)::GetDefault();
    return value;
}
 
 
NCBI_PARAM_DECL(bool, BAM, OMIT_AMBIGUOUS_MATCH_CIGAR);
NCBI_PARAM_DEF(bool, BAM, OMIT_AMBIGUOUS_MATCH_CIGAR, false);
 
 
static bool s_OmitAmbiguousMatchCigar(void)
{
    static bool value = NCBI_PARAM_TYPE(BAM, OMIT_AMBIGUOUS_MATCH_CIGAR)::GetDefault();
    return value;
}
 
 
NCBI_PARAM_DECL(int, BAM, DEBUG);
NCBI_PARAM_DEF_EX(int, BAM, DEBUG, 0, eParam_NoThread, BAM_DEBUG);
 
 
int CBamDb::GetDebugLevel(void)
{
    static int value = NCBI_PARAM_TYPE(BAM, DEBUG)::GetDefault();
    return value;
}
 
 
NCBI_PARAM_DECL(bool, BAM, USE_RAW_INDEX);
NCBI_PARAM_DEF_EX(bool, BAM, USE_RAW_INDEX, true,
                  eParam_NoThread, BAM_USE_RAW_INDEX);
 
 
bool CBamDb::UseRawIndex(EUseAPI use_api)
{
    if ( use_api == eUseDefaultAPI ) {
        static bool value = NCBI_PARAM_TYPE(BAM, USE_RAW_INDEX)::GetDefault();
        return value;
    }
    else {
        return use_api == eUseRawIndex;
    }
}
 
 
NCBI_PARAM_DECL(bool, BAM, EXPLICIT_MATE_INFO);
NCBI_PARAM_DEF_EX(bool, BAM, EXPLICIT_MATE_INFO, false,
                  eParam_NoThread, BAM_EXPLICIT_MATE_INFO);
 
 
static bool s_ExplicitMateInfo(void)
{
    static CSafeStatic<NCBI_PARAM_TYPE(BAM, EXPLICIT_MATE_INFO)> s_Value;
    return s_Value->Get();
}
 
 
static
void sx_MapId(CSeq_id& id, IIdMapper* idmapper)
{
    if ( idmapper ) {
        try {
            idmapper->MapObject(id);
        }
        catch ( CException& /*ignored*/ ) {
        }
    }
}
 
 
static
CRef<CSeq_id> sx_GetRefSeq_id(const string& str, IIdMapper* idmapper)
{
    CRef<CSeq_id> id;
    try {
        id = new CSeq_id(str);
    }
    catch ( CException& /*ignored*/ ) {
    }
    if ( !id && str.find('|') != NPOS ) {
        try {
            CBioseq::TId ids;
            CSeq_id::ParseIDs(ids, str);
            if ( !ids.empty() ) {
                id = *ids.begin();
            }
        }
        catch ( CException& /*ignored*/ ) {
        }
    }
    if ( !id || (id->IsGi() && id->GetGi() < GI_CONST(1000) ) ) {
        id = new CSeq_id(CSeq_id::e_Local, str);
    }
    sx_MapId(*id, idmapper);
    return id;
}
 
 
static
CRef<CSeq_id> sx_GetShortSeq_id(const string& str, IIdMapper* idmapper, bool external)
{
    if ( external || str.find('|') != NPOS ) {
        try {
            CRef<CSeq_id> id(new CSeq_id(str));
            return id;
        }
        catch ( CException& /*ignored*/ ) {
            // continue with local id
        }
    }
    CRef<CSeq_id> id(new CSeq_id(CSeq_id::e_Local, str));
    //sx_MapId(*id, idmapper);
    return id;
}
 
 
/////////////////////////////////////////////////////////////////////////////
// VDB library initialization code
// similar code is located in vdbread.cpp
/////////////////////////////////////////////////////////////////////////////
 
DEFINE_STATIC_FAST_MUTEX(sx_SDKMutex);
 
static char s_VDBVersion[32]; // enough for 255.255.65535-dev4000000000
 
static
void s_InitVDBVersion()
{
    if ( !s_VDBVersion[0] ) {
        ostringstream s;
        {{ // format VDB version string
            SraReleaseVersion release_version;
            SraReleaseVersionGet(&release_version);
            s << (release_version.version>>24) << '.'
              << ((release_version.version>>16)&0xff) << '.'
              << (release_version.version&0xffff);
            if ( release_version.revision != 0 ||
                 release_version.type != SraReleaseVersion::eSraReleaseVersionTypeFinal ) {
                const char* type = "";
                switch ( release_version.type ) {
                case SraReleaseVersion::eSraReleaseVersionTypeDev:   type = "dev"; break;
                case SraReleaseVersion::eSraReleaseVersionTypeAlpha: type = "a"; break;
                case SraReleaseVersion::eSraReleaseVersionTypeBeta:  type = "b"; break;
                case SraReleaseVersion::eSraReleaseVersionTypeRC:    type = "RC"; break;
                default:                                             type = ""; break;
                }
                s << '-' << type << release_version.revision;
            }
        }}
        string v = s.str();
        if ( !v.empty() ) {
            if ( v.size() >= sizeof(s_VDBVersion) ) {
                v.resize(sizeof(s_VDBVersion)-1);
            }
            copy(v.begin()+1, v.end(), s_VDBVersion+1);
            s_VDBVersion[0] = v[0];
        }
    }
}
 
struct SVDBSeverityTag {
    const char* tag;
    CNcbiDiag::FManip manip;
};
static const SVDBSeverityTag kSeverityTags[] = {
    { "err:", Error },
    { "int:", Error },
    { "sys:", Error },
    { "info:", Info },
    { "warn:", Warning },
    { "debug:", Trace },
    { "fatal:", Fatal },
};
static const SVDBSeverityTag* s_GetVDBSeverityTag(CTempString token)
{
    if ( !token.empty() && token[token.size()-1] == ':' ) {
        for ( auto& tag : kSeverityTags ) {
            if ( token == tag.tag ) {
                return &tag;
            }
        }
    }
    return 0;
}
 
#ifndef NCBI_THREADS
static thread::id s_DiagCheckThreadID;
#endif
 
static inline void s_InitDiagCheck()
{
#ifndef NCBI_THREADS
    s_DiagCheckThreadID = this_thread::get_id();
#endif
}
 
static inline bool s_DiagIsSafe()
{
#ifndef NCBI_THREADS
    return s_DiagCheckThreadID == this_thread::get_id();
#else
    return true;
#endif
}
 
 
static
rc_t VDBLogWriter(void* /*data*/, const char* buffer, size_t size, size_t* written)
{
    CTempString msg(buffer, size);
    NStr::TruncateSpacesInPlace(msg);
    CNcbiDiag::FManip sev_manip = Error;
    
    for ( SIZE_TYPE token_pos = 0, token_end; token_pos < msg.size(); token_pos = token_end + 1 ) {
        token_end = msg.find(' ', token_pos);
        if ( token_end == NPOS ) {
            token_end = msg.size();
        }
        if ( auto tag = s_GetVDBSeverityTag(CTempString(msg, token_pos, token_end-token_pos)) ) {
            sev_manip = tag->manip;
            break;
        }
    }
    if ( sev_manip == Trace ) {
        if ( s_DiagIsSafe() ) {
            _TRACE("VDB "<<s_VDBVersion<<": "<<msg);
        }
    }
    else {
        if ( s_DiagIsSafe() ) {
            ERR_POST(sev_manip<<"VDB "<<s_VDBVersion<<": "<<msg);
        }
    }
    *written = size;
    return 0;
}
 
 
static CBamRef<KConfig> s_InitProxyConfig()
{
    CBamRef<KConfig> config;
    if ( CNcbiApplicationGuard app = CNcbiApplication::InstanceGuard() ) {
        string host = app->GetConfig().GetString("CONN", "HTTP_PROXY_HOST", kEmptyStr);
        int port = app->GetConfig().GetInt("CONN", "HTTP_PROXY_PORT", 0);
        if ( !host.empty() && port != 0 ) {
            if ( rc_t rc = KConfigMake(config.x_InitPtr(), NULL) ) {
                NCBI_THROW2(CBamException, eInitFailed,
                            "Cannot create KConfig singleton", rc);
            }
            string path = host + ':' + NStr::IntToString(port);
            if ( rc_t rc = KConfigWriteString(config,
                                              "/http/proxy/path", path.c_str()) ) {
                NCBI_THROW2(CBamException, eInitFailed,
                            "Cannot set KConfig proxy path", rc);
            }
            if ( rc_t rc = KConfigWriteBool(config,
                                            "/http/proxy/enabled", true) ) {
                NCBI_THROW2(CBamException, eInitFailed,
                            "Cannot set KConfig proxy enabled", rc);
            }
        }
    }
    return config;
}
 
 
static DECLARE_TLS_VAR(const CRequestContext*, s_LastRequestContext);
static DECLARE_TLS_VAR(CRequestContext::TVersion, s_LastRequestContextVersion);
 
static void s_UpdateVDBRequestContext(void)
{
    CRequestContext& req_ctx = CDiagContext::GetRequestContext();
    auto req_ctx_version = req_ctx.GetVersion();
    if ( &req_ctx == s_LastRequestContext && req_ctx_version == s_LastRequestContextVersion ) {
        return;
    }
    _TRACE("CVDBMgr: Updating request context with version: "<<req_ctx_version);
    s_LastRequestContext = &req_ctx;
    s_LastRequestContextVersion = req_ctx_version;
    CBamRef<KNSManager> kns_mgr;
    if ( rc_t rc = KNSManagerMake(kns_mgr.x_InitPtr()) ) {
        NCBI_THROW2(CBamException, eInitFailed,
                    "Cannot create KNSManager singleton", rc);
    }
    if ( req_ctx.IsSetSessionID() ) {
        _TRACE("CVDBMgr: Updating session ID: "<<req_ctx.GetSessionID());
        KNSManagerSetSessionID(kns_mgr, req_ctx.GetSessionID().c_str());
    }
    if ( req_ctx.IsSetClientIP() ) {
        _TRACE("CVDBMgr: Updating client IP: "<<req_ctx.GetClientIP());
        KNSManagerSetClientIP(kns_mgr, req_ctx.GetClientIP().c_str());
    }
    if ( req_ctx.IsSetHitID() ) {
        _TRACE("CVDBMgr: Updating hit ID: "<<req_ctx.GetHitID());
        KNSManagerSetPageHitID(kns_mgr, req_ctx.GetHitID().c_str());
    }
}
 
 
static void s_InitAllKNS(KNSManager* kns_mgr)
{
    CNcbiApplicationGuard app = CNcbiApplication::InstanceGuard();
    if ( app && app->GetConfig().GetBool("VDB", "ALLOW_ALL_CERTS", false) ) {
        if ( rc_t rc = KNSManagerSetAllowAllCerts(kns_mgr, true) ) {
            NCBI_THROW2(CBamException, eInitFailed,
                        "Cannot enable all HTTPS certificates in KNSManager", rc);
        }
    }
    {{ // set user agent
        CNcbiOstrstream str;
        if ( app ) {
            str << app->GetAppName() << ": " << app->GetVersion().Print() << "; ";
        }
#if NCBI_PACKAGE
        str << "Package: " << NCBI_PACKAGE_NAME << ' ' <<
            NCBI_PACKAGE_VERSION << "; ";
#endif
        str << "C++ ";
#ifdef NCBI_PRODUCTION_VER
        str << NCBI_PRODUCTION_VER << "/";
#endif
#ifdef NCBI_DEVELOPMENT_VER
        str << NCBI_DEVELOPMENT_VER;
#endif
        string prefix = CNcbiOstrstreamToString(str);
        KNSManagerSetUserAgent(kns_mgr, "%s; VDB %s",
                               prefix.c_str(),
                               s_VDBVersion);
    }}
}
 
