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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.
*
* ===========================================================================
*
*/
struct AlignIdColReader;
#define COLREADER_IMPL struct AlignIdColReader
#include "ref-alignid-col.h"
#include "glob-poslen.h"
#include "csra-tbl.h"
#include "csra-pair.h"
#include "ctx.h"
#include "caps.h"
#include "except.h"
#include "status.h"
#include "mem.h"
#include "idx-mapping.h"
#include "map-file.h"
#include "sra-sort.h"
#include <vdb/cursor.h>
#include <kapp/main.h>
#include <klib/sort.h>
#include <klib/rc.h>
#include <string.h>
#include <assert.h>
FILE_ENTRY ( ref-alignid-col );
/*--------------------------------------------------------------------------
* IdPosLen
*/
typedef struct IdPosLen IdPosLen;
struct IdPosLen
{
int64_t id;
uint64_t poslen;
};
#if USE_OLD_KSORT
static
int64_t CC IdPosLenCmpPos ( const void *a, const void *b, void *data )
{
const IdPosLen *ap = a;
const IdPosLen *bp = b;
if ( ap -> poslen < bp -> poslen )
return -1;
if ( ap -> poslen > bp -> poslen )
return 1;
return ap -> id < bp -> id ? -1 : ap -> id > bp -> id;
}
static
int64_t CC cmp_int64_t ( const void *a, const void *b, void *data )
{
const int64_t *ap = a;
const int64_t *bp = b;
return * ap < * bp ? -1 : * ap > * bp;
}
#else
static
void ksort_IdPosLen_pos ( IdPosLen *pbase, size_t total_elems )
{
#define SWAP( a, b, off, size ) \
do \
{ \
IdPosLen tmp = * ( const IdPosLen* ) ( a ); \
* ( IdPosLen* ) ( a ) = * ( const IdPosLen* ) ( b ); \
* ( IdPosLen* ) ( b ) = tmp; \
} while ( 0 )
#define CMP( a, b ) \
( ( ( ( const IdPosLen* ) ( a ) ) -> poslen == ( ( const IdPosLen* ) ( b ) ) -> poslen ) ? \
( ( ( const IdPosLen* ) ( a ) ) -> id < ( ( const IdPosLen* ) ( b ) ) -> id ) ? -1 : \
( ( ( const IdPosLen* ) ( a ) ) -> id > ( ( const IdPosLen* ) ( b ) ) -> id ) \
: ( ( ( const IdPosLen* ) ( a ) ) -> poslen < ( ( const IdPosLen* ) ( b ) ) -> poslen ) ? -1 : \
( ( ( const IdPosLen* ) ( a ) ) -> poslen > ( ( const IdPosLen* ) ( b ) ) -> poslen ) )
KSORT ( pbase, total_elems, sizeof * pbase, 0, sizeof * pbase );
#undef SWAP
#undef CMP
}
#endif
/*--------------------------------------------------------------------------
* AlignIdColReader
*/
typedef struct AlignIdColReader AlignIdColReader;
struct AlignIdColReader
{
ColumnReader dad;
/* state for id range:
first = slot [ 0 ] of map
row_id = needs to match request - we only accept serial scans
next_id = next id to fetch from "ids"
last_excl = end of "ids" */
int64_t first, row_id, next_id, last_excl;
/* sequence for handing out new ids */
int64_t new_id;
/* reader onto our join index column */
ColumnReader *ids;
/* reader onto alignment table
to retrieve GLOBAL_REF_START + REF_LEN */
ColumnReader *poslen;
/* bi-directional index for writing
new=>old and old=>new mappings */
MapFile *idx;
/* buffer for sorted data */
union
{
int64_t *ids;
IdPosLen *id_poslen;
IdxMapping *id_map;
} u;
size_t max_elems;
size_t num_elems;
size_t cur_elem;
/* buffer for id row */
int64_t *row;
size_t max_row_len;
/* chunk-size */
size_t chunk_size;
/* whether we have all ids or not */
bool entire_table;
};
static
void AlignIdColReaderDestroy ( AlignIdColReader *self, const ctx_t *ctx )
{
if ( self -> ids != NULL )
{
FUNC_ENTRY ( ctx );
STATUS ( 4, "destroying align-column reader '%s'", ColumnReaderFullSpec ( self -> ids, ctx ) );
/* tear everything down */
