static rc_t vdb_fasta_loop_with_name( const p_dump_context ctx, const fastq_ctx * fctx )
{
rc_t rc = 0;
int64_t row_id;
vdn_start( ctx->row_generator );
while ( vdn_next( ctx->row_generator, (uint64_t*)&row_id ) && rc == 0 )
{
rc = Quitting();
if ( rc == 0 )
{
uint32_t elem_bits, boff, row_len, name_len;
const char * data;
const char * name;
rc = VCursorCellDataDirect( fctx->cursor, row_id, fctx->idx_name, &elem_bits,
(const void**)&name, &boff, &name_len );
if ( rc != 0 )
vdb_fastq_row_error( "VCursorCellDataDirect( row#$(row_nr), NAME ) failed", rc, row_id );
else
{
rc = VCursorCellDataDirect( fctx->cursor, row_id, fctx->idx_read, &elem_bits,
(const void**)&data, &boff, &row_len );
if ( rc != 0 )
vdb_fastq_row_error( "VCursorCellDataDirect( row#$(row_nr), READ ) failed", rc, row_id );
else
{
uint32_t idx = 0;
int32_t to_print = row_len;
rc = KOutMsg( ">%s.%li %.*s length=%u\n",
fctx->run_name, row_id, name_len, name, row_len );
if ( to_print > ctx->max_line_len )
to_print = ctx->max_line_len;
while ( rc == 0 && to_print > 0 )
{
rc = KOutMsg( "%.*s\n", to_print, &data[ idx ] );
if ( rc == 0 )
{
idx += ctx->max_line_len;
to_print = ( row_len - idx );
if ( to_print > ctx->max_line_len )
to_print = ctx->max_line_len;
}
}
}
}
}
}
return rc;
}
rc_t runChecks(const TestCase& test_case, const VCursor * cursor, uint32_t name_idx, uint32_t name_range_idx)
{
rc_t rc;
int64_t first_id;
uint64_t count_id;
rc = VCursorIdRange( cursor, name_idx, &first_id, &count_id );
if (rc != 0)
{
LOGERR( klogInt, rc, "VCursorIdRange() failed" );
return rc;
}
for (uint64_t row_id = first_id; row_id < first_id + count_id; ++row_id)
{
const char * name = NULL;
uint32_t name_len;
RowRange *row_range;
rc = VCursorCellDataDirect( cursor, row_id, name_idx, NULL, (void const **)&name, NULL, &name_len );
if ( rc != 0 )
return rc;
rc = VCursorParamsSet( ( struct VCursorParams const * )cursor, "QUERY_NAME", "%.*s", name_len, name );
if ( rc != 0 )
return rc;
rc = VCursorCellDataDirect( cursor, row_id, name_range_idx, NULL, (void const **)&row_range, NULL, NULL );
if ( rc != 0 )
return rc;
std::string name_str(name, name_len);
if (test_case.key_ranges.find(name_str) == test_case.key_ranges.end())
{
PLOGMSG( klogInt, (klogErr, "Unexpected name '$(NAME)' in test case '$(TC_NAME)'", "TC_NAME=%s,NAME=%s", test_case_name, name_str.c_str()) );
return 1;
}
RowRange row_range_exp = test_case.key_ranges.find(name_str)->second;
if (row_range->start_id != row_range_exp.start_id || row_range->stop_id != row_range_exp.stop_id)
{
PLOGMSG( klogInt, (klogErr, "Row range for name '$(NAME)' in test case '$(TC_NAME)' does not match. Expected: $(EXP_S)-$(EXP_F), actual: $(ACT_S)-$(ACT_F)",
"TC_NAME=%s,NAME=%s,EXP_S=%ld,EXP_F=%ld,ACT_S=%ld,ACT_F=%ld",
test_case_name, name_str.c_str(), row_range_exp.start_id, row_range_exp.stop_id, row_range->start_id, row_range->stop_id) );
return 1;
}
}
return rc;
}
rc_t read_INSDC_dna_text_ptr( int64_t row_id, const VCursor * cursor, uint32_t idx, const INSDC_dna_text **res, uint32_t *len, const char * hint )
{
rc_t rc;
if ( idx == INVALID_COLUMN )
{
rc = RC( rcExe, rcNoTarg, rcReading, rcItem, rcInvalid );
(void)PLOGERR( klogInt, ( klogInt, rc, "column idx invalid at row#$(tr) . $(hi) ) INSDC_dna_text (ptr)",
"tr=%li,hi=%s", row_id, hint ) );
}
else
{
const INSDC_dna_text * value;
uint32_t elem_bits, boff, row_len;
rc = VCursorCellDataDirect( cursor, row_id, idx, &elem_bits, (const void**)&value, &boff, &row_len );
if ( rc != 0 )
{
(void)PLOGERR( klogInt, ( klogInt, rc, "VCursorCellDataDirect( row#$(tr) . idx#$(ti) . $(hi) ) INSDC_dna_text (ptr) failed",
"tr=%li,ti=%u,hi=%s", row_id, idx, hint ) );
}
else
{
if ( row_len > 0 )
*res = value;
if ( len != NULL )
*len = row_len;
}
}
return rc;
}
rc_t read_uint8( int64_t row_id, const VCursor * cursor, uint32_t idx, uint8_t *res, uint8_t dflt, const char * hint )
{
rc_t rc;
if ( idx == INVALID_COLUMN )
{
rc = RC( rcExe, rcNoTarg, rcReading, rcItem, rcInvalid );
(void)PLOGERR( klogInt, ( klogInt, rc, "column idx invalid at row#$(tr) . $(hi) ) uint8",
"tr=%li,hi=%s", row_id, hint ) );
}
else
{
const uint8_t * value;
uint32_t elem_bits, boff, row_len;
rc = VCursorCellDataDirect( cursor, row_id, idx, &elem_bits, (const void**)&value, &boff, &row_len );
if ( rc != 0 )
{
(void)PLOGERR( klogInt, ( klogInt, rc, "VCursorCellDataDirect( row#$(tr) . idx#$(ti) . $(hi) ) char_ptr failed",
"tr=%li,ti=%u,hi=%s", row_id, idx, hint ) );
}
else
{
*res = ( row_len > 0 ) ? *value : dflt;
}
}
return rc;
}
static const char * get_platform( const VTable * tab )
{
const char * res = PT_NONE;
const VCursor * cur;
rc_t rc = VTableCreateCursorRead( tab, &cur );
if ( rc == 0 )
{
uint32_t idx;
rc = VCursorAddColumn( cur, &idx, "PLATFORM" );
if ( rc == 0 )
{
rc = VCursorOpen( cur );
if ( rc == 0 )
{
const uint8_t * pf;
rc = VCursorCellDataDirect( cur, 1, idx, NULL, (const void**)&pf, NULL, NULL );
if ( rc == 0 )
{
res = vdcd_get_platform_txt( *pf );
}
}
}
VCursorRelease( cur );
}
return res;
}
static rc_t get_idx_and_read( struct VCursor const *curs,
const char * name,
int64_t row_id,
const void ** base,
uint32_t * len )
{
uint32_t column_idx;
rc_t rc = VCursorGetColumnIdx ( curs, &column_idx, name );
if ( rc != 0 )
LOGERR( klogInt, rc, "VCursorGetColumnIdx() failed" );