 
static void s_InitStaticKNS(KNSManager* kns_mgr)
{
    s_InitAllKNS(kns_mgr);
}
 
 
static void s_InitLocalKNS(KNSManager* kns_mgr)
{
    s_InitAllKNS(kns_mgr);
}
 
 
namespace {
    NCBI_PARAM_DECL(int, VDB, DIAG_HANDLER);
    NCBI_PARAM_DEF(int, VDB, DIAG_HANDLER, 1);
}
 
 
static int s_GetDiagHandler(void)
{
    static CSafeStatic<NCBI_PARAM_TYPE(VDB, DIAG_HANDLER)> s_Value;
    return s_Value->Get();
}
 
 
static void s_VDBInit()
{
    CFastMutexGuard guard(sx_SDKMutex);
    static bool initialized = false;
    if ( !initialized ) {
        s_InitVDBVersion();
        // redirect VDB log to C++ Toolkit
        if ( s_GetDiagHandler() ) {
            KLogInit();
            KLogLevel ask_level;
#ifdef _DEBUG
            ask_level = klogDebug;
#else
            ask_level = klogInfo;
#endif
            s_InitDiagCheck();
            KLogLevelSet(ask_level);
            KLogHandlerSet(VDBLogWriter, 0);
            KLogLibHandlerSet(VDBLogWriter, 0);
            if ( CBamDb::GetDebugLevel() >= 2 ) {
                const char* msg = "info: VDB initialized";
                size_t written;
                VDBLogWriter(0, msg, strlen(msg), &written);
            }
        }
        auto config = s_InitProxyConfig();
        CBamRef<KNSManager> kns_mgr;
        if ( rc_t rc = KNSManagerMake(kns_mgr.x_InitPtr()) ) {
            NCBI_THROW2(CBamException, eInitFailed,
                        "Cannot create KNSManager singleton", rc);
        }
        s_InitStaticKNS(kns_mgr);
        initialized = true;
    }
}
 
/////////////////////////////////////////////////////////////////////////////
// end of VDB library initialization code
/////////////////////////////////////////////////////////////////////////////
        
 
void CBamVFSManager::x_Init()
{
    s_VDBInit();
    if ( rc_t rc = VFSManagerMake(x_InitPtr()) ) {
        NCBI_THROW2_FMT(CBamException, eInitFailed,
                        "CBamVFSManager: "
                        "cannot get VFSManager", rc);
    }
    VFSManagerLogNamesServiceErrors(*this, false);
    CBamRef<KNSManager> kns_mgr;
    if ( rc_t rc = VFSManagerGetKNSMgr(*this, kns_mgr.x_InitPtr()) ) {
        NCBI_THROW2(CBamException, eInitFailed,
                    "Cannot get KNSManager", rc);
    }
    s_InitLocalKNS(kns_mgr);
}
 
 
CBamMgr::CBamMgr(void)
{
    if ( rc_t rc = AlignAccessMgrMake(m_AlignAccessMgr.x_InitPtr()) ) {
        *m_AlignAccessMgr.x_InitPtr() = 0;
        NCBI_THROW2(CBamException, eInitFailed,
                    "Cannot create AlignAccessMgr", rc);
    }
}
 
 
#ifdef NCBI_OS_MSWIN
static inline
bool s_HasWindowsDriveLetter(const string& s)
{
    // first symbol is letter, and second symbol is colon (':')
    return s.length() >= 2 && isalpha(Uchar(s[0])) && s[1] == ':';
}
 
 
static
bool s_IsSysPath(const string& s)
{
    if ( s_HasWindowsDriveLetter(s) ) {
        return true;
    }
    if ( s.find_first_of("/\\") == NPOS ) {
        // may be plain accession or local file
        if ( CDirEntry(s).Exists() ) {
            // file -> sys path
            return true;
        }
        else {
            // accession
            return false;
        }
    }
    else {
        // may be path or URI
        if ( s[0] == 'h' &&
             (NStr::StartsWith(s, "http://") ||
              NStr::StartsWith(s, "https://")) ) {
            // URI
            return false;
        }
        if ( s[0] == 'f' &&
             NStr::StartsWith(s, "ftp://") ) {
            // URI
            return false;
        }
        // path
        return true;
    }
}
#endif
 
 
static VPath* sx_GetVPath(const CBamVFSManager& mgr,
                          const string& path)
{
#ifdef NCBI_OS_MSWIN
    // SRA SDK doesn't work with UNC paths with backslashes:
    // \\host\share\dir\file
    // As a workaroung we'll replace backslashes with forward slashes.
    string fixed_path = path;
    if ( s_IsSysPath(path) ) {
        try {
            fixed_path = CDirEntry::CreateAbsolutePath(path);
        }
        catch (exception&) {
            // CDirEntry::CreateAbsolutePath() can fail on remote access URL
        }
        replace(fixed_path.begin(), fixed_path.end(), '\\', '/');
        if ( s_HasWindowsDriveLetter(fixed_path) ) {
            // move drive letter from first symbol to second (in place of ':')
            fixed_path[1] = toupper(Uchar(fixed_path[0]));
            // add leading slash
            fixed_path[0] = '/';
        }
    }
    const char* c_path = fixed_path.c_str();
#else
    const char* c_path = path.c_str();
#endif
 
    VPath* kpath;
    if ( rc_t rc = VFSManagerMakePath(mgr, &kpath, c_path) ) {
        NCBI_THROW2(CBamException, eInitFailed,
                    "Cannot create VPath object", rc);
    }
    return kpath;
}
 
struct VPathReleaser
{
    static void Delete(const VPath* kpath)
        { VPathRelease(kpath); }
};
 
 
CBamDb::SAADBImpl::SAADBImpl(const CBamMgr& mgr,
                             const string& db_name)
{
    AutoPtr<VPath, VPathReleaser> kdb_name(sx_GetVPath(mgr.GetVFSManager(),
                                                       db_name));
    if ( rc_t rc = AlignAccessMgrMakeBAMDB(mgr.GetAlignAccessMgr(),
                                           m_DB.x_InitPtr(),
                                           kdb_name.get()) ) {
        *m_DB.x_InitPtr() = 0;
        NCBI_THROW3(CBamException, eInitFailed,
                    "Cannot open BAM DB", rc, db_name);
    }
}
 
 
static void s_AddReplacedExt(vector<string>& dst,
                             const string& base_name,
                             CTempString old_ext,
                             CTempString new_ext)
{
    if ( NStr::EndsWith(base_name, old_ext) ) {
        dst.push_back(base_name.substr(0, base_name.size()-old_ext.size())+new_ext);
    }
}
 
 
CBamDb::SAADBImpl::SAADBImpl(const CBamMgr& mgr,
                             const string& db_name,
                             string& idx_name)
{
    AutoPtr<VPath, VPathReleaser> kdb_name (sx_GetVPath(mgr.GetVFSManager(),
                                                        db_name));
    vector<string> index_name_candidates;
    if ( idx_name.empty() || idx_name == db_name ) {
        index_name_candidates.push_back(db_name+kBaiExt);
        s_AddReplacedExt(index_name_candidates, db_name, kBamExt, kBaiExt);
    }
    else {
        index_name_candidates.push_back(idx_name);
    }
    for ( size_t i = 0; i < index_name_candidates.size(); ++i ) {
        AutoPtr<VPath, VPathReleaser> kidx_name(sx_GetVPath(mgr.GetVFSManager(),
                                                            index_name_candidates[i]));
        if ( rc_t rc = AlignAccessMgrMakeIndexBAMDB(mgr.GetAlignAccessMgr(),
                                                    m_DB.x_InitPtr(),
                                                    kdb_name.get(),
                                                    kidx_name.get()) ) {
            if ( i < index_name_candidates.size()-1 &&
                 GetRCTarget(rc) == rcFile &&
                 GetRCState(rc) == rcNotFound ) {
                // try next index file name candidate
                continue;
            }
            else {
                *m_DB.x_InitPtr() = 0;
                NCBI_THROW3(CBamException, eInitFailed,
                            "Cannot open BAM DB", rc, db_name);
            }
        }
        else {
            idx_name = index_name_candidates[i];
            break;
        }
    }
}
 
 
CBamDb::CBamDb(const CBamMgr& mgr,
               const string& db_name,
               EUseAPI use_api)
    : m_DbName(db_name)
{
    s_UpdateVDBRequestContext();
    if ( UseRawIndex(use_api) ) {
        m_RawDB = new CObjectFor<CBamRawDb>(db_name);
    }
    else {
        m_AADB = new SAADBImpl(mgr, db_name);
    }
}
 
 
CBamDb::CBamDb(const CBamMgr& mgr,
               const string& db_name,
               const string& idx_name,
               EUseAPI use_api)
    : m_DbName(db_name),
      m_IndexName(idx_name)
{
    s_UpdateVDBRequestContext();
    if ( UseRawIndex(use_api) ) {
        m_RawDB = new CObjectFor<CBamRawDb>(db_name, m_IndexName);
        m_IndexName = m_RawDB->GetData().GetIndexName();
    }
    else {
        m_AADB = new SAADBImpl(mgr, db_name, m_IndexName);
    }
}
 
 
CRef<CSeq_id> CBamDb::GetRefSeq_id(const string& label) const
{
    if ( !m_RefSeqIds ) {
        DEFINE_STATIC_FAST_MUTEX(sx_RefSeqMutex);
        CFastMutexGuard guard(sx_RefSeqMutex);
        if ( !m_RefSeqIds ) {
            AutoPtr<TRefSeqIds> ids(new TRefSeqIds);
            for ( CBamRefSeqIterator it(*this); it; ++it ) {
                string label = it.GetRefSeqId();
                (*ids)[label] = sx_GetRefSeq_id(label, GetIdMapper());
            }
            m_RefSeqIds = ids;
        }
    }
    TRefSeqIds::const_iterator it = m_RefSeqIds->find(label);
    if ( it != m_RefSeqIds->end() ) {
        return it->second;
    }
    return sx_GetRefSeq_id(label, GetIdMapper());
}
 
 
CRef<CSeq_id> CBamDb::GetShortSeq_id(const string& str, bool external) const
{
    return sx_GetShortSeq_id(str, GetIdMapper(), external);
}
 
 
TSeqPos CBamDb::GetRefSeqLength(const string& id) const
{
    if ( !m_RefSeqLengths ) {
        DEFINE_STATIC_FAST_MUTEX(sx_RefSeqMutex);
        CFastMutexGuard guard(sx_RefSeqMutex);
        if ( !m_RefSeqLengths ) {
            AutoPtr<TRefSeqLengths> lengths(new TRefSeqLengths);
            for ( CBamRefSeqIterator it(*this); it; ++it ) {
                TSeqPos len;
                try {
                    len = it.GetLength();
                }
                catch ( CBamException& /*ignored*/ ) {
                    len = kInvalidSeqPos;
                }
                (*lengths)[it.GetRefSeqId()] = len;
            }
            m_RefSeqLengths = lengths;
        }
    }
    TRefSeqLengths::const_iterator it = m_RefSeqLengths->find(id);
    return it == m_RefSeqLengths->end()? kInvalidSeqPos: it->second;
}
 
 
string CBamDb::GetHeaderText(void) const
{
    if ( UsesRawIndex() ) {
        return m_RawDB->GetData().GetHeader().GetText();
    }
    else {
        CMutexGuard guard(m_AADB->m_Mutex);
        s_UpdateVDBRequestContext();
        CBamRef<const BAMFile> file;
        if ( rc_t rc = AlignAccessDBExportBAMFile(m_AADB->m_DB, file.x_InitPtr()) ) {
            NCBI_THROW2(CBamException, eOtherError,
                        "Cannot get BAMFile pointer", rc);
        }
        const char* header;
        size_t size;
        if ( rc_t rc = BAMFileGetHeaderText(file, &header, &size) ) {
            NCBI_THROW2(CBamException, eOtherError,
                        "Cannot get BAM header text", rc);
        }
        return string(header, size);
    }
}
 