MapFileRelease ( self -> idx, ctx );
self -> idx = NULL;
ColumnReaderRelease ( self -> poslen, ctx );
self -> poslen = NULL;
ColumnReaderRelease ( self -> ids, ctx );
self -> ids = NULL;
if ( self -> u . id_poslen != NULL )
{
MemFree ( ctx, self -> u . id_poslen, sizeof * self -> u . id_poslen * self -> max_elems );
self -> u . id_poslen = NULL;
}
if ( self -> row != NULL )
{
MemFree ( ctx, self -> row, sizeof self -> row [ 0 ] * self -> max_row_len );
self -> row = NULL;
}
}
}
static
void AlignIdColReaderWhack ( AlignIdColReader *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
/* tear down self */
AlignIdColReaderDestroy ( self, ctx );
/* tear down super-class */
ColumnReaderDestroy ( & self -> dad, ctx );
/* gone */
MemFree ( ctx, self, sizeof * self );
}
static
const char *AlignIdColReaderFullSpec ( const AlignIdColReader *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
return ColumnReaderFullSpec ( self -> ids, ctx );
}
static
uint64_t AlignIdColReaderIdRange ( const AlignIdColReader *self, const ctx_t *ctx, int64_t *opt_first )
{
FUNC_ENTRY ( ctx );
return ColumnReaderIdRange ( self -> ids, ctx, opt_first );
}
static
void AlignIdColReaderFlushToIdx ( AlignIdColReader *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
if ( self -> idx != NULL )
{
const Tool *tp = ctx -> caps -> tool;
/* write new=>old ids */
STATUS ( 3, "%s new=>old id map", tp -> write_new_to_old ? "writing" : "setting" );
ON_FAIL ( MapFileSetNewToOld ( self -> idx, ctx, self -> u . id_map, self -> num_elems ) )
{
ANNOTATE ( "failed to record new to old id mappings for '%s'", ColumnReaderFullSpec ( self -> ids, ctx ) );
return;
}
if ( tp -> sort_before_old2new )
{
/* sort by old ids */
STATUS ( 3, "sorting id-map by old-id" );
#if USE_OLD_KSORT
ksort ( self -> u . id_map, self -> num_elems, sizeof self -> u . id_map [ 0 ], IdxMappingCmpOld, ( void* ) ctx );
#else
IdxMappingSortOld ( self -> u . id_map, ctx, self -> num_elems );
#endif
}
/* write old=>new ids */
STATUS ( 3, "writing old=>new id map" );
ON_FAIL ( MapFileSetOldToNew ( self -> idx, ctx, self -> u . id_map, self -> num_elems ) )
{
ANNOTATE ( "failed to record old to new id mappings for '%s'", ColumnReaderFullSpec ( self -> ids, ctx ) );
return;
}
STATUS ( 3, "done writing id maps" );
}
/* empty buffer */
self -> first = self -> next_id;
}
static
void AlignIdColReaderPreCopy ( AlignIdColReader *self, const ctx_t *ctx )
{
/* TBD - a good place to allocate memory */
}
static
void AlignIdColReaderPostCopy ( AlignIdColReader *self, const ctx_t *ctx )
{
FUNC_ENTRY ( ctx );
/* called after a single copy
assumes that entire row-range of table has been copied */
/* tear down self */
AlignIdColReaderDestroy ( self, ctx );
}
static
const void *AlignIdColReaderRead ( AlignIdColReader *self, const ctx_t *ctx,
int64_t row_id, uint32_t *elem_bits, uint32_t *boff, uint32_t *row_len )
{
FUNC_ENTRY ( ctx );
rc_t rc;
const void *base;
uint32_t num_read32;
size_t i, num_read;
/* handle bad parameters */
uint32_t dummy [ 3 ];
if ( elem_bits == NULL )
elem_bits = & dummy [ 0 ];
if ( boff == NULL )
boff = & dummy [ 1 ];
if ( row_len == NULL )
row_len = & dummy [ 2 ];
/* THERE ARE three stages to this method:
1a. detect need to allocate id map
1b. detect need to flush to index
2. detect need to refresh id map
3. respond to read request
*/
if ( row_id != self -> row_id )
{
/* error condition */