else
{
uint32_t elem_bits, boff, len_intern;
const void * ptr;
rc = VCursorCellDataDirect ( curs, row_id, column_idx,
&elem_bits, &ptr, &boff, &len_intern );
if ( rc != 0 )
LOGERR( klogInt, rc, "VCursorCellDataDirect() failed" );
else
{
assert( boff == 0 );
if ( len != NULL ) *len = len_intern;
if ( base != NULL ) *base = ptr;
}
}
return rc;
}
static void get_string_cell( char * buffer, size_t buffer_size, const VTable * tab, int64_t row, const char * column )
{
if ( has_col( tab, column ) )
{
const VCursor * cur;
rc_t rc = VTableCreateCursorRead( tab, &cur );
if ( rc == 0 )
{
uint32_t idx;
rc = VCursorAddColumn( cur, &idx, column );
if ( rc == 0 )
{
rc = VCursorOpen( cur );
if ( rc == 0 )
{
const char * src;
uint32_t row_len;
rc = VCursorCellDataDirect( cur, row, idx, NULL, (const void**)&src, NULL, &row_len );
if ( rc == 0 )
{
size_t num_writ;
string_printf( buffer, buffer_size, &num_writ, "%.*s", row_len, src );
}
}
}
VCursorRelease( cur );
}
}
}
static rc_t cigar_loop( const VCursor *cur,
uint32_t cigar_idx,
int64_t first,
uint64_t count,
uint32_t min_len )
{
rc_t rc = 0;
int64_t row_id, last_row = ( first + count );
rna_splice_candidates candidates;
for ( row_id = first; ( row_id < last_row ) && ( rc == 0 ) && ( Quitting() == 0 ); row_id++ )
{
const char * cigar;
uint32_t row_len;
rc = VCursorCellDataDirect ( cur, row_id, cigar_idx, NULL, ( const void ** )&cigar, NULL, &row_len );
if ( rc == 0 )
{
candidates.count = 0;
candidates.fwd_matched = 0;
candidates.rev_matched = 0;
rc = discover_rna_splicing_candidates( row_len, cigar, min_len, &candidates );
if ( rc == 0 && candidates.count > 0 )
{
rc = KOutMsg( "%d rna-splice-candidates at row #%ld : %.*s\n", candidates.count, row_id, row_len, cigar );
}
}
}
return rc;
}
static rc_t vdb_fastq_loop_with_name( const p_dump_context ctx, const fastq_ctx * fctx )
{
rc_t rc = 0;
int64_t row_id;
vdn_start( ctx->row_generator );
while ( vdn_next( ctx->row_generator, (uint64_t*)&row_id ) && rc == 0 )
{
rc = Quitting();
if ( rc == 0 )
{
uint32_t elem_bits, boff, row_len, name_len;
const char * data;
const char * name;
rc = VCursorCellDataDirect( fctx->cursor, row_id, fctx->idx_name, &elem_bits,
(const void**)&name, &boff, &name_len );
if ( rc != 0 )
vdb_fastq_row_error( "VCursorCellDataDirect( row#$(row_nr), NAME ) failed", rc, row_id );
else
{
rc = VCursorCellDataDirect( fctx->cursor, row_id, fctx->idx_read, &elem_bits,
(const void**)&data, &boff, &row_len );
if ( rc != 0 )
vdb_fastq_row_error( "VCursorCellDataDirect( row#$(row_nr), READ ) failed", rc, row_id );
else
{
rc = KOutMsg( "@%s.%li %.*s length=%u\n%.*s\n",
fctx->run_name, row_id, name_len, name, row_len, row_len, data );
if ( rc == 0 )
{
rc = VCursorCellDataDirect( fctx->cursor, row_id, fctx->idx_qual, &elem_bits,
(const void**)&data, &boff, &row_len );
if ( rc != 0 )
vdb_fastq_row_error( "VCursorCellDataDirect( row#$(row_nr), QUALITY ) failed", rc, row_id );
else
rc = KOutMsg( "+%s.%li %.*s length=%u\n%.*s\n",
fctx->run_name, row_id, name_len, name, row_len, row_len, data );
}
}
}
}
}
return rc;
}
static
rc_t RefPosMake ( RefPos **objp, const VTable *tbl, const VCursor *native_curs )
{
rc_t rc;
/* create the object */
RefPos *obj = malloc ( sizeof * obj );
if ( obj == NULL ) {
rc = RC ( rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted );
} else {
obj->curs=NULL;
BSTreeInit(&obj->tr_range);
/* open the reference table cursor*/
if( (rc = AlignRefTableCursor(tbl, native_curs, &obj->curs, NULL)) == 0 ) {
uint32_t itmp;
if( (rc = VCursorAddColumn(obj->curs, &itmp, "(U32)MAX_SEQ_LEN")) == 0 || GetRCState(rc) == rcExists) {
const void *base;
uint32_t row_len;
rc = VCursorCellDataDirect(obj->curs, 1, itmp, NULL, &base, NULL, &row_len);
if(rc == 0) {
assert(row_len == 1);
memcpy(&obj->max_seq_len, base, 4);
}
}
if( GetRCObject(rc) == rcColumn && GetRCState(rc) == rcNotFound ) {
/*** no MAX_SEQ_LEN means that REF_POS==REF_START **/
VCursorRelease(obj->curs);
obj->curs = NULL;
obj->max_seq_len = 0;
obj->name_range_idx = 0;
obj->name_idx = 0;
rc = 0;
} else if( rc == 0 ) {
/* add columns to cursor */
rc = VCursorAddColumn(obj->curs, &obj->name_idx, "(utf8)NAME");
if(rc == 0 || GetRCState(rc) == rcExists)
rc = VCursorAddColumn(obj->curs, &obj->name_range_idx, "NAME_RANGE");
if(GetRCState(rc) == rcExists)
rc = 0;
}
}
if( rc == 0 ) {
*objp = obj;
} else {
VCursorRelease(obj->curs);
free(obj);
}
}
return rc;
}
rc_t read_cell( const VCursor *my_cursor,
int64_t row_id,
col *column,
const char * name )
{
rc_t rc = VCursorCellDataDirect ( my_cursor, row_id,
column->idx, &column->elem_bits, &column->base,
&column->bit_offset, &column->row_len );
if ( rc != 0 )
PLOGERR( klogInt, ( klogInt, rc,
"VCursorCellDataDirect($(name),$(rowid)) failed",
"name=%s,rowid=%lu", name, row_id ) );
return rc;
}
static rc_t report_ref_row( const VCursor *cur, report_row_ctx * row_ctx )
{
rc_t rc = 0;
uint32_t elem_bits, boff, prim_count, sec_count;
const void *base;
rc = VCursorCellDataDirect ( cur, row_ctx->row_id, row_ctx->prim_idx, &elem_bits, &base, &boff, &prim_count );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot read colum >PRIMARY_ALIGNMENT_IDS<" );
}
else
{
rc = VCursorCellDataDirect ( cur, row_ctx->row_id, row_ctx->sec_idx, &elem_bits, &base, &boff, &sec_count );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot read colum >SECONDARY_ALIGNMENT_IDS<" );