 
#ifdef HAVE_NEW_PILEUP_COLLECTOR
CBamDb::ICollectPileupCallback::~ICollectPileupCallback()
{
}
 
 
CBamDb::SPileupValues::SPileupValues()
{
}
 
 
CBamDb::SPileupValues::SPileupValues(CRange<TSeqPos> ref_range,
                                     EIntronMode intron_mode)
{
    initialize(ref_range, intron_mode);
}
 
 
void CBamDb::SPileupValues::initialize(CRange<TSeqPos> ref_range,
                                       EIntronMode intron_mode)
{
    m_RefToOpen = m_RefFrom = ref_range.GetFrom();
    m_RefStop = ref_range.GetToOpen();
    m_IntronMode = intron_mode;
    TSeqPos len = ref_range.GetLength()+32;
    for ( auto& c : max_count ) c = 0;
    cc_acgt.clear();
    cc_acgt.resize(len);
    cc_match.clear();
    cc_match.resize(len);
    cc_gap.clear();
    cc_gap.resize(len);
    cc_gap[0] = 0;
    cc_intron.clear();
    if ( count_introns() ) {
        cc_intron.resize(len);
        cc_intron[0] = 0;
    }
}
 
 
void CBamDb::SPileupValues::decode_gap(TSeqPos len)
{
    _ASSERT(len <= (m_RefToOpen-m_RefFrom));
    _ASSERT(accumulate(&cc_gap[0], &cc_gap[m_RefToOpen-m_RefFrom+1], 0) == 0);
    // restore gap counts from delta encoding
    TCount g = 0;
    for ( TSeqPos i = 0; i <= len; ++i ) {
        g += cc_gap[i];
        cc_gap[i] = g;
    }
    _ASSERT(accumulate(&cc_gap[len], &cc_gap[m_RefToOpen-m_RefFrom+1], 0) == 0);
}
 
 
void CBamDb::SPileupValues::decode_intron(TSeqPos len)
{
    _ASSERT(len <= (m_RefToOpen-m_RefFrom));
    _ASSERT(accumulate(&cc_intron[0], &cc_intron[m_RefToOpen-m_RefFrom+1], 0) == 0);
    // restore intron counts from delta encoding
    TCount g = 0;
    for ( TSeqPos i = 0; i <= len; ++i ) {
        g += cc_intron[i];
        cc_intron[i] = g;
    }
    _ASSERT(accumulate(&cc_intron[len], &cc_intron[m_RefToOpen-m_RefFrom+1], 0) == 0);
}
 
#ifdef USE_SSE
static inline
void add_bases_acgt(CBamDb::SPileupValues::SCountACGT* dst1, unsigned b, __m128i bits, __m128i mask)
{
    __m128i add = _mm_and_si128(_mm_srl_epi32(bits, _mm_cvtsi32_si128(b)), mask);
    __m128i* dst = (__m128i*)dst1;
    __m128i cnt = _mm_load_si128(dst);
    cnt = _mm_add_epi32(cnt, add);
    _mm_store_si128(dst, cnt);
}
#else
static inline
void add_bases_acgt(CBamDb::SPileupValues::SCountACGT* dst, unsigned b)
{
    dst->cc[CBamDb::SPileupValues::kStat_A] += b == ('A' & 0x1f);
    dst->cc[CBamDb::SPileupValues::kStat_C] += b == ('C' & 0x1f);
    dst->cc[CBamDb::SPileupValues::kStat_G] += b == ('G' & 0x1f);
    dst->cc[CBamDb::SPileupValues::kStat_T] += b == ('T' & 0x1f);
}
static inline
void add_bases_acgt_raw(CBamDb::SPileupValues::SCountACGT* dst, unsigned b)
{
    dst->cc[CBamDb::SPileupValues::kStat_A] += (b     ) & 1;
    dst->cc[CBamDb::SPileupValues::kStat_C] += (b >> 1) & 1;
    dst->cc[CBamDb::SPileupValues::kStat_G] += (b >> 2) & 1;
    dst->cc[CBamDb::SPileupValues::kStat_T] += (b >> 3) & 1;
}
#endif
 
void CBamDb::SPileupValues::add_bases_graph_range(TSeqPos pos, TSeqPos end,
                                                  CTempString read, TSeqPos read_pos)
{
    _ASSERT(pos < end);
    const char* src = read.data()+read_pos;
    SPileupValues::SCountACGT* dst = cc_acgt.data()+pos;
    SPileupValues::SCountACGT* dst_end = cc_acgt.data()+end;
    TCount* dst_match = cc_match.data()+pos;
#ifdef USE_SSE
    /* bits = Tth, Gth, Cth, and Ath bits */
    __m128i bits = _mm_set_epi32(1<<('T'&0x1f), 1<<('G'&0x1f), 1<<('C'&0x1f), 1<<('A'&0x1f));
    __m128i mask = _mm_set1_epi32(1);
#endif
    for ( ; dst < dst_end; ++src, ++dst, ++dst_match ) {
        // use only low 5 bits of base character, it's sufficient to distinguish all letters
        // and allows to use 32-bit masks
        unsigned b = *src & 0x1f;
        dst_match[0] += b == ('=' & 0x1f);
#ifdef USE_SSE
        add_bases_acgt(dst, b, bits, mask);
#else
        add_bases_acgt(dst, b);
#endif
    }
}
 
 
static inline unsigned get_raw_base0(unsigned bb)
{
    return bb >> 4;
}
 
 
static inline unsigned get_raw_base1(unsigned bb)
{
    return bb & 0xf;
}
 
 
static inline TSeqPos align_to_16_down(TSeqPos size)
{
    return size & ~0xf;
}
 
 
static inline TSeqPos align_to_16_up(TSeqPos size)
{
    return (size + 0xf) & ~0xf;
}
 
void CBamDb::SPileupValues::add_bases_graph_range_raw(TSeqPos pos, TSeqPos end,
                                                      CTempString read, TSeqPos read_pos)
{
    _ASSERT(pos < end);
#ifdef USE_SSE
    __m128i bits = _mm_set_epi32(0x100, 0x10, 0x4, 0x2); /* 8th, 4th, 2nd, and 1st bits */
    __m128i mask = _mm_set1_epi32(1);
#endif
    const char* src = read.data()+read_pos/2;
    SPileupValues::SCountACGT* dst = cc_acgt.data()+pos;
    SPileupValues::SCountACGT* dst_end = cc_acgt.data()+end-1;
    TCount* dst_match = cc_match.data()+pos;
    if ( read_pos%2 ) {
        unsigned bb = Uint1(*src);
        unsigned b = get_raw_base1(bb);
        dst_match[0] += b == 0;
#ifdef USE_SSE
        add_bases_acgt(dst, b, bits, mask);
#else
        add_bases_acgt_raw(dst, b);
#endif
        
        ++src;
        ++dst;
        ++dst_match;
    }
    for ( ; dst < dst_end; ++src, dst += 2, dst_match += 2 ) {
        unsigned bb = Uint1(*src);
        unsigned b0 = get_raw_base0(bb);
        unsigned b1 = get_raw_base1(bb);
        dst_match[0] += b0 == 0;
        dst_match[1] += b1 == 0;
#ifdef USE_SSE
        add_bases_acgt(dst+0, b0, bits, mask);
        add_bases_acgt(dst+1, b1, bits, mask);
#else
        add_bases_acgt_raw(dst+0, b0);
        add_bases_acgt_raw(dst+1, b1);
#endif
    }
    if ( dst <= dst_end ) {
        unsigned bb = Uint1(*src);
        unsigned b = get_raw_base0(bb);
        dst_match[0] += b == 0;
#ifdef USE_SSE
        add_bases_acgt(dst, b, bits, mask);
#else
        add_bases_acgt_raw(dst, b);
#endif
    }
}
 
 
void CBamDb::SPileupValues::advance_current_beg(TSeqPos ref_pos, ICollectPileupCallback* callback)
{
    if ( ref_pos > m_RefToOpen ) {
        // gap must be filled with zeros
        if ( ref_pos > m_RefToOpen+FLUSH_SIZE ) {
            // gap is big enough to call AddZeros()
            if ( m_RefToOpen != m_RefFrom ) {
                // flush non-zero part
                advance_current_beg(m_RefToOpen, callback);
            }
            _ASSERT(m_RefToOpen == m_RefFrom);
            TSeqPos add_zeros = ref_pos-m_RefToOpen;
            TSeqPos flush_zeros = align_to_16_down(add_zeros);
            _ASSERT(flush_zeros%16 == 0);
            callback->AddZerosBy16(flush_zeros);
            m_RefToOpen = m_RefFrom += flush_zeros;
            if ( ref_pos > m_RefToOpen ) {
                advance_current_end(ref_pos);
            }
            return;
        }
        advance_current_end(ref_pos);
    }
    TSeqPos flush = ref_pos-m_RefFrom;
    if ( ref_pos != m_RefStop ) {
        flush = align_to_16_down(flush);
    }
    if ( flush ) {
        decode_gap(flush);
        if ( count_introns() ) {
            decode_intron(flush);
        }
        TSeqPos total = m_RefToOpen-m_RefFrom;
        if ( flush >= 16 ) {
            _ASSERT(flush%16 == 0);
            update_max_counts(flush);
            callback->AddValuesBy16(flush, *this);
            TSeqPos copy = total-flush;
            TSeqPos copy16 = align_to_16_up(copy);
            if ( copy ) {
                NFast::MoveBuffer(cc_acgt[flush].cc, copy16*4, cc_acgt[0].cc);
                NFast::MoveBuffer(cc_match.data()+flush, copy16, cc_match.data());
            }
            {
                TCount gap_save = cc_gap[total];
                if ( copy ) {
                    NFast::MoveBuffer(cc_gap.data()+flush, copy16, cc_gap.data());
                }
                cc_gap[copy] = gap_save;
            }
            if ( count_introns() ) {
                TCount intron_save = cc_intron[total];
                if ( copy ) {
                    NFast::MoveBuffer(cc_intron.data()+flush, copy16, cc_intron.data());
                }
                cc_intron[copy] = intron_save;
            }
            m_RefFrom += flush;
            _ASSERT(accumulate(&cc_gap[0], &cc_gap[m_RefToOpen-m_RefFrom+1], 0) == 0);
            _ASSERT(!count_introns() ||
                    accumulate(&cc_intron[0], &cc_intron[m_RefToOpen-m_RefFrom+1], 0) == 0);
        }
        else {
            _ASSERT(ref_pos == m_RefStop);
            _ASSERT(ref_pos == m_RefToOpen);
            update_max_counts(flush);
            callback->AddValuesTail(flush, *this);
            m_RefFrom = m_RefStop;
        }
    }
}
 
 
void CBamDb::SPileupValues::advance_current_end(TSeqPos ref_end)
{
    _ASSERT(ref_end > m_RefToOpen);
    _ASSERT(ref_end <= m_RefStop);
    TSeqPos cur_pos = m_RefToOpen-m_RefFrom;
    TSeqPos new_pos = (min(m_RefStop + 15, ref_end + FLUSH_SIZE) - m_RefFrom) & ~15;
 