rc = RC ( rcExe, rcCursor, rcReading, rcParam, rcIncorrect );
INTERNAL_ERROR ( rc, "AlignIdColReader only supports serial access" );
return NULL;
}
/* stage 1 - allocate or flush */
if ( self -> u . ids == NULL && ! self -> entire_table )
{
/* limit ids to actual count */
uint64_t num_ids = MapFileCount ( self -> idx, ctx );
self -> max_elems = ctx -> caps -> tool -> max_ref_idx_ids;
if ( ( uint64_t ) self -> max_elems > num_ids )
self -> max_elems = ( size_t ) num_ids;
/* allocate the buffer */
do
{
CLEAR ();
TRY ( self -> u . id_poslen = MemAlloc ( ctx, sizeof self -> u . id_poslen [ 0 ] * self -> max_elems, false ) )
{
STATUS ( 4, "allocated map buffer with %,zu elements", self -> max_elems );
break;
}
self -> max_elems >>= 1;
}
while ( self -> max_elems >= 1024 * 1024 );
if ( FAILED () )
{
ANNOTATE ( "failed to allocate id buffer" );
return NULL;
}
/* notice if we have the entire table */
if ( ( uint64_t ) self -> max_elems == num_ids )
self -> entire_table = true;
/* allocate a row buffer */
self -> max_row_len = 8 * 1024;
ON_FAIL ( self -> row = MemAlloc ( ctx, sizeof self -> row [ 8 ] * self -> max_row_len, false ) )
{
ANNOTATE ( "failed to allocate row buffer" );
return NULL;
}
assert ( self -> first == self -> next_id );
assert ( self -> first == row_id );
}
else if ( row_id == self -> next_id && self -> first < row_id )
{
ON_FAIL ( AlignIdColReaderFlushToIdx ( self, ctx ) )
return NULL;
}
/* stage 2 - refresh */
if ( self -> first == self -> next_id )
{
/* if there are no more rows, return NULL */
if ( self -> next_id == self -> last_excl )
{
STATUS ( 3, "done reading '%s'", ColumnReaderFullSpec ( self -> ids, ctx ) );
return NULL;
}
self -> cur_elem = 0;
/* if the entire table will be read into memory,
there is no point in reading/sorting the ids */
if ( self -> entire_table )
{
STATUS ( 3, "auto-generating %,zu ids for '%s'", self -> max_elems, ColumnReaderFullSpec ( self -> ids, ctx ) );
for ( i = 0; i < self -> max_elems; ++ i )
{
self -> u . id_poslen [ i ] . id = self -> first + i;
#if _DEBUGGING
self -> u . id_poslen [ i ] . poslen = 0;
#endif
}
self -> num_elems = self -> max_elems;
self -> next_id = self -> last_excl;
}
else
{
/* read up to max_elems into id array */
STATUS ( 3, "reading ids from '%s'", ColumnReaderFullSpec ( self -> ids, ctx ) );
for ( self -> num_elems = 0; self -> next_id < self -> last_excl; self -> num_elems += num_read, ++ self -> next_id )
{
/* read a row of ids */
ON_FAIL ( base = ColumnReaderRead ( self -> ids, ctx, self -> next_id, elem_bits, boff, & num_read32 ) )
{
ANNOTATE ( "failed to read id column" );
return NULL;
}
/* we expect empty rows */
num_read = num_read32;
if ( num_read == 0 )
continue;
assert ( * elem_bits == sizeof self -> u . ids [ 0 ] * 8 );
assert ( * boff == 0 );
/* detect when buffer is full */
if ( self -> num_elems + num_read > self -> max_elems )
{
/* if we've read at least one row, then we're okay */
if ( self -> first < self -> next_id )
break;
/* error condition - buffer was too small to read a single row */
rc = RC ( rcExe, rcCursor, rcReading, rcBuffer, rcInsufficient );
ERROR ( rc, "allocated buffer was too small ( %zu elems ) to read a single row ( id %ld, row-len %zu )",
self -> max_elems, self -> next_id, num_read );
return NULL;
}
/* bring them in */
memmove ( & self -> u . ids [ self -> num_elems ], base, num_read * sizeof self -> u . ids [ 0 ] );
}
/* sort to produce sparse but ordered list */