}
else if ( prim_count > 0 || sec_count > 0 )
{
rc = KOutMsg( "ROW[ %,lu ]: PRIM:%,u SEC:%,u\n", row_ctx->row_id, prim_count, sec_count );
}
}
return rc;
}
static
rc_t LocalRefIDMake ( LocalRefID **objp, const VTable *tbl, const VCursor *native_curs)
{
rc_t rc;
/* create the object */
LocalRefID *obj = malloc ( sizeof * obj );
if ( obj == NULL )
{
rc = RC( rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted );
}
else
{
const VCursor *curs=NULL;
/* open the reference table cursor*/
rc = AlignRefTableCursor( tbl, native_curs, &curs, NULL );
if ( rc == 0 )
{
uint32_t itmp;
rc = VCursorAddColumn( curs, &itmp, "(U32)MAX_SEQ_LEN" );
if ( rc == 0 || GetRCState( rc ) == rcExists )
{
const void *base;
uint32_t row_len;
rc = VCursorCellDataDirect( curs, 1, itmp, NULL, &base, NULL, &row_len );
if ( rc == 0 )
{
assert( row_len == 1 );
memmove( &obj->max_seq_len, base, 4 );
}
}
if ( ( GetRCObject( rc ) == ( enum RCObject )rcColumn ) && ( GetRCState( rc ) == rcNotFound ) )
{
obj->max_seq_len = 0;
rc = 0;
}
VCursorRelease( curs );
if ( rc == 0 )
{
*objp = obj;
return 0;
}
}
free ( obj );
}
return rc;
}
/*
function ascii NCBI:align:ref_seq_id ( I64 ref_id );
*/
static
rc_t CC align_ref_seq_id ( void *data, const VXformInfo *info,
int64_t row_id, VRowResult *rslt, uint32_t argc, const VRowData argv[] )
{
rc_t rc;
RefSeqID const *self = ( void const * )data;
char const *name = NULL;
uint32_t name_len;
/* get start and length of reference segment */
int64_t const *ref_id = argv[REF_ID].u.data.base;
assert( argv[ REF_ID ].u.data.elem_bits == sizeof( *ref_id ) * 8) ;
if ( self->curs == NULL || argv[ REF_ID ].u.data.elem_count == 0 )
{
rslt->elem_count = 0;
return 0;
}
ref_id += argv[ REF_ID] .u.data.first_elem;
SUB_DEBUG( ( "SUB.Rd in 'align_ref_seq_id.c' at #%lu\n", ref_id[ 0 ] ) );
rc = VCursorCellDataDirect( self->curs, ref_id[ 0 ], self->seqID_idx, NULL, (void const **)&name, NULL, &name_len );
if ( GetRCState( rc ) == rcNotFound && GetRCObject( rc ) == rcRow )
{
name = "";
name_len = 0;
}
else if ( rc != 0 )
{
return rc;
}
rc = KDataBufferCast( rslt->data, rslt->data, sizeof( name[ 0 ] ) * 8, true );
if ( rc != 0 )
return rc;
rc = KDataBufferResize( rslt->data, name_len );
if ( rc != 0 )
return rc;
memmove( rslt->data->base, name, sizeof( name[ 0 ] ) * name_len );
rslt->elem_count = name_len;
rslt->elem_bits = sizeof( name[ 0 ] ) * 8;
return rc;
}
/* Read - PRIVATE
* column message sent via table
*/
rc_t SRATableRead ( const SRATable *self, spotid_t id, uint32_t idx,
const void **base, bitsz_t *offset, bitsz_t *size )
{
rc_t rc;
if ( base == NULL || offset == NULL || size == NULL )
rc = RC ( rcSRA, rcColumn, rcReading, rcParam, rcNull );
else if ( self == NULL )
rc = RC ( rcSRA, rcTable, rcAccessing, rcSelf, rcNull );
else
{
rc = 0;
/* open cursor */
if ( ! self -> curs_open )
{
rc = VCursorOpen(self->curs);
if ( rc == 0 )
((SRATable *)self)->curs_open = true;
}
if ( rc == 0 )
{
uint32_t elem_bits, elem_off, elem_cnt;
rc = VCursorCellDataDirect ( self -> curs, id, idx,
& elem_bits, base, & elem_off, & elem_cnt );
if ( rc == 0 )
{
* offset = elem_off * elem_bits;
* size = elem_cnt * elem_bits;
return 0;
} else if( UIError(rc, NULL, self->vtbl) ) {
UITableLOGError(rc, self->vtbl, true);
}
}
}
if ( base != NULL )
* base = NULL;
if ( offset != NULL )
* offset = 0;
if ( size != NULL )
* size = 0;
return rc;
}
static
rc_t fetch_all_rows(const VCursor *curs, unsigned ncol, const uint32_t cid[/* ncol */])
{
int64_t start;
int64_t stop;
int64_t row;
unsigned i;
rc_t rc;
for (i = 0; i != ncol; ++i) {
int64_t cstart;
uint64_t ccount;
rc = VCursorIdRange(curs, cid[i], &cstart, &ccount);
if (rc)
return rc;
if (i == 0) {
start = cstart;
stop = cstart + ccount;
}
else {
if (start > cstart)
start = cstart;
if (stop < cstart + ccount)
stop = cstart + ccount;
}
}
for (row = start; row != stop; ++row) {
for (i = 0; i != ncol; ++i) {
uint32_t elem_bits;
const void *base;
uint32_t offset;
uint32_t length;
rc = VCursorCellDataDirect(curs, row, cid[i], &elem_bits,
&base, &offset, &length);
if (rc)
return rc;
}
}
return 0;
}
static bool rr_store_alignment( rr_store * rr, int64_t align_id, const VCursor * curs, uint32_t read_idx )
{
bool res = false;
const INSDC_4na_bin * read = NULL;
uint32_t read_len;
rc_t rc = VCursorCellDataDirect( curs, align_id, read_idx, NULL, ( const void** ) &read, NULL, &read_len );
if ( rc == 0 )
{
rr_entry * entry;
res = rr_entry_make ( &entry, read, read_len );
if ( res )
{
uint64_t key = ( uint64_t ) align_id;
res = ( KVectorSetPtr ( rr -> v, key, entry ) == 0 );
if ( !res )
rr_entry_release( key, entry, NULL );
}
}
return res;
}
static rc_t read_base_and_len( struct VCursor const *curs,
uint32_t column_idx,
int64_t row_id,
const void ** base,
uint32_t * len )
{
uint32_t elem_bits, boff, len_intern;
const void * ptr;
rc_t rc = VCursorCellDataDirect ( curs, row_id, column_idx, &elem_bits, &ptr, &boff, &len_intern );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "VCursorCellDataDirect() failed" );
}
else
{
if ( len != NULL ) *len = len_intern;
if ( base != NULL ) *base = ptr;
}
return rc;
}
static rc_t cg_dump_row( cg_dump_opts * opts, cg_dump_ctx * cg_ctx, uint64_t row_id )