    NFast::ClearBuffer(cc_acgt[cur_pos].cc, (new_pos-cur_pos)*4);
    NFast::ClearBuffer(cc_match.data()+cur_pos, (new_pos-cur_pos));
    {
        TCount gap_save = cc_gap[cur_pos];
        NFast::ClearBuffer(cc_gap.data()+cur_pos, (new_pos-cur_pos));
        cc_gap[cur_pos] = gap_save;
        cc_gap[new_pos] = 0;
    }
    if ( count_introns() ) {
        TCount intron_save = cc_intron[cur_pos];
        NFast::ClearBuffer(cc_intron.data()+cur_pos, (new_pos-cur_pos));
        cc_intron[cur_pos] = intron_save;
        cc_intron[new_pos] = 0;
    }
    m_RefToOpen = min(m_RefStop, m_RefFrom + new_pos);
}
 
 
void CBamDb::SPileupValues::finalize(ICollectPileupCallback* callback)
{
    if ( m_RefToOpen < m_RefStop ) {
        advance_current_end(m_RefStop);
    }
    _ASSERT(m_RefToOpen == m_RefStop);
    decode_gap(m_RefStop - m_RefFrom);
    if ( callback ) {
        if ( TSeqPos flush = m_RefToOpen-m_RefFrom ) {
            _ASSERT(flush < 16);
            update_max_counts(flush);
            callback->AddValuesTail(flush, *this);
            m_RefFrom += flush;
        }
    }
    else {
        update_max_counts(m_RefStop - m_RefFrom);
    }
}
 
 
void CBamDb::SPileupValues::update_max_counts(TSeqPos length)
{
    _ASSERT(m_RefFrom+length <= m_RefToOpen);
    _ASSERT(length % 16 == 0 || m_RefToOpen == m_RefStop);
    length = align_to_16_up(length);
    NFast::Find4MaxElements(cc_acgt[0].cc, length, max_count);
    NFast::FindMaxElement(cc_match.data(), length, max_count[kStat_Match]);
    NFast::FindMaxElement(cc_gap.data(), length, max_count[kStat_Gap]);
    if ( count_introns() ) {
        NFast::FindMaxElement(cc_intron.data(), length, max_count[kStat_Intron]);
    }
    else {
        max_count[kStat_Intron] = 0;
    }
    m_SplitACGTLen = 0;
}
 
 
void CBamDb::SPileupValues::make_split_acgt(TSeqPos len)
{
    if ( m_SplitACGTLen < len ) {
        TSeqPos len16 = align_to_16_up(len);
        for ( int k = 0; k < kNumStat_ACGT; ++k ) {
            cc_split_acgt[k].clear();
            cc_split_acgt[k].resize(len16);
        }
        NFast::SplitBufferInto4(get_acgt_counts(), len16,
                           cc_split_acgt[0].data(),
                           cc_split_acgt[1].data(),
                           cc_split_acgt[2].data(),
                           cc_split_acgt[3].data());
        m_SplitACGTLen = len;
    }
}
 
 
size_t CBamDb::CollectPileup(SPileupValues& values,
                             const string& ref_id,
                             CRange<TSeqPos> graph_range,
                             Uint1 min_quality,
                             ICollectPileupCallback* callback,
                             SPileupValues::EIntronMode intron_mode,
                             TSeqPos gap_to_intron_threshold) const
{
    values.initialize(graph_range, intron_mode);
    
    size_t count = 0;
 
    CBamAlignIterator ait(*this, ref_id, graph_range.GetFrom(), graph_range.GetLength());
    if ( CBamRawAlignIterator* rit = ait.GetRawIndexIteratorPtr() ) {
        for( ; *rit; ++*rit ){
            if ( min_quality > 0 && rit->GetMapQuality() < min_quality ) {
                continue;
            }
            ++count;
 
            TSeqPos ref_pos = rit->GetRefSeqPos();
            values.update_current_ref_start(ref_pos, callback);
            TSeqPos read_len = rit->GetShortSequenceLength();
            CTempString read_raw = rit->GetShortSequenceRaw();
            TSeqPos read_pos = 0;
            for ( Uint2 i = 0, count = rit->GetCIGAROpsCount(); i < count; ++i ) {
                if ( ref_pos >= graph_range.GetToOpen() ) {
                    // passed beyond the end of graph range
                    break;
                }
                Uint4 op = rit->GetCIGAROp(i);
                Uint4 seglen = op >> 4;
                op &= 0xf;
                
                TSeqPos ref_end = ref_pos + seglen;
                switch ( op ) {
                case SBamAlignInfo::kCIGAR_eq: // =
                    // match
                    values.add_match_ref_range(ref_pos, ref_end);
                    ref_pos += seglen;
                    read_pos += seglen;
                    break;
                case SBamAlignInfo::kCIGAR_M: // M
                case SBamAlignInfo::kCIGAR_X: // X
                    // mismatch ('X') or
                    // unspecified 'alignment match' ('M') that can be a mismatch too
                    if ( read_pos+ref_end > read_len+ref_pos ) {
                        // range is out of read bounds -> keep it unspecified
                        values.add_match_ref_range(ref_pos, ref_end);
                    }
                    else {
                        values.add_bases_ref_range_raw(ref_pos, ref_end, read_raw, read_pos);
                    }
                    ref_pos += seglen;
                    read_pos += seglen;
                    break;
                case SBamAlignInfo::kCIGAR_I: // I
                case SBamAlignInfo::kCIGAR_S: // S
                    read_pos += seglen;
                    break;
                case SBamAlignInfo::kCIGAR_N: // N
                    // intron
                    values.add_intron_ref_range(ref_pos, ref_end);
                    ref_pos += seglen;
                    break;
                case SBamAlignInfo::kCIGAR_D: // D
                    // gap or intron
                    if ( seglen > gap_to_intron_threshold ) {
                        values.add_intron_ref_range(ref_pos, ref_end);
                    }
                    else {
                        values.add_gap_ref_range(ref_pos, ref_end);
                    }
                    ref_pos += seglen;
                    break;
                default: // P
                    break;
                }
            }
        }
    }
    else {
        for( ; ait; ++ait ){
            if ( min_quality > 0 && ait.GetMapQuality() < min_quality ) {
                continue;
            }
            ++count;
 
            TSeqPos ref_pos = ait.GetRefSeqPos();
            values.update_current_ref_start(ref_pos, callback);
            _ASSERT((values.m_RefFrom-graph_range.GetFrom())%16 == 0);
            _ASSERT((values.m_RefToOpen-values.m_RefFrom)%16 == 0 || values.m_RefToOpen == values.m_RefStop);
            TSeqPos read_len = ait.GetShortSequenceLength();
            CTempString read = ait.GetShortSequence();
            TSeqPos read_pos = ait.GetCIGARPos();
            CTempString cigar = ait.GetCIGAR();
            const char* ptr = cigar.data();
            const char* end = ptr + cigar.size();
            while ( ptr != end ) {
                if ( ref_pos >= graph_range.GetToOpen() ) {
                    // passed beyond the end of graph range
                    break;
                }
                char type = *ptr;
                TSeqPos seglen = 0;
                for ( ; ++ptr != end; ) {
                    char c = *ptr;
                    if ( c >= '0' && c <= '9' ) {
                        seglen = seglen*10+(c-'0');
                    }
                    else {
                        break;
                    }
                }
                if ( seglen == 0 ) {
                    ERR_POST("Bad CIGAR length: "<<type<<"0 in "<<cigar);
                    break;
                }
 
                TSeqPos ref_end = ref_pos + seglen;
                if ( type == '=' ) {
                    // match
                    values.add_match_ref_range(ref_pos, ref_end);
                    ref_pos += seglen;
                    read_pos += seglen;
                }
                else if ( type == 'M' || type == 'X' ) {
                    // mismatch ('X') or
                    // unspecified 'alignment match' ('M') that can be a mismatch too
                    if ( read_pos+ref_end > read_len+ref_pos ) {
                        // range is out of read bounds -> keep it unspecified
                        values.add_match_ref_range(ref_pos, ref_end);
                    }
                    else {
                        values.add_bases_ref_range(ref_pos, ref_end, read, read_pos);
                    }
                    ref_pos += seglen;
                    read_pos += seglen;
                }
                else if ( type == 'S' ) {
                    // soft clipping already accounted in seqpos
                }
                else if ( type == 'I' ) {
                    read_pos += seglen;
                }
                else if ( type == 'N' ) {
                    // intron
                    values.add_intron_ref_range(ref_pos, ref_end);
                    ref_pos += seglen;
                }
                else if ( type == 'D' ) {
                    // gap or intron
                    if ( seglen > gap_to_intron_threshold ) {
                        values.add_intron_ref_range(ref_pos, ref_end);
                    }
                    else {
                        values.add_gap_ref_range(ref_pos, ref_end);
                    }
                    ref_pos += seglen;
                }
                else if ( type != 'P' ) {
                    ERR_POST("Bad CIGAR char: "<<type<<" in "<<cigar);
                    break;
                }
                _ASSERT((values.m_RefFrom-graph_range.GetFrom())%16 == 0);
                _ASSERT((values.m_RefToOpen-values.m_RefFrom)%16 == 0 || values.m_RefToOpen == values.m_RefStop);
            }
        }
    }
    if ( count ) {
        //values.update_current_ref_start(graph_range.GetToOpen(), callback);
        if ( callback && graph_range.GetToOpen() != values.m_RefFrom ) {
            TSeqPos flush = graph_range.GetToOpen() - values.m_RefFrom;
            TSeqPos flush16 = align_to_16_down(flush);
            TSeqPos flush_tail = flush - flush16;
            if ( flush16 ) {
                values.advance_current_beg(values.m_RefFrom+flush16, callback);
            }
            if ( flush_tail ) {
                values.advance_current_beg(values.m_RefFrom+flush_tail, callback);
            }
            _ASSERT(values.m_RefFrom == graph_range.GetToOpen());
        }
        values.finalize(callback);
    }
    return count;
}
#endif // HAVE_NEW_PILEUP_COLLECTOR
 
bool CBamDb::IncludeAlignTag(CTempString tag)
{
    if ( tag.size() != 2 ) {
        NCBI_THROW_FMT(CBamException, eInvalidArg, "Tag name must have 2 characters: \""<<tag<<'"');
    }
    auto iter = find(m_IncludedAlignTags.begin(), m_IncludedAlignTags.end(), tag);
    if ( iter != m_IncludedAlignTags.end() ) {
        // already included
        return false;
    }
    STagInfo info;
    info.name[0] = tag[0];
    info.name[1] = tag[1];
    m_IncludedAlignTags.push_back(info);
    return true;
}
 
 
bool CBamDb::ExcludeAlignTag(CTempString tag)
{
    if ( tag.size() != 2 ) {
        NCBI_THROW_FMT(CBamException, eInvalidArg, "Tag name must have 2 characters: \""<<tag<<'"');
    }
    auto iter = find(m_IncludedAlignTags.begin(), m_IncludedAlignTags.end(), tag);
    if ( iter == m_IncludedAlignTags.end() ) {
        // already excluded
        return false;
    }
    m_IncludedAlignTags.erase(iter);
    return true;
}
 
/////////////////////////////////////////////////////////////////////////////
 
CBamRefSeqIterator::CBamRefSeqIterator()
    : m_DB(0)
{
}
 
 
CBamRefSeqIterator::CBamRefSeqIterator(const CBamDb& bam_db)
    : m_DB(&bam_db)
{
    if ( bam_db.UsesRawIndex() ) {
        m_RawDB = bam_db.m_RawDB;
        if ( m_RawDB->GetData().GetHeader().GetRefs().empty() ) {
            m_RawDB = null;
        }
        m_RefIndex = 0;
    }
    else {
        CMutexGuard guard(bam_db.m_AADB->m_Mutex);
        s_UpdateVDBRequestContext();
        AlignAccessRefSeqEnumerator* ptr = 0;
        if ( rc_t rc = AlignAccessDBEnumerateRefSequences(bam_db.m_AADB->m_DB, &ptr) ) {
            if ( !(GetRCObject(rc) == rcRow &&
                   GetRCState(rc) == rcNotFound) ) {
                // error
                NCBI_THROW2(CBamException, eOtherError, "Cannot find first refseq", rc);
            }
            // no reference sequences found
        }
        else {
            // found first reference sequences
            m_AADBImpl = new SAADBImpl();
            m_AADBImpl->m_Iter.SetReferencedPointer(ptr);
            x_AllocBuffers();
        }
    }
}
 
 
void CBamRefSeqIterator::x_AllocBuffers(void)
{
    m_AADBImpl->m_RefSeqIdBuffer.reserve(32);
}
 
 
void CBamRefSeqIterator::x_InvalidateBuffers(void)
{
    m_AADBImpl->m_RefSeqIdBuffer.clear();
}
 
