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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.
*
* ===========================================================================
*
*/
typedef struct CaptureFirstHalfAlignedColWriter CaptureFirstHalfAlignedColWriter;
#define COLWRITER_IMPL CaptureFirstHalfAlignedColWriter
#include "csra-pair.h"
#include "col-pair.h"
#include "ctx.h"
#include "caps.h"
#include "except.h"
#include "status.h"
#include "mem.h"
#include "sra-sort.h"
#include <klib/rc.h>
FILE_ENTRY ( capture-first-half-aligned );
/*--------------------------------------------------------------------------
* CaptureFirstHalfAlignedColWriter
*/
struct CaptureFirstHalfAlignedColWriter
{
ColumnWriter dad;
int64_t row_id;
cSRAPair *csra;
ColumnWriter *writer;
};
static
void CaptureFirstHalfAlignedColWriterWhack ( CaptureFirstHalfAlignedColWriter *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
ColumnWriterRelease ( self -> writer, ctx );
self -> csra = NULL;
self -> writer = NULL;
MemFree ( ctx, self, sizeof * self );
}
static
const char *CaptureFirstHalfAlignedColWriterFullSpec ( const CaptureFirstHalfAlignedColWriter *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
return ColumnWriterFullSpec ( self -> writer, ctx );
}
static
void CaptureFirstHalfAlignedColWriterPreCopy ( CaptureFirstHalfAlignedColWriter *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
ColumnWriterPreCopy ( self -> writer, ctx );
}
static
void CaptureFirstHalfAlignedColWriterPostCopy ( CaptureFirstHalfAlignedColWriter *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
ColumnWriterPostCopy ( self -> writer, ctx );
}
static
void CaptureFirstHalfAlignedColWriterWrite ( CaptureFirstHalfAlignedColWriter *self, const ctx_t *ctx,
uint32_t elem_bits, const void *data, uint32_t boff, uint32_t row_len )
{
FUNC_ENTRY ( ctx );
cSRAPair *csra = self -> csra;
if ( csra -> first_half_aligned_spot == 0 )
{
uint32_t i;
const int64_t *row = data;
for ( i = 0; i < row_len; ++ i )
{
if ( row [ i ] == 0 )
{
csra -> first_half_aligned_spot = self -> row_id;
break;
}
}
}
TRY ( ColumnWriterWrite ( self -> writer, ctx, elem_bits, data, boff, row_len ) )
{
++ self -> row_id;
}
}
static
void CaptureFirstHalfAlignedColWriterWriteStatic ( CaptureFirstHalfAlignedColWriter *self, const ctx_t *ctx,
uint32_t elem_bits, const void *data, uint32_t boff, uint32_t row_len, uint64_t count )
{
FUNC_ENTRY ( ctx );
cSRAPair *csra = self -> csra;
if ( csra -> first_half_aligned_spot == 0 )
{
uint32_t i;
const int64_t *row = data;
for ( i = 0; i < row_len; ++ i )
{
if ( row [ i ] == 0 )
{
csra -> first_half_aligned_spot = self -> row_id;
break;
}
}
}
TRY ( ColumnWriterWriteStatic ( self -> writer, ctx, elem_bits, data, boff, row_len, count ) )
{
self -> row_id += count;
}
}
static
void CaptureFirstHalfAlignedColWriterCommit ( CaptureFirstHalfAlignedColWriter *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
ColumnWriterCommit ( self -> writer, ctx );
}
static ColumnWriter_vt CaptureFirstHalfAlignedColWriter_vt =
{
CaptureFirstHalfAlignedColWriterWhack,
CaptureFirstHalfAlignedColWriterFullSpec,
CaptureFirstHalfAlignedColWriterPreCopy,
CaptureFirstHalfAlignedColWriterPostCopy,
CaptureFirstHalfAlignedColWriterWrite,
CaptureFirstHalfAlignedColWriterWriteStatic,
CaptureFirstHalfAlignedColWriterCommit
};
/*--------------------------------------------------------------------------
* cSRAPair
*/
/* MakeFirstHalfAlignedRowIdCaptureWriter
* a simple monitor on SEQUENCE.PRIMARY_ALIGNMENT_ID looking for
* half-aligned spots and capturing the first occurrence.
*/
ColumnWriter *cSRAPairMakeFirstHalfAlignedRowIdCaptureWriter ( cSRAPair *self,
const ctx_t *ctx, ColumnWriter *writer )
{
FUNC_ENTRY ( ctx );
CaptureFirstHalfAlignedColWriter *mon;
TRY ( mon = MemAlloc ( ctx, sizeof * mon, false ) )
{
TRY ( ColumnWriterInit ( & mon -> dad, ctx, & CaptureFirstHalfAlignedColWriter_vt, false ) )
{
mon -> row_id = 1;
mon -> csra = self;
TRY ( mon -> writer = ColumnWriterDuplicate ( writer, ctx ) )
{
return & mon -> dad;
}
}
MemFree ( ctx, mon, sizeof * mon );
}
return NULL;
}
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