{
uint32_t elem_bits, boff, sg_len;
const char * sg;
rc_t rc = VCursorCellDataDirect( cg_ctx->seq_cur, row_id, cg_ctx->seq_sg_idx, &elem_bits, (const void**)&sg, &boff, &sg_len );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot read spot-group in row #$(row_id)", "row_id=%lu", row_id ) );
}
else
{
String spot_group;
lane * sg_lane;
StringInit( &spot_group, sg, sg_len, sg_len );
sg_lane = ( lane * )BSTreeFind ( &cg_ctx->lanes, &spot_group, String_lane_cmp );
if ( sg_lane == NULL )
{
/* KOutMsg( "row %lu (%S) not found, create it\n", row_id, &spot_group ); */
rc = make_lane( opts, cg_ctx->lookup, cg_ctx->out_dir, &spot_group, &sg_lane );
if ( rc == 0 )
{
rc = BSTreeInsert ( &cg_ctx->lanes, ( BSTNode * )sg_lane, lane_lane_cmp );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot insert new lane" );
whack_lane( sg_lane );
}
}
}
else
{
/* KOutMsg( "row %lu (%S) found, use it\n", row_id, &spot_group ); */
}
if ( rc == 0 )
{
cg_dump_write_spot( opts, cg_ctx, row_id, sg_lane ); /* <================== */
}
}
return rc;
}
/*
function ascii NCBI:align:ref_name ( I64 ref_id );
*/
static
rc_t CC align_ref_name ( void *data, const VXformInfo *info,
int64_t row_id, VRowResult *rslt, uint32_t argc, const VRowData argv[] )
{
rc_t rc;
RefName const *self = (void const *)data;
char const *name = NULL;
uint32_t name_len;
/* get start and length of reference segment */
int64_t const *ref_id = argv[REF_ID].u.data.base;
if (argv[REF_ID].u.data.elem_count == 0)
rc = RC(rcAlign, rcFunction, rcExecuting, rcRow, rcNotFound);
else {
assert(argv[REF_ID].u.data.elem_bits == sizeof(*ref_id) * 8);
ref_id += argv[REF_ID].u.data.first_elem;
rc = VCursorCellDataDirect(self->curs, ref_id[0], self->name_idx, NULL, (void const **)&name, NULL, &name_len);
}
if (GetRCState(rc) == rcNotFound && GetRCObject(rc) == rcRow) {
name = "";
name_len = 0;
}
else if (rc) return rc;
rc = KDataBufferCast(rslt->data, rslt->data, sizeof(name[0]) * 8, true);
if (rc) return rc;
rc = KDataBufferResize(rslt->data, name_len);
if (rc) return rc;
memcpy(rslt->data->base, name, sizeof(name[0]) * name_len);
rslt->elem_count = name_len;
rslt->elem_bits = sizeof(name[0]) * 8;
return rc;
}
static rc_t read_from_ref_node( ref_node * node,
int32_t ref_offset, uint32_t ref_len,
uint8_t *exclude_vector,
uint32_t *active )
{
rc_t rc = 0;
uint64_t row_id = ( ref_offset / node->read_len ) + 1;
uint8_t *dst = exclude_vector;
uint32_t remaining = ref_len;
uint32_t src_ofs = ref_offset % node->read_len;
while ( remaining > 0 && rc == 0 )
{
uint32_t elem_bits, boff, rlen;
const uint8_t *src;
rc = VCursorCellDataDirect ( node->cur, row_id, node->hits_idx,
&elem_bits, (const void**)&src, &boff, &rlen );
if ( rc != 0 )
{
PLOGERR( klogInt, ( klogInt, rc,
"error to read $(col_name) from 1st row in table $(db_name).$(tab_name)",
"col_name=%s,db_name=%S,tab_name=%s",
HITS_COLUMN, node->name, HITMAP_TAB ) );
}
else
{
if ( src_ofs >= rlen )
{
rc = RC( rcApp, rcNoTarg, rcReading, rcParam, rcInvalid );
PLOGERR( klogInt, ( klogInt, rc,
"error: try to read more data than are in var-loc $(tab_name)",
"tab_name=%S", node->name ) );
}
else
{
uint32_t to_copy = ( rlen - src_ofs );
if ( to_copy > remaining )
{
to_copy = remaining;
}
src += src_ofs;
memmove( dst, src, to_copy );
dst += to_copy;
remaining -= to_copy;
src_ofs = 0;
row_id ++;
node->bytes_requested += to_copy;
}
}
}
*active = 0;
if ( rc == 0 )
{
for ( src_ofs = 0; src_ofs < ref_len; ++src_ofs )
{
if ( exclude_vector[ src_ofs ] > 0 )
{
( *active )++;
}
}
}
return rc;
}
bool nextPileup (
PileupIteratorState* pileup_state,
VCursor const* cursor_ref, VCursor const* cursor_pa,
char const* const* column_names_ref, uint32_t* column_index_ref, size_t column_count_ref,
char const* const* column_names_pa, uint32_t* column_index_pa, size_t column_count_pa,
char* error_buf,
size_t error_buf_size
)
{
int64_t ref_row_id; /* current row_id */
int64_t prev_ref_row_id;
uint64_t ref_pos = pileup_state->ref_pos;
rc_t rc;
/* TODO: check the case when slice_end is beyond the reference end*/
if ( pileup_state->slice_length && pileup_state->ref_pos == pileup_state->slice_start + pileup_state->slice_length )
{
error_buf[0] = '\0'; /* indicating that no error has occured */
return false;
}
/* drop cached alignments that we will not need anymore */
remove_unneeded_alignments ( pileup_state, ref_pos, error_buf, error_buf_size ); /* it's not an issue but this action is not rolled backed in the case of error below */
/* Check if we moved to the next reference row_id,
if yes - read it and add appropriate alignments to cache
*/
prev_ref_row_id = pileup_state->reference_start_id + ref_pos / pileup_state->max_seq_len;
++ ref_pos;
ref_row_id = pileup_state->reference_start_id + ref_pos / pileup_state->max_seq_len;
if ( ref_row_id != prev_ref_row_id ) /* moved to the next row_id */
{
uint32_t dummy;
uint32_t row_len;
uint32_t seq_start;
#if USE_SINGLE_BLOB_FOR_ALIGNMENT_IDS != 1
int64_t const* alignment_ids;
#endif
char ref_name[ countof (pileup_state->ref_name) ];
/* TODO: consider storing this in pileup_state (don't need to calculate every time)*/
/*slice_start_id = pileup_state->reference_start_id + pileup_state->slice_start/pileup_state->max_seq_len;
slice_end_id = pileup_state->slice_length != 0 ?