 
CBamRefSeqIterator::CBamRefSeqIterator(const CBamRefSeqIterator& iter)
{
    *this = iter;
}
 
 
CBamRefSeqIterator& CBamRefSeqIterator::operator=(const CBamRefSeqIterator& iter)
{
    if ( this != &iter ) {
        m_DB = iter.m_DB;
        m_AADBImpl = iter.m_AADBImpl;
        m_RawDB = iter.m_RawDB;
        m_RefIndex = iter.m_RefIndex;
        m_CachedRefSeq_id.Reset();
    }
    return *this;
}
 
 
void CBamRefSeqIterator::x_CheckValid(void) const
{
    if ( !*this ) {
        NCBI_THROW(CBamException, eNoData, "CBamRefSeqIterator is invalid");
    }
}
 
 
CBamRefSeqIterator& CBamRefSeqIterator::operator++(void)
{
    if ( m_AADBImpl ) {
        x_InvalidateBuffers();
        s_UpdateVDBRequestContext();
        if ( rc_t rc = AlignAccessRefSeqEnumeratorNext(m_AADBImpl->m_Iter) ) {
            m_AADBImpl.Reset();
            if ( !(GetRCObject(rc) == rcRow &&
                   GetRCState(rc) == rcNotFound) ) {
                // error
                NCBI_THROW2(CBamException, eOtherError,
                            "Cannot find next refseq", rc);
            }
            // no more reference sequences
        }
    }
    else {
        if( ++m_RefIndex == m_RawDB->GetData().GetHeader().GetRefs().size() ) {
            // no more reference sequences
            m_RawDB.Reset();
        }
    }
    m_CachedRefSeq_id.Reset();
    return *this;
}
 
 
bool CBamRefSeqIterator::x_CheckRC(CBamString& buf,
                                   rc_t rc,
                                   size_t size,
                                   const char* msg) const
{
    if ( rc == 0 ) {
        // no error, update size and finish
        if ( size > 0 ) {
            // omit trailing zero char
            if ( buf[size-1] ) {
                ERR_POST("No zero at the end: " << string(buf.data(), size-1));
            }
            _ASSERT(buf[size-1] == '\0');
            buf.resize(size-1);
        }
        else {
            buf.clear();
        }
        return true;
    }
    else if ( GetRCState(rc) == rcInsufficient && size > buf.capacity() ) {
        // buffer too small, realloc and repeat
        buf.reserve(size);
        return false;
    }
    else {
        // other failure
        NCBI_THROW3(CBamException, eNoData,
                    "Cannot get value", rc, msg);
    }
}
 
 
void CBamRefSeqIterator::x_GetString(CBamString& buf,
                                     const char* msg, TGetString func) const
{
    x_CheckValid();
    while ( buf.empty() ) {
        size_t size = 0;
        rc_t rc = func(m_AADBImpl->m_Iter, buf.data(), buf.capacity(), &size);
        if ( x_CheckRC(buf, rc, size, msg) ) {
            break;
        }
    }
}
 
 
CTempString CBamRefSeqIterator::GetRefSeqId(void) const
{
    if ( m_AADBImpl ) {
        x_GetString(m_AADBImpl->m_RefSeqIdBuffer, "RefSeqId",
                    AlignAccessRefSeqEnumeratorGetID);
        return m_AADBImpl->m_RefSeqIdBuffer;
    }
    else {
        return m_RawDB->GetData().GetHeader().GetRefName(m_RefIndex);
    }
}
 
 
CRef<CSeq_id> CBamRefSeqIterator::GetRefSeq_id(void) const
{
    if ( !m_CachedRefSeq_id ) {
        m_CachedRefSeq_id = m_DB->GetRefSeq_id(GetRefSeqId());
    }
    return m_CachedRefSeq_id;
}
 
 
TSeqPos CBamRefSeqIterator::GetLength(void) const
{
    if ( m_AADBImpl ) {
        uint64_t length;
        if ( rc_t rc = AlignAccessRefSeqEnumeratorGetLength(m_AADBImpl->m_Iter, &length) ) {
            NCBI_THROW2(CBamException, eNoData,
                        "CBamRefSeqIterator::GetLength() cannot get length", rc);
        }
        if ( length >= kInvalidSeqPos ) {
            NCBI_THROW(CBamException, eOtherError,
                       "CBamRefSeqIterator::GetLength() length is too big");
        }
        return TSeqPos(length);
    }
    else {
        return m_RawDB->GetData().GetHeader().GetRefLength(m_RefIndex);
    }
}
 
 
/////////////////////////////////////////////////////////////////////////////
 
CBamAlignIterator::SRawImpl::SRawImpl(CObjectFor<CBamRawDb>& db)
    : m_RawDB(&db),
      m_Iter(db)
{
}
 
 
CBamAlignIterator::SRawImpl::SRawImpl(CObjectFor<CBamRawDb>& db,
                                      const string& ref_label,
                                      TSeqPos ref_pos,
                                      TSeqPos window,
                                      CBamAlignIterator::ESearchMode search_mode)
    : m_RawDB(&db),
      m_Iter(db, ref_label, ref_pos, window, CBamRawAlignIterator::ESearchMode(search_mode))
{
    m_ShortSequence.reserve(256);
    m_CIGAR.reserve(32);
}
 
 
CBamAlignIterator::SRawImpl::SRawImpl(CObjectFor<CBamRawDb>& db,
                                      const string& ref_label,
                                      TSeqPos ref_pos,
                                      TSeqPos window,
                                      CBamIndex::EIndexLevel min_level,
                                      CBamIndex::EIndexLevel max_level,
                                      CBamAlignIterator::ESearchMode search_mode)
    : m_RawDB(&db),
      m_Iter(db, ref_label, ref_pos, window, min_level, max_level, CBamRawAlignIterator::ESearchMode(search_mode))
{
    m_ShortSequence.reserve(256);
    m_CIGAR.reserve(32);
}
 
 
void CBamAlignIterator::SRawImpl::x_InvalidateBuffers()
{
    m_ShortSequence.clear();
    m_CIGAR.clear();
}
 
 
CBamAlignIterator::SAADBImpl::SAADBImpl(const CBamDb::SAADBImpl& db,
                                        AlignAccessAlignmentEnumerator* ptr)
    : m_DB(&db),
      m_Guard(db.m_Mutex)
{
    m_Iter.SetReferencedPointer(ptr);
    m_RefSeqId.reserve(32);
    m_ShortSeqId.reserve(32);
    m_ShortSeqAcc.reserve(32);
    m_ShortSequence.reserve(256);
    m_CIGAR.reserve(32);
    m_Strand = eStrand_not_read;
}
 
 
void CBamAlignIterator::SAADBImpl::x_InvalidateBuffers()
{
    m_RefSeqId.clear();
    m_ShortSeqId.clear();
    m_ShortSeqAcc.clear();
    m_ShortSequence.clear();
    m_CIGAR.clear();
    m_Strand = eStrand_not_read;
}
 
 
bool CBamAlignIterator::SAADBImpl::x_HasAmbiguousMatch() const
{
    for ( size_t i = 0; i < m_CIGAR.size(); ++i ) {
        if ( m_CIGAR[i] == 'M' ) {
            return true;
        }
    }
    return false;
}
 
 
TSeqPos CBamAlignIterator::SAADBImpl::GetRefSeqPos() const
{
    uint64_t pos = 0;
    if ( rc_t rc = AlignAccessAlignmentEnumeratorGetRefSeqPos(m_Iter, &pos) ) {
        if ( GetRCObject(rc) == RCObject(rcData) &&
             GetRCState(rc) == rcNotFound ) {
            return kInvalidSeqPos;
        }
        NCBI_THROW2(CBamException, eNoData,
                    "Cannot get RefSeqPos", rc);
    }
    return TSeqPos(pos);
}
 
 
CBamAlignIterator::~CBamAlignIterator()
{
}
 
 
CBamAlignIterator::CBamAlignIterator(void)
    : m_DB(0),
      m_BamFlagsAvailability(eBamFlags_NotTried)
{
}
 
 
CBamAlignIterator::CBamAlignIterator(const CBamDb& bam_db)
    : m_DB(&bam_db),
      m_BamFlagsAvailability(eBamFlags_NotTried)
{
    s_UpdateVDBRequestContext();
    if ( bam_db.UsesRawIndex() ) {
        m_RawImpl = new SRawImpl(bam_db.m_RawDB.GetNCObject());
        if ( !m_RawImpl->m_Iter ) {
            m_RawImpl.Reset();
        }
    }
    else {
        CMutexGuard guard(bam_db.m_AADB->m_Mutex);
        AlignAccessAlignmentEnumerator* ptr = 0;
        if ( rc_t rc = AlignAccessDBEnumerateAlignments(bam_db.m_AADB->m_DB, &ptr) ) {
            if ( !AlignAccessAlignmentEnumeratorIsEOF(rc) ) {
                // error
                NCBI_THROW2(CBamException, eNoData, "Cannot find first alignment", rc);
            }
            // no alignments
        }
        else {
            // found first alignment
            m_AADBImpl = new SAADBImpl(*bam_db.m_AADB, ptr);
        }
    }
}
 
 
CBamAlignIterator::CBamAlignIterator(const CBamDb& bam_db,
                                     const string& ref_id,
                                     TSeqPos ref_pos,
                                     TSeqPos window,
                                     ESearchMode search_mode)
    : m_DB(&bam_db),
      m_BamFlagsAvailability(eBamFlags_NotTried)
{
    s_UpdateVDBRequestContext();
    if ( bam_db.UsesRawIndex() ) {
        m_RawImpl = new SRawImpl(bam_db.m_RawDB.GetNCObject(), ref_id, ref_pos, window, search_mode);
        if ( !m_RawImpl->m_Iter ) {
            m_RawImpl.Reset();
        }
    }
    else {
        CMutexGuard guard(bam_db.m_AADB->m_Mutex);
        AlignAccessAlignmentEnumerator* ptr = 0;
        if ( rc_t rc = AlignAccessDBWindowedAlignments(bam_db.m_AADB->m_DB, &ptr,
                                                       ref_id.c_str(), ref_pos, window) ) {
            if ( ptr ) {
                AlignAccessAlignmentEnumeratorRelease(ptr);
                ptr = 0;
            }
            if ( !AlignAccessAlignmentEnumeratorIsEOF(rc) ) {
                // error
                NCBI_THROW2(CBamException, eNoData, "Cannot find first alignment", rc);
            }
            // no alignments
            return;
        }
        // found first alignment
        m_AADBImpl = new SAADBImpl(*bam_db.m_AADB, ptr);
        if ( search_mode == eSearchByStart ) {
            // skip alignments that start before the requested range
            while ( m_AADBImpl->GetRefSeqPos() < ref_pos ) {
                if ( rc_t rc = AlignAccessAlignmentEnumeratorNext(ptr) ) {
                    m_AADBImpl.Reset();
                    if ( !AlignAccessAlignmentEnumeratorIsEOF(rc) ) {
                        // error
                        NCBI_THROW2(CBamException, eOtherError, "Cannot find first alignment", rc);
                    }
                    else {
                        // no matching alignment found
                        return;
                    }
                }
            }
        }
    }
}
 