STATUS ( 3, "sorting %,zu 64-bit ids", self -> num_elems );
#if USE_OLD_KSORT
ksort ( self -> u . ids, self -> num_elems, sizeof self -> u . ids [ 0 ], cmp_int64_t, ( void* ) ctx );
#else
ksort_int64_t ( self -> u . ids, self -> num_elems );
#endif
/* transform from ids to id_poslen */
STATUS ( 3, "expanding ids to ( id, position, len ) tuples" );
for ( i = self -> num_elems; i > 1 ; )
{
-- i;
self -> u . id_poslen [ i ] . id = self -> u . ids [ i ];
}
}
/* read num_elems from poslen */
STATUS ( 3, "reading ( position, len ) pairs from '%s'", ColumnReaderFullSpec ( self -> poslen, ctx ) );
for ( i = 0; i < self -> num_elems; ++ i )
{
ON_FAIL ( base = ColumnReaderRead ( self -> poslen, ctx, self -> u . id_poslen [ i ] . id, elem_bits, boff, & num_read32 ) )
{
ANNOTATE ( "failed to read global ref-start from alignment table" );
return NULL;
}
num_read = num_read32;
assert ( * elem_bits == sizeof self -> u . id_poslen [ 0 ] . poslen * 8 );
assert ( * boff == 0 );
assert ( num_read == 1 );
self -> u . id_poslen [ i ] . poslen = * ( uint64_t* ) base;
}
/* sort by poslen */
STATUS ( 3, "sorting ( id, position, len ) tuples on position, len DESC" );
#if USE_OLD_KSORT
ksort ( self -> u . id_poslen, self -> num_elems, sizeof self -> u . id_poslen [ 0 ], IdPosLenCmpPos, ( void* ) ctx );
#else
ksort_IdPosLen_pos ( self -> u . id_poslen, self -> num_elems );
#endif
/* write poslen to temp column */
STATUS ( 3, "writing ( position, len ) to temp column" );
ON_FAIL ( MapFileSetPoslen ( self -> idx, ctx, self -> u . id_map, self -> num_elems ) )
{
ANNOTATE ( "failed to write temporary poslen column for '%s'", ColumnReaderFullSpec ( self -> ids, ctx ) );
return NULL;
}
STATUS ( 3, "done writing ( position, len )" );
}
/* stage 3 - build a row */
for ( num_read = ( size_t ) ( self -> num_elems - self -> cur_elem ), i = 0; i < num_read; ++ i )
{
/* whatever the current element is, it must belong to this row */
uint64_t pos = decode_pos_len ( self -> u . id_poslen [ self -> cur_elem + i ] . poslen );
int64_t cur_row_id = global_to_row_id ( pos, self -> chunk_size );
if ( cur_row_id != row_id )
{
num_read = i;
break;
}
}
/* "num_read" now has the number of elements in this row */
if ( num_read > self -> max_row_len )
{
STATUS ( 4, "reallocating row buffer for row-length %,zu", num_read );
/* realloc the row buffer */
MemFree ( ctx, self -> row, self -> max_row_len * sizeof self -> row [ 0 ] );
self -> max_row_len = ( num_read + 4095 ) & ~ ( size_t ) 4095;
ON_FAIL ( self -> row = MemAlloc ( ctx, sizeof self -> row [ 0 ] * self -> max_row_len, false ) )
{
ANNOTATE ( "failed to reallocate row buffer" );
return NULL;
}
}
/* build the row, assigning new ids */
for ( i = 0; i < num_read; ++ i )
{
self -> row [ i ] = ++ self -> new_id;
self -> u . id_map [ self -> cur_elem + i ] . new_id = self -> new_id;
}
/* advance row_id */
self -> cur_elem += num_read;
if ( ++ self -> row_id == self -> last_excl )
{
/* if this was the last row, flush index */
ON_FAIL ( AlignIdColReaderFlushToIdx ( self, ctx ) )
return NULL;
if ( ctx -> caps -> tool -> idx_consistency_check && self -> idx != NULL )
{
ON_FAIL ( MapFileConsistencyCheck ( self -> idx, ctx ) )
return NULL;
}
}
/* return row */
* elem_bits = sizeof self -> row [ 0 ] * 8;
* boff = 0;
* row_len = num_read;
return self -> row;
}
static ColumnReader_vt AlignIdColReader_vt =
{
AlignIdColReaderWhack,
AlignIdColReaderFullSpec,