pileup_state->reference_start_id + (pileup_state->slice_start + (int64_t)pileup_state->slice_length)/pileup_state->max_seq_len :
(int64_t)pileup_state->total_row_count;*/
if ( ref_row_id < pileup_state->slice_start_id || ref_row_id > pileup_state->slice_end_id )
{
error_buf[0] = '\0'; /* indicating that no error has occured */
return false;
}
rc = VCursorReadDirect ( cursor_ref, ref_row_id, column_index_ref [COL_NAME],
sizeof (ref_name[0]) * 8, ref_name, countof(ref_name), & row_len );
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: VCursorReadDirect(ref) failed with error: 0x%08x (%u) [%R]", rc, rc, rc);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return false;
}
ref_name[ min ( countof(ref_name) - 1, row_len) ] = '\0';
if ( strcmp (ref_name, pileup_state->ref_name) )
{
/*Alignment_Init ( & pileup_state->cache_alignment);
strncpy ( pileup_state->ref_name, ref_name, countof (pileup_state->ref_name) - 1 );
pileup_state->reference_start_id = ref_row_id;*/
error_buf[0] = '\0'; /* indicating that no error has occured */
return false;
}
#if USE_SINGLE_BLOB_FOR_ALIGNMENT_IDS == 1
rc = open_blob_for_current_id ( ref_row_id,
cursor_ref, & pileup_state->blob_alignment_ids,
column_index_ref [COL_PRIMARY_ALIGNMENT_IDS],
error_buf, error_buf_size );
if (rc != 0)
return false;
#endif
/* Read new SEQ_START */
rc = VCursorReadDirect ( cursor_ref, ref_row_id,
column_index_ref [COL_SEQ_START],
sizeof (seq_start) * 8, & seq_start, 1, & row_len );
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: VCursorReadDirect(ref-seq_start) failed with error: 0x%08x (%u) [%R]",
rc, rc, rc);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return false;
}
pileup_state->current_seq_start = seq_start;
/* Read REFERENCE row's PRIMARY_ALIGNMENT_IDS column to iterate through them */
/* elem_bits = sizeof (*pileup_state->alignment_ids) * 8; */
#if USE_SINGLE_BLOB_FOR_ALIGNMENT_IDS == 1
rc = VBlobCellData ( pileup_state->blob_alignment_ids, ref_row_id,
& dummy, & pileup_state->alignment_ids, NULL, & row_len );
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: VBlobCellData(ref-pa_ids) failed with error: 0x%08x (%u) [%R], row_len=%u",
rc, rc, rc, row_len);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return false;
}
pileup_state -> size_alignment_ids = row_len;
#else
rc = VCursorCellDataDirect ( cursor_ref, ref_row_id,
column_index_ref [COL_PRIMARY_ALIGNMENT_IDS],
NULL,
(void const**)(& alignment_ids), 0, & row_len );
/*rc = VCursorReadDirect ( cursor_ref, ref_row_id,
column_index_ref [COL_PRIMARY_ALIGNMENT_IDS],
sizeof (*pileup_state->alignment_ids) * 8,
pileup_state->alignment_ids,
countof (pileup_state->alignment_ids),
& row_len );*/
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: VCursorCellDataDirect(ref-pa_ids) failed with error: 0x%08x (%u) [%R], row_len=%u",
rc, rc, rc, row_len);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return false;
}
rc = PileupIteratorState_SetAlignmentIds ( pileup_state, alignment_ids, row_len );
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: PileupIteratorState_SetAlignmentIds failed with error: 0x%08x (%u), row_len=%u",
rc, rc, row_len);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return rc;
}
#endif
pileup_state->next_alignment_idx = 0;
/*pileup_state->size_alignment_ids = row_len;*/
printf ("Read %lu PRIMARY_ALIGNMENT_IDS for REFERENCE row_id=%lld\n", row_len, ref_row_id);
/* For each PRIMARY_ALIGNMENT_ID in pa_ids: read its start, length and
cache it if it intersects the slice
*/
rc = add_ref_row_to_cache ( pileup_state, cursor_pa, seq_start, ref_pos,
pileup_state->alignment_ids, row_len,
column_names_pa, column_index_pa, column_count_pa,
error_buf, error_buf_size );
if ( rc != 0 )
return false;
/*pileup_state -> seq_start = seq_start;*/
}
else
{
/* read remaining alignment_ids and check if they must be cached */
size_t count = pileup_state->size_alignment_ids - pileup_state->next_alignment_idx;
if (count > 0)
{
rc_t rc = add_ref_row_to_cache ( pileup_state, cursor_pa,
pileup_state->current_seq_start, ref_pos,
& pileup_state->alignment_ids[ pileup_state->next_alignment_idx ],
(uint32_t)count,
column_names_pa, column_index_pa, column_count_pa,
error_buf, error_buf_size );
if ( rc != 0 )
return false;
}
}
++ pileup_state->ref_pos;
return true;
}
static
rc_t build_scaffold_read_impl(self_t const *const self, void *const Dst,
unsigned const components,
INSDC_coord_one const Start[/* components */],
INSDC_coord_len const Length[/* components */],
NCBI_WGS_component_props const Props[/* components */],
int64_t const join[/* components */])
{
INSDC_4na_bin *const dst = Dst;
unsigned i;
unsigned j;
unsigned id;
rc_t rc;
for (rc = 0, id = j = i = 0; rc == 0 && i != components; ++i) {
INSDC_coord_len const length = Length[i];
int const props = Props[i];
if (props < 0) {
/* gap */
memset(dst + j, READ_GAP_VALUE, length);
}
else if (self->curs == NULL) {
memset(dst + j, 15, length);
}
else {
int const type = props & 0x0F;
int const strand = (props & ~(NCBI_WGS_strand_plus | NCBI_WGS_strand_minus)) >> 4;
if (type != 0 || strand == 3)
rc = RC(rcXF, rcFunction, rcExecuting, rcType, rcInvalid);
else {
int64_t const row = join[id++];
uint32_t elem_bits;
uint32_t bit_offset;
uint32_t elem_count;
void const *base;
rc = VCursorCellDataDirect(self->curs, row, self->col_idx,
&elem_bits, &base, &bit_offset,
&elem_count);
assert(bit_offset == 0);
if (rc == 0) {
INSDC_coord_one const start = Start[i] - 1;
if (elem_count < start + length)
rc = RC(rcXF, rcFunction, rcExecuting, rcData, rcInsufficient);
else {
INSDC_4na_bin const *const src = base;
if (strand == 2) {
static INSDC_4na_bin const complement[] = {
/* 0 0000 - 0000*/ 0,
/* 1 0001 - 1000*/ 8,
/* 2 0010 - 0100*/ 4,
/* 3 0011 - 1100*/ 12,
/* 4 0100 - 0010*/ 2,
/* 5 0101 - 1010*/ 10,