 
CBamAlignIterator::CBamAlignIterator(const CBamDb& bam_db,
                                     const string& ref_id,
                                     TSeqPos ref_pos,
                                     TSeqPos window,
                                     CBamIndex::EIndexLevel min_level,
                                     CBamIndex::EIndexLevel max_level,
                                     ESearchMode search_mode)
    : m_DB(&bam_db),
      m_BamFlagsAvailability(eBamFlags_NotTried)
{
    s_UpdateVDBRequestContext();
    if ( bam_db.UsesRawIndex() ) {
        m_RawImpl = new SRawImpl(bam_db.m_RawDB.GetNCObject(), ref_id, ref_pos, window, min_level, max_level, search_mode);
        if ( !m_RawImpl->m_Iter ) {
            m_RawImpl.Reset();
        }
    }
    else {
        NCBI_THROW(CBamException, eInvalidArg, "BAM index levels are supported only in raw index mode");
    }
}
 
 
CBamAlignIterator::CBamAlignIterator(const CBamAlignIterator& iter)
{
    *this = iter;
}
 
 
CBamAlignIterator& CBamAlignIterator::operator=(const CBamAlignIterator& iter)
{
    if ( this != &iter ) {
        m_DB = iter.m_DB;
        m_AADBImpl = iter.m_AADBImpl;
        m_RawImpl = iter.m_RawImpl;
        m_SpotIdDetector = iter.m_SpotIdDetector;
        m_BamFlagsAvailability = iter.m_BamFlagsAvailability;
    }
    return *this;
}
 
 
void CBamAlignIterator::x_CheckValid(void) const
{
    if ( !*this ) {
        NCBI_THROW(CBamException, eNoData, "CBamAlignIterator is invalid");
    }
}
 
 
CBamAlignIterator& CBamAlignIterator::operator++(void)
{
    x_CheckValid();
    m_RefSeq_id.Reset();
    m_ShortSeq_id.Reset();
    s_UpdateVDBRequestContext();
    if ( m_AADBImpl ) {
        if ( rc_t rc = AlignAccessAlignmentEnumeratorNext(m_AADBImpl->m_Iter) ) {
            m_AADBImpl.Reset();
            if ( !(GetRCObject(rc) == rcRow &&
                   GetRCState(rc) == rcNotFound) ) {
                // error
                NCBI_THROW2(CBamException, eOtherError, "Cannot find next alignment", rc);
            }
            // end of iteration, keep the error code
        }
        else {
            // next alignment
            m_AADBImpl->x_InvalidateBuffers();
        }
    }
    else {
        if ( !++m_RawImpl->m_Iter ) {
            m_RawImpl.Reset();
        }
        else {
            m_RawImpl->x_InvalidateBuffers();
        }
    }
    return *this;
}
 
 
bool CBamAlignIterator::x_CheckRC(CBamString& buf,
                                  rc_t rc,
                                  size_t size,
                                  const char* msg) const
{
    if ( rc == 0 ) {
        // no error, update size and finish
        if ( size > 0 ) {
            // omit trailing zero char
            if ( buf[size-1] ) {
                ERR_POST("No zero at the end: " << string(buf.data(), size-1));
            }
            _ASSERT(buf[size-1] == '\0');
            buf.resize(size-1);
        }
        else {
            buf.clear();
        }
        return true;
    }
    else if ( GetRCState(rc) == rcInsufficient && size > buf.capacity() ) {
        // buffer too small, realloc and repeat
        buf.reserve(size);
        return false;
    }
    else {
        // other failure
        NCBI_THROW3(CBamException, eNoData,
                    "Cannot get value", rc, msg);
    }
}
 
 
void CBamAlignIterator::x_GetString(CBamString& buf,
                                    const char* msg, TGetString func) const
{
    x_CheckValid();
    while ( buf.empty() ) {
        size_t size = 0;
        rc_t rc = func(m_AADBImpl->m_Iter, buf.data(), buf.capacity(), &size);
        if ( x_CheckRC(buf, rc, size, msg) ) {
            break;
        }
    }
}
 
 
void CBamAlignIterator::x_GetString(CBamString& buf, uint64_t& pos,
                                    const char* msg, TGetString2 func) const
{
    x_CheckValid();
    while ( buf.empty() ) {
        size_t size = 0;
        rc_t rc = func(m_AADBImpl->m_Iter, &pos, buf.data(), buf.capacity(), &size);
        if ( x_CheckRC(buf, rc, size, msg) ) {
            break;
        }
    }
}
 
 
CTempString CBamAlignIterator::GetRefSeqId(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_RawDB->GetData().GetHeader().GetRefName(m_RawImpl->m_Iter.GetRefSeqIndex());
    }
    else {
        x_GetString(m_AADBImpl->m_RefSeqId, "RefSeqId",
                    AlignAccessAlignmentEnumeratorGetRefSeqID);
        return m_AADBImpl->m_RefSeqId;
    }
}
 
 
TSeqPos CBamAlignIterator::GetRefSeqPos(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetRefSeqPos();
    }
    else {
        return m_AADBImpl->GetRefSeqPos();
    }
}
 
 
Int4 CBamAlignIterator::GetNextRefSeqIndex(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetNextRefSeqIndex();
    }
    else {
        // not implemented
        return -1;
    }
}
 
 
CTempString CBamAlignIterator::GetNextRefSeqId(void) const
{
    if ( m_RawImpl ) {
        Int4 next_ref_index = m_RawImpl->m_Iter.GetNextRefSeqIndex();
        if ( next_ref_index == -1 ) {
            // no next segment
            return CTempString();
        }
        else {
            return m_RawImpl->m_RawDB->GetData().GetHeader().GetRefName(next_ref_index);
        }
    }
    else {
        // not implemented
        return CTempString();
    }
}
 
 
TSeqPos CBamAlignIterator::GetNextRefSeqPos(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetNextRefSeqPos();
    }
    else {
        // not implemented
        return kInvalidSeqPos;
    }
}
 
 
CTempString CBamAlignIterator::GetShortSeqId(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetShortSeqId();
    }
    else {
        x_GetString(m_AADBImpl->m_ShortSeqId, "ShortSeqId",
                    AlignAccessAlignmentEnumeratorGetShortSeqID);
        return m_AADBImpl->m_ShortSeqId;
    }
}
 
 
CTempString CBamAlignIterator::GetShortSeqAcc(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetShortSeqAcc();
    }
    else {
        x_GetString(m_AADBImpl->m_ShortSeqAcc, "ShortSeqAcc",
                    AlignAccessAlignmentEnumeratorGetShortSeqAccessionID);
        return m_AADBImpl->m_ShortSeqAcc;
    }
}
 
 
CTempString CBamAlignIterator::GetShortSequence(void) const
{
    if ( m_RawImpl ) {
        if ( m_RawImpl->m_ShortSequence.empty() ) {
            m_RawImpl->m_Iter.GetShortSequence(m_RawImpl->m_ShortSequence);
        }
        return m_RawImpl->m_ShortSequence;
    }
    else {
        if ( m_AADBImpl->m_ShortSequence.empty() ) {
            x_GetString(m_AADBImpl->m_ShortSequence, "ShortSequence",
                        AlignAccessAlignmentEnumeratorGetShortSequence);
        }
        return m_AADBImpl->m_ShortSequence;
    }
}
 
 
TSeqPos CBamAlignIterator::GetShortSequenceLength(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetShortSequenceLength();
    }
    else {
        return TSeqPos(GetShortSequence().size());
    }
}
 
 
inline void CBamAlignIterator::x_GetCIGAR(void) const
{
    x_GetString(m_AADBImpl->m_CIGAR, m_AADBImpl->m_CIGARPos, "CIGAR",
                AlignAccessAlignmentEnumeratorGetCIGAR);
}
 
 
bool CBamAlignIterator::x_HasAmbiguousMatch() const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.HasAmbiguousMatch();
    }
    else {
        x_GetCIGAR();
        return m_AADBImpl->x_HasAmbiguousMatch();
    }
}
 
 
TSeqPos CBamAlignIterator::GetCIGARPos(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetCIGARPos();
    }
    else {
        x_GetCIGAR();
        return TSeqPos(m_AADBImpl->m_CIGARPos);
    }
}
 
 
CTempString CBamAlignIterator::GetCIGAR(void) const
{
    if ( m_RawImpl ) {
        if ( m_RawImpl->m_CIGAR.empty() ) {
            m_RawImpl->m_Iter.GetCIGAR(m_RawImpl->m_CIGAR);
        }
        return m_RawImpl->m_CIGAR;
    }
    else {
        x_GetCIGAR();
        return m_AADBImpl->m_CIGAR;
    }
}
 
 
void CBamAlignIterator::GetRawCIGAR(vector<Uint4>& raw_cigar) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetCIGAR(raw_cigar);
    }
    else {
        x_GetCIGAR();
        raw_cigar.clear();
        const char* ptr = m_AADBImpl->m_CIGAR.data();
        const char* end = ptr + m_AADBImpl->m_CIGAR.size();
        char type;
        TSeqPos len;
        while ( ptr != end ) {
            type = *ptr;
            for ( len = 0; ++ptr != end; ) {
                char c = *ptr;
                if ( c >= '0' && c <= '9' ) {
                    len = len*10+(c-'0');
                }
                else {
                    break;
                }
            }
            const char* types = "MIDNSHP=X";
            const char* ptr = strchr(types, type);
            unsigned op = ptr? unsigned(ptr-types): 15u;
            raw_cigar.push_back((len<<4)|(op));
        }
    }
}
 
 
TSeqPos CBamAlignIterator::GetCIGARRefSize(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetCIGARRefSize();
    }
    else {
        TSeqPos ref_size = 0;
        x_GetCIGAR();
        const char* ptr = m_AADBImpl->m_CIGAR.data();
        const char* end = ptr + m_AADBImpl->m_CIGAR.size();
        char type;
        TSeqPos len;
        while ( ptr != end ) {
            type = *ptr;
            for ( len = 0; ++ptr != end; ) {
                char c = *ptr;
                if ( c >= '0' && c <= '9' ) {
                    len = len*10+(c-'0');
                }
                else {
                    break;
                }
            }
            if ( type == 'M' || type == '=' || type == 'X' ) {
                // match
                ref_size += len;
            }
            else if ( type == 'I' || type == 'S' ) {
                // insert
            }
            else if ( type == 'D' || type == 'N' ) {
                // delete
                ref_size += len;
            }
            else if ( type != 'P' ) {
                NCBI_THROW_FMT(CBamException, eBadCIGAR,
                               "Bad CIGAR char: " << type << " in " << m_AADBImpl->m_CIGAR);
            }
            if ( len == 0 ) {
                NCBI_THROW_FMT(CBamException, eBadCIGAR,
                               "Bad CIGAR length: " << type << "0 in " << m_AADBImpl->m_CIGAR);
            }
        }
        return ref_size;
    }
}
 
