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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_bam_reader_
#define _h_bam_reader_
#include <klib/rc.h>
#include <kfs/directory.h>
#include <align/extern.h>
#include <align/bam.h>
#include <loader/common-reader-priv.h>
#ifdef __cplusplus
extern "C" {
#endif
rc_t CC BamReaderFileMake( const ReaderFile **self, char const headerText[], char const path[] );
/* temporary crutches for refactoring: */
const BAMFile* ToBam(const ReaderFile *self);
const BAMAlignment *ToBamAlignment(const Record* record);
#if 0
#ifdef TENTATIVE
/*--------------------------------------------------------------------------
* BAMReader, a parsing thread adapter for BAMFile.
* Creates a thread that does reading and parsing of BAM files, provides access to parsed data one record at a time.
*/
typedef struct BAMReader BAMReader;
rc_t BAMReaderMake( const BAMReader **result,
char const headerText[],
char const path[] );
/* AddRef
* Release
*/
rc_t BAMReaderAddRef ( const BAMReader *self );
rc_t AMReaderRelease ( const BAMReader *self );
/* GetBAMFile
*/
const BAMFile* BAMReaderGetBAMFile ( const BAMReader *self );
/* Read
* read an aligment
*
* "result" [ OUT ] - return param for BAMAlignment object
* must be released with BAMAlignmentRelease
*
* returns RC(..., ..., ..., rcRow, rcNotFound) at end
*/
rc_t BAMReaderRead ( const BAMReader *self, const BAMAlignment **result );
#else /*TENTATIVE*/
/* use BAMFile directly, as in the earlier version */
typedef struct BAMFile BAMReader;
#define BAMReaderMake BAMFileMakeWithHeader
#define BAMReaderAddRef BAMFileAddRef
#define BAMReaderRelease BAMFileRelease
#define BAMReaderGetBAMFile(p) (p)
#define BAMReaderRead BAMFileRead
#endif
#endif
#ifdef __cplusplus
}
#endif
#endif /* _h_bam_reader_ */
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