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/*===========================================================================
*
* 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.
*
* ===========================================================================
*
*/
#ifndef _h_pl_context_
#define _h_pl_context_
#ifdef __cplusplus
extern "C" {
#endif
#include <klib/out.h>
#include <klib/rc.h>
#include <klib/text.h>
#include <klib/log.h>
#include <klib/namelist.h>
#include <kapp/args.h>
#define OPTION_SCHEMA "schema"
#define OPTION_FORCE "force"
#define OPTION_TABS "tabs"
#define OPTION_WITH_PROGRESS "with_progressbar"
#define OPTION_OUTPUT "output"
#define ALIAS_SCHEMA "S"
#define ALIAS_FORCE "f"
#define ALIAS_TABS "t"
#define ALIAS_WITH_PROGRESS "p"
#define ALIAS_OUTPUT "o"
#define DFLT_SCHEMA "/usr/lib/ncbi-vdb/sra/pacbio.vschema"
#define PACBIO_SCHEMA_DB "NCBI:SRA:PacBio:smrt:db"
/* *******************************************************************
the parameter-context contains all informations needed to load
******************************************************************* */
typedef struct context
{
char *dst_path; /* the vdb-database-path to create */
char *schema_name; /* name of a schema-file to use", if different from std */
char *tabs; /* load only these tabs... */
VNamelist * src_paths; /* list of source-paths */
bool force; /* if true", overwrite eventually existing output-db */
bool with_progress; /* if true", use the pl_progressbar */
} context;
rc_t ctx_init( const Args * args, context *ctx );
void ctx_free( context *ctx );
rc_t ctx_show( context * ctx );
bool ctx_ld_sequence( context * ctx );
bool ctx_ld_consensus( context * ctx );
bool ctx_ld_passes( context * ctx );
bool ctx_ld_metrics( context * ctx );
#ifdef __cplusplus
}
#endif
#endif
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