 
TSeqPos CBamAlignIterator::GetCIGARShortSize(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetCIGARShortSize();
    }
    else {
        TSeqPos short_size = 0;
        x_GetCIGAR();
        const char* ptr = m_AADBImpl->m_CIGAR.data();
        const char* end = ptr + m_AADBImpl->m_CIGAR.size();
        char type;
        TSeqPos len;
        while ( ptr != end ) {
            type = *ptr;
            for ( len = 0; ++ptr != end; ) {
                char c = *ptr;
                if ( c >= '0' && c <= '9' ) {
                    len = len*10+(c-'0');
                }
                else {
                    break;
                }
            }
            if ( type == 'M' || type == '=' || type == 'X' ) {
                // match
                short_size += len;
            }
            else if ( type == 'I' || type == 'S' ) {
                // insert
                short_size += len;
            }
            else if ( type == 'D' || type == 'N' ) {
                // delete
            }
            else if ( type != 'P' ) {
                NCBI_THROW_FMT(CBamException, eBadCIGAR,
                               "Bad CIGAR char: " << type << " in " << m_AADBImpl->m_CIGAR);
            }
            if ( len == 0 ) {
                NCBI_THROW_FMT(CBamException, eBadCIGAR,
                               "Bad CIGAR length: " << type << "0 in " << m_AADBImpl->m_CIGAR);
            }
        }
        return short_size;
    }
}
 
 
pair< COpenRange<TSeqPos>, COpenRange<TSeqPos> >
CBamAlignIterator::GetCIGARAlignment(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetCIGARAlignment();
    }
    else {
        pair< COpenRange<TSeqPos>, COpenRange<TSeqPos> > ret;
        ret.first.SetFrom(GetRefSeqPos());
        x_GetCIGAR();
        ret.second.SetFrom(TSeqPos(m_AADBImpl->m_CIGARPos));
        TSeqPos ref_size = 0, short_size = 0;
        const char* ptr = m_AADBImpl->m_CIGAR.data();
        const char* end = ptr + m_AADBImpl->m_CIGAR.size();
        char type;
        TSeqPos len;
        while ( ptr != end ) {
            type = *ptr;
            for ( len = 0; ++ptr != end; ) {
                char c = *ptr;
                if ( c >= '0' && c <= '9' ) {
                    len = len*10+(c-'0');
                }
                else {
                    break;
                }
            }
            if ( type == 'M' || type == '=' || type == 'X' ) {
                // match
                ref_size += len;
                short_size += len;
            }
            else if ( type == 'I' || type == 'S' ) {
                // insert
                short_size += len;
            }
            else if ( type == 'D' || type == 'N' ) {
                // delete
                ref_size += len;
            }
            else if ( type != 'P' ) {
                NCBI_THROW_FMT(CBamException, eBadCIGAR,
                               "Bad CIGAR char: " << type << " in " << m_AADBImpl->m_CIGAR);
            }
            if ( len == 0 ) {
                NCBI_THROW_FMT(CBamException, eBadCIGAR,
                               "Bad CIGAR length: " << type << "0 in " << m_AADBImpl->m_CIGAR);
            }
        }
        ret.first.SetLength(ref_size);
        ret.second.SetLength(short_size);
        return ret;
    }
}
 
 
CRef<CSeq_id> CBamAlignIterator::GetRefSeq_id(void) const
{
    if ( !m_RefSeq_id ) {
        m_RefSeq_id = m_DB->GetRefSeq_id(GetRefSeqId());
    }
    return m_RefSeq_id;
}
 
 
CRef<CSeq_id> CBamAlignIterator::GetShortSeq_id(const string& str) const
{
    return sx_GetShortSeq_id(str, GetIdMapper(), GetShortSequenceLength() == 0);
}
 
 
CRef<CSeq_id> CBamAlignIterator::GetShortSeq_id(void) const
{
    if ( !m_ShortSeq_id ) {
        string id = GetShortSeqId();
        bool paired = IsPaired(), is_1st = false, is_2nd = false;
        if ( paired ) {
            // regular way to get pairing info
            is_1st = IsFirstInPair();
            is_2nd = IsSecondInPair();
        }
        else {
            // more pairing info may be available via BAM file flags
            Uint2 flags;
            if ( TryGetFlags(flags) ) {
                // use flags to get pairing info faster
                paired = (flags & (BAMFlags_WasPaired |
                                   BAMFlags_IsMappedAsPair)) != 0;
                is_1st = (flags & BAMFlags_IsFirst) != 0;
                is_2nd = (flags & BAMFlags_IsSecond) != 0;
            }
        }
        if ( paired ) {
            if ( is_1st && !is_2nd ) {
                id += ".1";
            }
            else if ( is_2nd && !is_1st ) {
                id += ".2";
            }
            else {
                // conflict
                if ( ISpotIdDetector* detector = GetSpotIdDetector() ) {
                    detector->AddSpotId(id, this);
                }
                else {
                    id += ".?";
                }
            }
        }
        m_ShortSeq_id = GetShortSeq_id(id);
    }
    return m_ShortSeq_id;
}
 
 
void CBamAlignIterator::SetRefSeq_id(CRef<CSeq_id> seq_id)
{
    m_RefSeq_id = seq_id;
}
 
 
void CBamAlignIterator::SetShortSeq_id(CRef<CSeq_id> seq_id)
{
    m_ShortSeq_id = seq_id;
}
 
 
void CBamAlignIterator::x_GetStrand(void) const
{
    x_CheckValid();
    if ( m_AADBImpl->m_Strand != eStrand_not_read ) {
        return;
    }
    
    m_AADBImpl->m_Strand = eStrand_not_set;
    AlignmentStrandDirection dir;
    if ( AlignAccessAlignmentEnumeratorGetStrandDirection(m_AADBImpl->m_Iter, &dir) != 0 ) {
        return;
    }
    
    switch ( dir ) {
    case asd_Forward:
        m_AADBImpl->m_Strand = eNa_strand_plus;
        break;
    case asd_Reverse:
        m_AADBImpl->m_Strand = eNa_strand_minus;
        break;
    default:
        m_AADBImpl->m_Strand = eNa_strand_unknown;
        break;
    }
}
 
 
bool CBamAlignIterator::IsSetStrand(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.IsSetStrand();
    }
    else {
        x_GetStrand();
        return m_AADBImpl->m_Strand != eStrand_not_set;
    }
}
 
 
ENa_strand CBamAlignIterator::GetStrand(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetStrand();
    }
    else {
        if ( !IsSetStrand() ) {
            NCBI_THROW(CBamException, eNoData,
                       "Strand is not set");
        }
        return ENa_strand(m_AADBImpl->m_Strand);
    }
}
 
 
Uint1 CBamAlignIterator::GetMapQuality(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetMapQuality();
    }
    else {
        x_CheckValid();
        uint8_t q = 0;
        if ( rc_t rc = AlignAccessAlignmentEnumeratorGetMapQuality(m_AADBImpl->m_Iter, &q) ) {
            NCBI_THROW2(CBamException, eNoData,
                        "Cannot get MapQuality", rc);
        }
        return q;
    }
}
 
 
bool CBamAlignIterator::IsPaired(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.IsPaired();
    }
    else {
        x_CheckValid();
        bool f;
        if ( rc_t rc = AlignAccessAlignmentEnumeratorGetIsPaired(m_AADBImpl->m_Iter, &f) ) {
            NCBI_THROW2(CBamException, eNoData,
                        "Cannot get IsPaired flag", rc);
        }
        return f;
    }
}
 
 
bool CBamAlignIterator::IsFirstInPair(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.IsFirstInPair();
    }
    else {
        x_CheckValid();
        bool f;
        if ( rc_t rc=AlignAccessAlignmentEnumeratorGetIsFirstInPair(m_AADBImpl->m_Iter, &f) ) {
            NCBI_THROW2(CBamException, eNoData,
                        "Cannot get IsFirstInPair flag", rc);
        }
        return f;
    }
}
 
 
bool CBamAlignIterator::IsSecondInPair(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.IsSecondInPair();
    }
    else {
        x_CheckValid();
        bool f;
        if ( rc_t rc=AlignAccessAlignmentEnumeratorGetIsSecondInPair(m_AADBImpl->m_Iter, &f) ) {
            NCBI_THROW2(CBamException, eNoData,
                        "Cannot get IsSecondInPair flag", rc);
        }
        return f;
    }
}
 
 
bool CBamAlignIterator::IsSecondary(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.IsSecondary();
    }
    else {
        x_CheckValid();
        Uint2 flags;
        if ( TryGetFlags(flags) ) {
            return (flags & BAMFlags_IsNotPrimary) != 0;
        }
        return false; // assume non-secondary
    }
}
 
 
CBamFileAlign::CBamFileAlign(const CBamAlignIterator& iter)
{
    if ( rc_t rc = AlignAccessAlignmentEnumeratorGetBAMAlignment(iter.m_AADBImpl->m_Iter, x_InitPtr()) ) {
        *x_InitPtr() = 0;
        NCBI_THROW2(CBamException, eNoData,
                    "Cannot get BAM file alignment", rc);
    }
}
 
 
Int4 CBamFileAlign::GetRefSeqIndex(void) const
{
    int32_t id;
    if ( rc_t rc = BAMAlignmentGetRefSeqId(*this, &id) ) {
        NCBI_THROW2(CBamException, eNoData,
                    "Cannot get BAM RefSeqIndex", rc);
    }
    return id;
}
 
 
Int4 CBamAlignIterator::GetRefSeqIndex(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetRefSeqIndex();
    }
    else {
        x_CheckValid();
        return CBamFileAlign(*this).GetRefSeqIndex();
    }
}
 
 
Uint2 CBamFileAlign::GetFlags(void) const
{
    uint16_t flags;
    if ( rc_t rc = BAMAlignmentGetFlags(*this, &flags) ) {
        NCBI_THROW2(CBamException, eNoData,
                    "Cannot get BAM flags", rc);
    }
    return flags;
}
 
 
bool CBamFileAlign::TryGetFlags(Uint2& flags) const
{
    return BAMAlignmentGetFlags(*this, &flags) == 0;
}
 
 
Uint2 CBamAlignIterator::GetFlags(void) const
{
    if ( m_RawImpl ) {
        return m_RawImpl->m_Iter.GetFlags();
    }
    else {
        x_CheckValid();
        try {
            Uint2 flags = CBamFileAlign(*this).GetFlags();
            if ( m_BamFlagsAvailability != eBamFlags_Available ) {
                m_BamFlagsAvailability = eBamFlags_Available;
            }
            return flags;
        }
        catch ( CBamException& /* will be rethrown */ ) {
            if ( m_BamFlagsAvailability != eBamFlags_NotAvailable ) {
                m_BamFlagsAvailability = eBamFlags_NotAvailable;
            }
            throw;
        }
    }
}
 
 
bool CBamAlignIterator::TryGetFlags(Uint2& flags) const
{
    if ( m_RawImpl ) {
        flags = m_RawImpl->m_Iter.GetFlags();
        return true;
    }
    else {
        if ( !*this || m_BamFlagsAvailability == eBamFlags_NotAvailable ) {
            return false;
        }
        if ( !CBamFileAlign(*this).TryGetFlags(flags) ) {
            m_BamFlagsAvailability = eBamFlags_NotAvailable;
            return false;
        }
        if ( m_BamFlagsAvailability != eBamFlags_Available ) {
            m_BamFlagsAvailability = eBamFlags_Available;
        }
        return true;
    }
}
 
 
CBamAuxIterator CBamAlignIterator::GetAuxIterator() const
{
    if ( auto impl = GetRawIndexIteratorPtr() ) {
        return impl->GetAuxIterator();
    }
    NCBI_THROW(CBamException, eInvalidArg, "BAM aux iterator is supported only in raw index mode");
}
 
 
CRef<CBioseq> CBamAlignIterator::GetShortBioseq(void) const
{
    CTempString data = GetShortSequence();
    TSeqPos length = TSeqPos(data.size());
    if ( length == 0 ) {
        // no actual sequence
        return null;
    }
    CRef<CBioseq> seq(new CBioseq);
    seq->SetId().push_back(GetShortSeq_id());
    CSeq_inst& inst = seq->SetInst();
    inst.SetRepr(inst.eRepr_raw);
    inst.SetMol(inst.eMol_na);
    inst.SetLength(length);
    string& iupac = inst.SetSeq_data().SetIupacna().Set();
    iupac.assign(data.data(), length);
    if ( GetStrand() == eNa_strand_minus ) {
        CSeqManip::ReverseComplement(iupac, CSeqUtil::e_Iupacna, 0, length);
    }
    return seq;
}
 
 
struct CBamAlignIterator::SCreateCache {
    TObjectIdCache m_ObjectIdTracebacks;
    TObjectIdCache m_ObjectIdCIGAR;
    TObjectIdCache m_ObjectIdHP;
    TObjectIdCache m_ObjectIdMateRead;
    TObjectIdCache m_ObjectIdRefId;
    TObjectIdCache m_ObjectIdRefPos;
    TObjectIdCache m_ObjectIdLcl;
    CRef<CUser_object> m_SecondaryIndicator;
    CRef<CAnnotdesc> m_MatchAnnotIndicator;
};
 