AlignIdColReaderIdRange,
AlignIdColReaderPreCopy,
AlignIdColReaderPostCopy,
AlignIdColReaderRead
};
/*--------------------------------------------------------------------------
* RefTblPair
*/
static
size_t RefTblPairGetChunkSize ( TablePair *self, const ctx_t *ctx, const VCursor **cursp )
{
FUNC_ENTRY ( ctx );
rc_t rc;
rc = VTableCreateCursorRead ( self -> stbl, cursp );
if ( rc != 0 )
ERROR ( rc, "failed to create cursor on '%s'", self -> full_spec );
else
{
uint32_t idx;
const VCursor *curs = * cursp;
rc = VCursorAddColumn ( curs, & idx, "MAX_SEQ_LEN" );
if ( rc != 0 )
rc = VCursorAddColumn ( curs, & idx, "CHUNK_SIZE" );
if ( rc != 0 )
ERROR ( rc, "VCursorAddColumn - failed to determine chunk size of '%s'", self -> full_spec );
else
{
rc = VCursorOpen ( curs );
if ( rc != 0 )
ERROR ( rc, "VCursorOpen - failed to determine chunk size of '%s'", self -> full_spec );
else
{
uint32_t row_len, chunk_size;
rc = VCursorReadDirect ( curs, 1, idx,
sizeof chunk_size * 8, & chunk_size, 1, & row_len );
if ( rc != 0 )
ERROR ( rc, "VCursorReadDirect - failed to determine chunk size of '%s'", self -> full_spec );
else if ( row_len != 1 )
{
rc = RC ( rcExe, rcCursor, rcReading, rcData, rcInsufficient );
ERROR ( rc, "VCursorReadDirect - failed to determine chunk size of '%s'", self -> full_spec );
}
else
{
STATUS ( 3, "'%s' chunk size determined to be %u", self -> full_spec, chunk_size );
return chunk_size;
}
}
}
VCursorRelease ( curs );
* cursp = NULL;
}
return 0;
}
/*--------------------------------------------------------------------------
* ColumnReader
* interface to read column in random order
*/
/* MakeAlignIdReader
*/
ColumnReader *TablePairMakeAlignIdReader ( TablePair *self,
const ctx_t *ctx, TablePair *align_tbl, MapFile *idx, const char *colspec )
{
FUNC_ENTRY ( ctx );
size_t chunk_size;
const VCursor *curs;
/* determine chunk size and keep cursor for id reader */
TRY ( chunk_size = RefTblPairGetChunkSize ( self, ctx, & curs ) )
{
ColumnReader *ids;
/* need to create a traditional reader on self */
TRY ( ids = TablePairMakeColumnReader ( self, ctx, curs, colspec, true ) )
{
ColumnReader *poslen;
/* need to create a poslen reader on align_tbl */
TRY ( poslen = TablePairMakeGlobalPosLenReader ( align_tbl, ctx, ( uint32_t ) chunk_size ) )
{
int64_t first;
uint64_t count;
/* need to create a mapfile based on range of poslen */
TRY ( count = ColumnReaderIdRange ( poslen, ctx, & first ) )
{
TRY ( MapFileSetIdRange ( idx, ctx, first, count ) )
{
AlignIdColReader *col;
TRY ( col = MemAlloc ( ctx, sizeof * col, true ) )
{
TRY ( ColumnReaderInit ( & col -> dad, ctx, & AlignIdColReader_vt ) )
{
/* one more point of failure when obtaining the id range */
TRY ( count = ColumnReaderIdRange ( ids, ctx, & first ) )
{
TRY ( col -> idx = MapFileDuplicate ( idx, ctx ) )
{
col -> first = col -> row_id = col -> next_id = first;
col -> last_excl = first + count;
col -> ids = ids;
col -> poslen = poslen;
col -> chunk_size = chunk_size;
col -> entire_table = false;
/* the actual working buffer is allocated upon demand
to avoid occupying space while waiting to execute */
/* douse the cursor here */
VCursorRelease ( curs );
return & col -> dad;
}
}
}
MemFree ( ctx, col, sizeof * col );
}
MapFileRelease ( idx, ctx );
}
}
ColumnReaderRelease ( poslen, ctx );
}
ColumnReaderRelease ( ids, ctx );
}
VCursorRelease ( curs );
}
return NULL;
}
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