/* 6 0110 - 0110*/ 6,
/* 7 0111 - 1110*/ 14,
/* 8 1000 - 0001*/ 1,
/* 9 1001 - 1001*/ 9,
/*10 1010 - 0101*/ 5,
/*11 1011 - 1101*/ 13,
/*12 1100 - 0011*/ 3,
/*13 1101 - 1011*/ 11,
/*14 1110 - 0111*/ 7,
/*15 1111 - 1111*/ 15
};
unsigned k;
unsigned jj;
for (jj = j + length, k = 0; k != length; ++k) {
INSDC_4na_bin const elem = src[start + k];
assert(/* 0 <= elem && */ elem <= 15);
--jj;
dst[jj] = complement[elem];
}
}
else
memcpy(&dst[j], &src[start], length);
}
}
}
}
j += length;
}
return rc;
}
static
rc_t CC seq_restore_read_impl1 ( void *data, const VXformInfo *info, int64_t row_id,
VRowResult *rslt, uint32_t argc, const VRowData argv [] )
{
rc_t rc;
int i;
Read_Restorer *self = data;
INSDC_4na_bin *dst;
INSDC_coord_len len;
uint32_t src_len = (uint32_t)argv[ 0 ].u.data.elem_count;
const INSDC_4na_bin *src = argv[ 0 ].u.data.base;
const uint32_t num_reads = (uint32_t)argv[ 1 ].u.data.elem_count;
const int64_t *align_id = argv[ 1 ].u.data.base;
const INSDC_coord_len *read_len = argv[ 2 ].u.data.base;
const uint8_t *read_type = argv[ 3 ].u.data.base;
bool is_sequential = false;
assert( argv[ 0 ].u.data.elem_bits == 8 );
assert( argv[ 1 ].u.data.elem_bits == 64 );
assert( argv[ 2 ].u.data.elem_bits == sizeof( INSDC_coord_len ) * 8 );
assert( argv[ 2 ].u.data.elem_count == num_reads );
assert( argv[ 3 ].u.data.elem_count == num_reads );
src += argv [ 0 ] . u . data . first_elem;
align_id += argv [ 1 ] . u . data . first_elem;
read_len += argv [ 2 ] . u . data . first_elem;
read_type += argv [ 3 ] . u . data . first_elem;
if ( row_id != self->last_row_id && row_id != self->last_row_id + 1 )
{
self->first_sequential_row_id = row_id;
is_sequential = false;
}
else if ( row_id > self->first_sequential_row_id + 100 )
{
is_sequential = true;
}
self->last_row_id = row_id;
/* is_sequential = false; forcing it to false ... Sept. 16th 2015 to analyze prefetching */
for ( i = 0, len = 0; i < (int)num_reads; i++ )
{
len += read_len[ i ];
}
/* resize output row */
rslt->data->elem_bits = 8;
rc = KDataBufferResize( rslt->data, len );
rslt->elem_count = len;
dst = rslt->data->base;
if ( rc == 0 && len > 0 )
{
if ( len == src_len ) /*** shortcut - all data is local ***/
{
memmove( dst, src, len );
}
else
{
if ( is_sequential &&
( row_id < self->prefetch_start_id || row_id > self->prefetch_stop_id ) )
{ /* do prefetch */
uint32_t num_rows = ( argv[ 1 ].u.data.base_elem_count - argv[ 1 ].u.data.first_elem );
/*
KTimeMs_t ts = KTimeMsStamp();
fprintf( stderr, "\nprefetch row_id #%lu ( start_id #%lu, stop_id #%lu ) num_rows = %d\n", row_id, self->prefetch_start_id, self->prefetch_stop_id, num_rows );
*/
VCursorDataPrefetch( self->curs,
align_id,
self->read_idx,
num_rows,
1,
INT64_MAX,
true );
/*
ts = KTimeMsStamp() - ts;
fprintf( stderr, "prefetch done in %lu ms\n", ts );
*/
self->prefetch_start_id=row_id;
self->prefetch_stop_id =argv[1].blob_stop_id;
}
for( i = 0; i < (int)num_reads && rc == 0; i++ ) /*** checking read by read ***/
{
if ( align_id[ i ] > 0 )
{
const INSDC_4na_bin *r_src;
uint32_t r_src_len;
SUB_DEBUG( ( "SUB.Rd in 'seq-restore-read.c' at #%lu\n", align_id[ i ] ) );
rc = VCursorCellDataDirect( self -> curs, align_id[ i ], self -> read_idx,
NULL, ( const void** ) &r_src, NULL, &r_src_len );
if ( rc == 0 )
{
if ( r_src_len == read_len[ i ] )
{
if ( read_type[ i ] & SRA_READ_TYPE_FORWARD )
{
memmove( dst, r_src, read_len[ i ] );
}
else if ( read_type[ i ] & SRA_READ_TYPE_REVERSE )
{
int j, k;
for( j = 0, k = read_len[ i ] - 1; j < (int)read_len[ i ]; j++, k-- )
{
dst[ j ] = map [ r_src[ k ] & 15 ];
}
}
else
{
rc = RC( rcXF, rcFunction, rcExecuting, rcData, rcInconsistent );
}
}
else
{
rc = RC( rcXF, rcFunction, rcExecuting, rcData, rcInconsistent );
}
}
}
else /*** data is in READ column **/
{
if ( src_len >= read_len[ i ] )
{
memmove( dst, src, read_len[ i ] );
src_len -= read_len[ i ];
src += read_len[ i ];
}
else
{
return RC( rcXF, rcFunction, rcExecuting, rcData, rcInconsistent );
}
}
dst += read_len[ i ];
}
}
}
return rc;
}
/* --------------------------------------------------------------------------------------
argv[ 0 ] ... CMP_READ
argv[ 1 ] ... PRIM_ALIG_ID
argv[ 2 ] ... READ_LEN
argv[ 3 ] ... READ_TYPE
-------------------------------------------------------------------------------------- */
static rc_t CC seq_restore_read_impl2 ( void *data, const VXformInfo *info, int64_t row_id,
VRowResult *rslt, uint32_t argc, const VRowData argv [] )
{
rc_t rc;
Read_Restorer *self = data;
INSDC_4na_bin *dst;
INSDC_coord_len len;
id_list align_ids;
uint32_t i;
uint32_t src_len = (uint32_t)argv[ 0 ] . u . data . elem_count;
const INSDC_4na_bin * src = argv[ 0 ] . u . data.base;
const uint32_t num_reads = (uint32_t)argv[ 1 ]. u . data . elem_count;
const INSDC_coord_len * read_len = argv[ 2 ] . u . data.base;
const uint8_t *read_type = argv[ 3 ] . u . data.base;
int64_t last_row_id = argv[ 1 ] . blob_stop_id;
align_ids.list = ( int64_t * )argv[ 1 ].u.data.base;
align_ids.count = ( uint32_t )( argv[ 1 ].u.data.base_elem_count - argv[ 1 ].u.data.first_elem );
assert( argv[ 0 ].u.data.elem_bits == 8 );
assert( argv[ 1 ].u.data.elem_bits == 64 );
assert( argv[ 2 ].u.data.elem_bits == sizeof( INSDC_coord_len ) * 8 );
assert( argv[ 2 ].u.data.elem_count == num_reads );
assert( argv[ 3 ].u.data.elem_count == num_reads );
src += argv [ 0 ] . u . data . first_elem;
align_ids.list += argv [ 1 ] . u . data . first_elem;
read_len += argv [ 2 ] . u . data . first_elem;
read_type += argv [ 3 ] . u . data . first_elem;
handle_caching( self, &align_ids, row_id, last_row_id );
for ( i = 0, len = 0; i < num_reads; i++ )
len += read_len[ i ];
/* resize output row */
rslt->data->elem_bits = 8;
rc = KDataBufferResize( rslt->data, len );
rslt->elem_count = len;
dst = rslt->data->base;