 
CBamAlignIterator::SCreateCache&
CBamAlignIterator::x_GetCreateCache(void) const
{
    if ( !m_CreateCache ) {
        m_CreateCache = new SCreateCache;
    }
    return *m_CreateCache;
}
 
 
static CObject_id& sx_GetObject_id(CTempString name,
                                   CRef<CObject_id>& cache)
{
    if ( !cache ) {
        cache = new CObject_id();
        cache->SetStr(name);
    }
    return *cache;
}
 
 
static CRef<CUser_object> sx_GetSecondaryIndicator(CRef<CUser_object>& cache)
{
    if ( !cache ) {
        cache = new CUser_object();
        cache->SetType().SetStr("Secondary");
        cache->SetData();
    }
    return cache;
}
 
 
static CRef<CAnnotdesc> sx_GetMatchAnnotIndicator(CRef<CAnnotdesc>& cache)
{
    if ( !cache ) {
        cache = new CAnnotdesc;
        CUser_object& obj = cache->SetUser();
        obj.SetType().SetStr("Mate read");
        obj.AddField("Match by local Seq-id", true);
    }
    return cache;
}
 
 
CRef<CSeq_align> CBamAlignIterator::GetMatchAlign(void) const
{
    if ( GetRefSeqPos() == kInvalidSeqPos ) {
        return null;
    }
    CRef<CSeq_align> align(new CSeq_align);
    align->SetType(CSeq_align::eType_diags);
    CDense_seg& denseg = align->SetSegs().SetDenseg();
    denseg.SetIds().push_back(GetRefSeq_id());
    denseg.SetIds().push_back(GetShortSeq_id());
    CDense_seg::TStarts& starts = denseg.SetStarts();
    CDense_seg::TLens& lens = denseg.SetLens();
 
    int segcount = 0;
    if ( m_RawImpl ) {
        m_RawImpl->m_Iter.GetSegments(starts, lens);
        segcount = int(lens.size());
    }
    else {
        TSeqPos refpos = GetRefSeqPos();
        TSeqPos seqpos = GetCIGARPos();
        const char* ptr = m_AADBImpl->m_CIGAR.data();
        const char* end = ptr + m_AADBImpl->m_CIGAR.size();
        char type;
        TSeqPos seglen;
        TSeqPos refstart = 0, seqstart = 0;
        while ( ptr != end ) {
            type = *ptr;
            for ( seglen = 0; ++ptr != end; ) {
                char c = *ptr;
                if ( c >= '0' && c <= '9' ) {
                    seglen = seglen*10+(c-'0');
                }
                else {
                    break;
                }
            }
            if ( type == 'M' || type == '=' || type == 'X' ) {
                // match
                refstart = refpos;
                refpos += seglen;
                seqstart = seqpos;
                seqpos += seglen;
            }
            else if ( type == 'I' || type == 'S' ) {
                refstart = kInvalidSeqPos;
                seqstart = seqpos;
                seqpos += seglen;
            }
            else if ( type == 'D' || type == 'N' ) {
                // delete
                refstart = refpos;
                refpos += seglen;
                seqstart = kInvalidSeqPos;
            }
            else if ( type == 'P' ) {
                continue;
            }
            else {
                NCBI_THROW_FMT(CBamException, eBadCIGAR,
                               "Bad CIGAR char: " <<type<< " in " <<m_AADBImpl->m_CIGAR);
            }
            if ( seglen == 0 ) {
                NCBI_THROW_FMT(CBamException, eBadCIGAR,
                               "Bad CIGAR length: " << type <<
                               "0 in " << m_AADBImpl->m_CIGAR);
            }
            starts.push_back(refstart);
            starts.push_back(seqstart);
            lens.push_back(seglen);
            ++segcount;
        }
    }
    if ( GetStrand() == eNa_strand_minus ) {
        CDense_seg::TStrands& strands = denseg.SetStrands();
        strands.reserve(2*segcount);
        TSeqPos end = GetShortSequenceLength();
        for ( int i = 0; i < segcount; ++i ) {
            strands.push_back(eNa_strand_plus);
            strands.push_back(eNa_strand_minus);
            TSeqPos pos = starts[i*2+1];
            TSeqPos len = lens[i];
            if ( pos != kInvalidSeqPos ) {
                starts[i*2+1] = end - (pos + len);
            }
        }
    }
 
    denseg.SetNumseg(segcount);
 
    bool add_cigar = s_GetCigarInAlignExt();
    const CBamDb::TTagList& tags = m_DB->GetIncludedAlignTags();
    bool add_aux = !tags.empty();
    if ( add_cigar && s_OmitAmbiguousMatchCigar() && x_HasAmbiguousMatch() ) {
        add_cigar = false;
    }
    if ( add_aux && !UsesRawIndex() ) {
        // only raw index API provides aux tags 
        add_aux = false;
    }
    bool add_mate = s_ExplicitMateInfo();
    if ( add_mate && !UsesRawIndex() ) {
        // only raw index API provides next segment info 
        add_mate = false;
    }
    Int4 next_ref_index = -1;
    CTempString next_ref_id;
    TSeqPos next_ref_pos = kInvalidSeqPos;
    if ( add_mate ) {
        next_ref_pos = GetNextRefSeqPos();
        if ( next_ref_pos != kInvalidSeqPos ) {
            next_ref_index = GetNextRefSeqIndex();
            next_ref_id = GetNextRefSeqId();
            if ( next_ref_id.empty() ) {
                next_ref_pos = kInvalidSeqPos;
            }
        }
        if ( next_ref_pos == kInvalidSeqPos ) {
            // no next segment
            add_mate = false;
        }
    }
    if ( add_cigar || add_aux ) {
        SCreateCache& cache = x_GetCreateCache();
        CRef<CUser_object> obj(new CUser_object);
        obj->SetType(sx_GetObject_id("Tracebacks", cache.m_ObjectIdTracebacks));
 
        if ( add_cigar ) {
            CRef<CUser_field> field(new CUser_field());
            field->SetLabel(sx_GetObject_id("CIGAR", cache.m_ObjectIdCIGAR));
            field->SetData().SetStr(GetCIGAR());
            obj->SetData().push_back(field);
        }
 
        if ( add_aux ) {
            for ( auto aux_it = GetAuxIterator(); aux_it; ++aux_it ) {
                CTempString name = aux_it->GetTag();
                CBamDb::TTagList::const_iterator info_iter = find(tags.begin(), tags.end(), name);
                if ( info_iter == tags.end() ) {
                    continue;
                }
                CRef<CUser_field> field(new CUser_field());
                field->SetLabel(sx_GetObject_id(name, info_iter->id_cache));
                if ( aux_it->IsArray() ) {
                    if ( aux_it->IsFloat() ) {
                        auto& arr = field->SetData().SetReals();
                        for ( size_t i = 0; i < aux_it->size(); ++i ) {
                            arr.push_back(aux_it->GetFloat(i));
                        }
                    }
                    else {
                        auto& arr = field->SetData().SetInts();
                        for ( size_t i = 0; i < aux_it->size(); ++i ) {
                            arr.push_back(CUser_field::TData::TInt(aux_it->GetInt(i)));
                        }
                    }
                }
                else {
                    if ( aux_it->IsChar() ) {
                        field->SetData().SetStr(string(1, aux_it->GetChar()));
                    }
                    else if ( aux_it->IsString() ) {
                        field->SetData().SetStr(aux_it->GetString());
                    }
                    else if ( aux_it->IsFloat() ) {
                        field->SetData().SetReal(aux_it->GetFloat());
                    }
                    else {
                        field->SetData().SetInt(CUser_field::TData::TInt(aux_it->GetInt()));
                    }
                }
                obj->SetData().push_back(field);
            }
        }
 
        if ( obj->IsSetData() ) {
            align->SetExt().push_back(obj);
        }
    }
    if ( add_mate ) {
        SCreateCache& cache = x_GetCreateCache();
        CRef<CUser_object> obj(new CUser_object);
        obj->SetType(sx_GetObject_id("Mate read", cache.m_ObjectIdMateRead));
        
        if ( next_ref_index != GetRefSeqIndex() ) {
            CRef<CUser_field> field(new CUser_field());
            field->SetLabel(sx_GetObject_id("RefId", cache.m_ObjectIdRefId));
            field->SetData().SetStr(m_DB->GetRefSeq_id(next_ref_id)->AsFastaString());
            obj->SetData().push_back(field);
        }
        {
            CRef<CUser_field> field(new CUser_field());
            field->SetLabel(sx_GetObject_id("RefPos", cache.m_ObjectIdRefPos));
            field->SetData().SetInt(next_ref_pos);
            obj->SetData().push_back(field);
        }
        {
            // search for mate read to determine its Seq-id
            auto this_ref_index = GetRefSeqIndex();
            TSeqPos this_ref_pos = GetRefSeqPos();
            CBamAlignIterator mate_iter(*m_DB, next_ref_id, next_ref_pos, 1, eSearchByStart);
            for ( ; mate_iter; ++mate_iter ) {
                if ( mate_iter.GetNextRefSeqPos() == this_ref_pos &&
                     mate_iter.GetNextRefSeqIndex() == this_ref_index ) {
                    // found mate read
                    CRef<CUser_field> field(new CUser_field());
                    field->SetLabel(sx_GetObject_id("lcl|", cache.m_ObjectIdLcl));
                    mate_iter.GetShortSeq_id()->GetLabel(&field->SetData().SetStr(),
                                                         CSeq_id::eContent);
                    obj->SetData().push_back(field);
                    break;
                }
            }
        }
        
        align->SetExt().push_back(obj);
    }
    if ( IsSecondary() ) {
        SCreateCache& cache = x_GetCreateCache();
        align->SetExt().push_back(sx_GetSecondaryIndicator(cache.m_SecondaryIndicator));
    }
    
    return align;
}
 
 
CRef<CSeq_annot>
CBamAlignIterator::x_GetSeq_annot(const string* annot_name) const
{
    CRef<CSeq_annot> annot(new CSeq_annot);
    annot->SetData().SetAlign();
    if ( annot_name ) {
        CRef<CAnnotdesc> desc(new CAnnotdesc);
        desc->SetName(*annot_name);
        annot->SetDesc().Set().push_back(desc);
    }
    if ( !s_ExplicitMateInfo() ) {
        SCreateCache& cache = x_GetCreateCache();
        annot->SetDesc().Set().push_back(sx_GetMatchAnnotIndicator(cache.m_MatchAnnotIndicator));
    }
    return annot;
}
 
 
CRef<CSeq_entry>
CBamAlignIterator::x_GetMatchEntry(const string* annot_name) const
{
    CRef<CSeq_entry> entry(new CSeq_entry);
    if ( CRef<CBioseq> seq = GetShortBioseq() ) {
        entry->SetSeq(*seq);
    }
    else {
        entry->SetSet().SetSeq_set();
    }
    if ( CRef<CSeq_align> align = GetMatchAlign() ) {
        CRef<CSeq_annot> annot = x_GetSeq_annot(annot_name);
        entry->SetAnnot().push_back(annot);
        annot->SetData().SetAlign().push_back(align);
    }
    return entry;
}
 
 
/////////////////////////////////////////////////////////////////////////////
// CBamAlignIterator::ISpotIdDetector
 
CBamAlignIterator::ISpotIdDetector::~ISpotIdDetector(void)
{
}
 
 
END_SCOPE(objects)
END_NCBI_SCOPE