#include <ncbi_pch.hpp>
#include "wgs_client.hpp"
#include "pubseq_gateway.hpp"
#include "pubseq_gateway_logging.hpp"
#include <objects/seqset/seqset__.hpp>
#include <objects/seqsplit/ID2S_Split_Info.hpp>
#include <sra/readers/sra/wgsresolver.hpp>
#include <objects/id2/ID2_Blob_Id.hpp>
#include <objects/id2/ID2_Blob_State.hpp>

Include dependency graph for wgs_client.cpp:

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Classes
class	CIndexUpdateThread

Typedefs
typedef int	TAllowSeqType

Enumerations
enum	EAddMasterDescr { eAddMasterDescr_none , eAddMasterDescr_detached , eAddMasterDescr_all }

enum	EResolveMaster { eResolveMaster_never , eResolveMaster_without_gi , eResolveMaster_always , eResolveMaster_never , eResolveMaster_without_gi , eResolveMaster_always }

enum	EAlligSeqType { fAllow_contig = 1 , fAllow_scaffold = 2 , fAllow_protein = 4 }

enum	EBlobType { eBlobType_none , eBlobType_Text , eBlobType_Binary , eBlobType_contig = 1 , eBlobType_scaffold = 2 , eBlobType_protein = 3 }

enum	EBlobIdBits { eBlobIdBits_type = 2 , eBlobIdBits_letter = 5 , eBlobIdBits_digit = 4 }

Functions
	BEGIN_NAMESPACE (psg)

	BEGIN_NAMESPACE (wgs)

	USING_SCOPE (objects)

	NCBI_PARAM_DECL (bool, WGS, FILTER_ALL)

	NCBI_PARAM_DEF_EX (bool, WGS, FILTER_ALL, false, eParam_NoThread, WGS_FILTER_ALL)

	NCBI_PARAM_DECL (bool, WGS, SPLIT_FEATURES)

	NCBI_PARAM_DEF (bool, WGS, SPLIT_FEATURES, true)

	NCBI_PARAM_DECL (bool, WGS, KEEP_REPLACED)

	NCBI_PARAM_DEF (bool, WGS, KEEP_REPLACED, true)

	NCBI_PARAM_DECL (bool, WGS, KEEP_MIGRATED)

	NCBI_PARAM_DEF (bool, WGS, KEEP_MIGRATED, false)

	NCBI_PARAM_DECL (bool, WGS, KEEP_EXTERNAL)

	NCBI_PARAM_DEF (bool, WGS, KEEP_EXTERNAL, true)

	NCBI_PARAM_DECL (string, WGS, ADD_MASTER_DESCR)

	NCBI_PARAM_DEF (string, WGS, ADD_MASTER_DESCR, "detached")

	NCBI_PARAM_DECL (bool, WGS, MARK_MASTER_DESCR)

	NCBI_PARAM_DEF (bool, WGS, MARK_MASTER_DESCR, false)

static bool	s_SplitFeatures (void)

static bool	s_KeepReplaced (void)

static bool	s_KeepMigrated (void)

static EAddMasterDescr	s_ProcessAddMasterDescr (void)

static EAddMasterDescr	s_AddMasterDescrLevel (void)

static bool	s_AddMasterDescrContig ()

static bool	s_AddMasterDescrScaffold ()

static bool	s_AddMasterDescrProtein ()

static bool	s_MarkMasterDescr (void)

static bool	s_IsEnabledOSGSat (CWGSClient::TEnabledFlags enabled_flags, Int4 sat)

static bool	s_IsOSGSat (Int4 sat)

static bool	s_Skip (CTempString &str, char c)

static bool	s_IsValidIntChar (char c)

template<class Int >
static bool	s_ParseInt (CTempString &str, Int &v)

static bool	s_IsOSGBlob (Int4 sat, Int4, Int4)

static bool	s_ParseOSGBlob (CTempString &s, Int4 &sat, Int4 &subsat, Int4 &satkey)

static void	s_FormatBlobId (ostream &s, const CID2_Blob_Id &blob_id)

static bool	IsWGSGeneral (const CDbtag &dbtag)

static bool	IsWGSAccession (const string &acc, const CTextseq_id &id, TAllowSeqType allow_seq_type)

static bool	IsWGSProtAccession (const CTextseq_id &id)

static bool	IsWGSAccession (const CTextseq_id &id)

static int	s_GBStateToID2 (NCBI_gb_state gb_state)

	END_NAMESPACE (wgs)

	END_NAMESPACE (psg)

Variables
	BEGIN_NCBI_NAMESPACE

static const EResolveMaster	kResolveMaster = eResolveMaster_never

static const char	kSubSatSeparator = '/'

static const int	kOSG_Sat_WGS_min = 1000

static const int	kOSG_Sat_WGS_max = 1130

static const int	kOSG_Sat_SNP_min = 2001

static const int	kOSG_Sat_SNP_max = 3999

static const int	kOSG_Sat_CDD_min = 8087

static const int	kOSG_Sat_CDD_max = 8088

static const size_t	kTypePrefixLen = 4

static const size_t	kNumLettersV1 = 4

static const size_t	kNumLettersV2 = 6

static const size_t	kVersionDigits = 2

static const size_t	kPrefixLenV1 = kNumLettersV1 + kVersionDigits

static const size_t	kPrefixLenV2 = kNumLettersV2 + kVersionDigits

static const size_t	kMinRowDigitsV1 = 6

static const size_t	kMaxRowDigitsV1 = 8

static const size_t	kMinRowDigitsV2 = 7

static const size_t	kMaxRowDigitsV2 = 9

static const size_t	kMinProtAccLen = 8

static const size_t	kMaxProtAccLen = 10

static const int	kBlobIdV1Sat = 1000

static const int	kBlobIdV2SatMin = 1001

static const int	kBlobIdV2SatMax = 1129

static const int	kBlobIdV2VersionScaffold = 0

static const int	kBlobIdV2VersionProtein = 1

static const int	kBlobIdV2VersionContig = 2

	BEGIN_LOCAL_NAMESPACE

	END_LOCAL_NAMESPACE

	END_NCBI_NAMESPACE