if ( rc == 0 && len > 0 )
{
if ( len == src_len ) /*** shortcut - all data is local ***/
memmove( dst, src, len );
else
{
rr_entry * ep;
const INSDC_4na_bin * rd;
uint32_t rd_len;
bool found_in_cache;
for ( i = 0; i < num_reads && rc == 0; i++ ) /*** checking read by read ***/
{
int64_t align_id = align_ids.list[ i ];
if ( align_id > 0 )
{
found_in_cache = false;
if ( self -> read_store != NULL )
found_in_cache = rr_get_read ( self -> read_store, align_id, &ep );
if ( found_in_cache )
{
/* we found it in the cache... */
rd = &( ep->read[ 0 ] );
rd_len = ep->read_len;
}
else
{
/* we did not find it in the cache, get it from the alignment-table... */
rc = VCursorCellDataDirect( self -> curs, align_id, self -> read_idx,
NULL, ( const void** ) &rd, NULL, &rd_len );
}
if ( rc == 0 )
{
if ( rd_len == read_len[ i ] )
{
if ( read_type[ i ] & SRA_READ_TYPE_FORWARD )
{
memmove( dst, rd, read_len[ i ] );
}
else if ( read_type[ i ] & SRA_READ_TYPE_REVERSE )
{
int j, k;
for( j = 0, k = read_len[ i ] - 1; j < (int)read_len[ i ]; j++, k-- )
{
dst[ j ] = map [ rd[ k ] & 15 ];
}
}
else
{
rc = RC( rcXF, rcFunction, rcExecuting, rcData, rcInconsistent );
}
}
else
{
rc = RC( rcXF, rcFunction, rcExecuting, rcData, rcInconsistent );
}
}
}
else /*** data is in READ column **/
{
if ( src_len >= read_len[ i ] )
{
memmove( dst, src, read_len[ i ] );
src_len -= read_len[ i ];
src += read_len[ i ];
}
else
{
return RC( rcXF, rcFunction, rcExecuting, rcData, rcInconsistent );
}
}
dst += read_len[ i ];
}
}
}
return rc;
}
static
rc_t build_scaffold_qual_impl(self_t const *const self, void *const Dst,
unsigned const components,
INSDC_coord_one const Start[/* components */],
INSDC_coord_len const Length[/* components */],
NCBI_WGS_component_props const Props[/* components */],
int64_t const join[/* components */])
{
INSDC_quality_phred *const dst = Dst;
unsigned i;
unsigned j;
unsigned id;
rc_t rc;
for (rc = 0, id = j = i = 0; rc == 0 && i != components; ++i) {
INSDC_coord_len const length = Length[i];
int const props = Props[i];
if (props < 0) {
/* gap */
memset(dst + j, QUAL_GAP_VALUE, length);
}
else if (self->curs == NULL) {
memset(dst + j, 30, length);
}
else {
int const type = props & 0x0F;
int const strand = (props & ~(NCBI_WGS_strand_plus | NCBI_WGS_strand_minus)) >> 4;
if (type != 0 || strand == 3)
rc = RC(rcXF, rcFunction, rcExecuting, rcType, rcInvalid);
else {
int64_t const row = join[id++];
uint32_t elem_bits;
uint32_t bit_offset;
uint32_t elem_count;
void const *base;
rc = VCursorCellDataDirect(self->curs, row, self->col_idx,
&elem_bits, &base, &bit_offset,
&elem_count);
assert(bit_offset == 0);
if (rc == 0) {
INSDC_quality_phred const start = Start[i] - 1;
if (elem_count < start + length)
rc = RC(rcXF, rcFunction, rcExecuting, rcData, rcInsufficient);
else {
INSDC_quality_phred const *const src = base;
if (strand == 2) {
unsigned k;
unsigned jj;
for (jj = j + length, k = 0; k != length; ++k) {
INSDC_quality_phred const elem = src[start + k];
--jj;
dst[jj] = elem;
}
}
else
memcpy(&dst[j], &src[start], length);
}
}
}
}
j += length;
}
return rc;
}
/**
* returns true if checks are passed
*/
void runChecks ( const char * accession, const CheckCorruptConfig * config, const VCursor * pa_cursor, const VCursor * sa_cursor, const VCursor * seq_cursor )
{
rc_t rc;
uint32_t pa_has_ref_offset_idx;
uint32_t sa_has_ref_offset_idx;
uint32_t sa_seq_spot_id_idx;
uint32_t sa_seq_read_id_idx;
uint32_t sa_pa_id_idx;
uint32_t sa_tmp_mismatch_idx;
uint32_t seq_pa_id_idx;
uint32_t seq_read_len_idx;
uint32_t seq_cmp_read_idx;
bool has_tmp_mismatch;
/* add columns to cursor */
#define add_column(tbl_name, cursor, idx, col_spec) \
rc = VCursorAddColumn( cursor, &idx, col_spec ); \
if ( rc != 0 ) \
throw VDB_ERROR("VCursorAddColumn() failed for " tbl_name " table, " col_spec " column", rc);
add_column( "PRIMARY_ALIGNMENT", pa_cursor, pa_has_ref_offset_idx, "(bool)HAS_REF_OFFSET" );
add_column( "SECONDARY_ALIGNMENT", sa_cursor, sa_has_ref_offset_idx, "(bool)HAS_REF_OFFSET" );
add_column( "SECONDARY_ALIGNMENT", sa_cursor, sa_seq_spot_id_idx, "SEQ_SPOT_ID" );
add_column( "SECONDARY_ALIGNMENT", sa_cursor, sa_seq_read_id_idx, "SEQ_READ_ID" );
add_column( "SECONDARY_ALIGNMENT", sa_cursor, sa_pa_id_idx, "PRIMARY_ALIGNMENT_ID" );
add_column( "SEQUENCE", seq_cursor, seq_pa_id_idx, "PRIMARY_ALIGNMENT_ID" );
add_column( "SEQUENCE", seq_cursor, seq_read_len_idx, "READ_LEN" );
add_column( "SEQUENCE", seq_cursor, seq_cmp_read_idx, "CMP_READ" );
// optional columns
rc = VCursorAddColumn( sa_cursor, &sa_tmp_mismatch_idx, "TMP_MISMATCH" );
if ( rc == 0 )
has_tmp_mismatch = true;
else
{
has_tmp_mismatch = false;
rc = 0;
}
#undef add_column
rc = VCursorOpen( pa_cursor );
if (rc != 0)
throw VDB_ERROR("VCursorOpen() failed for PRIMARY_ALIGNMENT table", rc);
rc = VCursorOpen( sa_cursor );
if (rc != 0)
throw VDB_ERROR("VCursorOpen() failed for SECONDARY_ALIGNMENT table", rc);
rc = VCursorOpen( seq_cursor );
if (rc != 0)
throw VDB_ERROR("VCursorOpen() failed for SEQUENCE table", rc);
int64_t sa_id_first;
uint64_t sa_row_count;
rc = VCursorIdRange( sa_cursor, sa_pa_id_idx, &sa_id_first, &sa_row_count );
if (rc != 0)
throw VDB_ERROR("VCursorIdRange() failed for SECONDARY_ALIGNMENT table, PRIMARY_ALIGNMENT_ID column", rc);
bool reported_about_no_pa = false;
uint64_t pa_longer_sa_rows = 0;
uint64_t pa_longer_sa_limit;
if (config->pa_len_threshold_percent > 0)
pa_longer_sa_limit = ceil( config->pa_len_threshold_percent * sa_row_count );
else if (config->pa_len_threshold_number == 0 || config->pa_len_threshold_number > sa_row_count)
pa_longer_sa_limit = sa_row_count;
else
pa_longer_sa_limit = config->pa_len_threshold_number;
uint64_t sa_row_limit;
if (config->sa_cutoff_percent > 0)
sa_row_limit = ceil( config->sa_cutoff_percent * sa_row_count );
else if (config->sa_cutoff_number == 0 || config->sa_cutoff_number > sa_row_count)
sa_row_limit = sa_row_count;
else
sa_row_limit = config->sa_cutoff_number;
for ( uint64_t i = 0; i < sa_row_count && i < sa_row_limit; ++i )
{
int64_t sa_row_id = i + sa_id_first;
const void * data_ptr = NULL;
uint32_t data_len;
uint32_t pa_row_len;
uint32_t sa_row_len;
uint32_t seq_read_len_len;
// SA:HAS_REF_OFFSET
rc = VCursorCellDataDirect ( sa_cursor, sa_row_id, sa_has_ref_offset_idx, NULL, (const void**)&data_ptr, NULL, &sa_row_len );
if ( rc != 0 )
throw VDB_ROW_ERROR("VCursorCellDataDirect() failed on SECONDARY_ALIGNMENT table, HAS_REF_OFFSET column", sa_row_id, rc);
const int64_t * p_seq_spot_id;
uint32_t seq_spot_id_len;
// SA:SEQ_SPOT_ID
rc = VCursorCellDataDirect ( sa_cursor, sa_row_id, sa_seq_spot_id_idx, NULL, (const void**)&p_seq_spot_id, NULL, &seq_spot_id_len );
if ( rc != 0 || p_seq_spot_id == NULL || seq_spot_id_len != 1 )
throw VDB_ROW_ERROR("VCursorCellDataDirect() failed on SECONDARY_ALIGNMENT table, SEQ_SPOT_ID column", sa_row_id, rc);
int64_t seq_spot_id = *p_seq_spot_id;
if (seq_spot_id == 0)
{
std::stringstream ss;
ss << "SECONDARY_ALIGNMENT:" << sa_row_id << " has SEQ_SPOT_ID = " << seq_spot_id;
throw DATA_ERROR(ss.str());
}
if ( has_tmp_mismatch )
{
const char * p_sa_tmp_mismatch;
// SA:TMP_MISMATCH
rc = VCursorCellDataDirect ( sa_cursor, sa_row_id, sa_tmp_mismatch_idx, NULL, (const void**)&p_sa_tmp_mismatch, NULL, &data_len );
if ( rc != 0 || p_sa_tmp_mismatch == NULL )
throw VDB_ROW_ERROR("VCursorCellDataDirect() failed on SECONDARY_ALIGNMENT table, TMP_MISMATCH column", sa_row_id, rc);
for ( uint32_t j = 0; j < data_len; ++j )
{
if ( p_sa_tmp_mismatch[j] == '=' )
{
std::stringstream ss;
ss << "SECONDARY_ALIGNMENT:" << sa_row_id << " TMP_MISMATCH contains '='";
throw DATA_ERROR(ss.str());
}
}
}
const int64_t * p_pa_row_id;
// SA:PRIMARY_ALIGNMENT_ID
rc = VCursorCellDataDirect ( sa_cursor, sa_row_id, sa_pa_id_idx, NULL, (const void**)&p_pa_row_id, NULL, &data_len );
if ( rc != 0 || p_pa_row_id == NULL || data_len != 1 )
throw VDB_ROW_ERROR("VCursorCellDataDirect() failed on SECONDARY_ALIGNMENT table, PRIMARY_ALIGNMENT_ID column", sa_row_id, rc);
int64_t pa_row_id = *p_pa_row_id;
if (pa_row_id == 0)
{
if (!reported_about_no_pa)
{
PLOGMSG (klogInfo, (klogInfo, "$(ACC) has secondary alignments without primary", "ACC=%s", accession));
reported_about_no_pa = true;
}
continue;
}
// PA:HAS_REF_OFFSET
rc = VCursorCellDataDirect ( pa_cursor, pa_row_id, pa_has_ref_offset_idx, NULL, &data_ptr, NULL, &pa_row_len );
if ( rc != 0 )
throw VDB_ROW_ERROR("VCursorCellDataDirect() failed on PRIMARY_ALIGNMENT table, HAS_REF_OFFSET column", pa_row_id, rc);
// move on when PA.len equal to SA.len
if (pa_row_len == sa_row_len)
continue;
if (pa_row_len < sa_row_len)
{
std::stringstream ss;
ss << "PRIMARY_ALIGNMENT:" << pa_row_id << " HAS_REF_OFFSET length (" << pa_row_len << ") less than SECONDARY_ALIGNMENT:" << sa_row_id << " HAS_REF_OFFSET length (" << sa_row_len << ")";
throw DATA_ERROR(ss.str());
}
// we already know that pa_row_len > sa_row_len
++pa_longer_sa_rows;
const int32_t * p_seq_read_id;
// SA:SEQ_READ_ID
rc = VCursorCellDataDirect ( sa_cursor, sa_row_id, sa_seq_read_id_idx, NULL, (const void**)&p_seq_read_id, NULL, &data_len );
if ( rc != 0 || p_seq_read_id == NULL || data_len != 1 )
throw VDB_ROW_ERROR("VCursorCellDataDirect() failed on SECONDARY_ALIGNMENT table, SEQ_READ_ID column", sa_row_id, rc);
// one-based read index
int32_t seq_read_id = *p_seq_read_id;
const uint32_t * p_seq_read_len;
// SEQ:READ_LEN
rc = VCursorCellDataDirect ( seq_cursor, seq_spot_id, seq_read_len_idx, NULL, (const void**)&p_seq_read_len, NULL, &seq_read_len_len );
if ( rc != 0 || p_seq_read_len == NULL )
throw VDB_ROW_ERROR("VCursorCellDataDirect() failed on SEQUENCE table, READ_LEN column", seq_spot_id, rc);
if ( seq_read_id < 1 || (uint32_t)seq_read_id > seq_read_len_len )
{
std::stringstream ss;
ss << "SECONDARY:" << sa_row_id << " SEQ_READ_ID value (" << seq_read_id << ") - 1 based, is out of SEQUENCE:" << seq_spot_id << " READ_LEN range (" << seq_read_len_len << ")";
throw DATA_ERROR(ss.str());
}
if (pa_row_len != p_seq_read_len[seq_read_id - 1])
{
std::stringstream ss;
ss << "PRIMARY_ALIGNMENT:" << pa_row_id << " HAS_REF_OFFSET length (" << pa_row_len << ") does not match its SEQUENCE:" << seq_spot_id << " READ_LEN[" << seq_read_id - 1 << "] value (" << p_seq_read_len[seq_read_id - 1] << ")";
throw DATA_ERROR(ss.str());
}
if (pa_longer_sa_rows >= pa_longer_sa_limit)
{
std::stringstream ss;
ss << "Limit violation (pa_longer_sa): there are at least " << pa_longer_sa_rows << " alignments where HAS_REF_OFFSET column is longer in PRIMARY_ALIGNMENT than in SECONDARY_ALIGNMENT";
throw DATA_ERROR(ss.str());
}
}
int64_t seq_id_first;
uint64_t seq_row_count;
rc = VCursorIdRange( seq_cursor, seq_pa_id_idx, &seq_id_first, &seq_row_count );
if (rc != 0)
throw VDB_ERROR("VCursorIdRange() failed for SEQUENCE table, PRIMARY_ALIGNMENT_ID column", rc);
uint64_t seq_row_limit;
if (config->seq_cutoff_percent > 0)
seq_row_limit = ceil( config->seq_cutoff_percent * seq_row_count );
else if (config->seq_cutoff_number == 0 || config->seq_cutoff_number > seq_row_count)
seq_row_limit = seq_row_count;
else
seq_row_limit = config->seq_cutoff_number;
for ( uint64_t i = 0; i < seq_row_count && i < seq_row_limit; ++i )
{
int64_t seq_row_id = i + seq_id_first;
const void * data_ptr = NULL;
uint32_t data_len;
const int64_t * p_seq_pa_id;
uint32_t seq_pa_id_len;
// SEQ:PRIMARY_ALIGNMENT_ID
rc = VCursorCellDataDirect ( seq_cursor, seq_row_id, seq_pa_id_idx, NULL, (const void**)&p_seq_pa_id, NULL, &seq_pa_id_len );
if ( rc != 0 || p_seq_pa_id == NULL )
throw VDB_ROW_ERROR("VCursorCellDataDirect() failed on SEQUENCE table, PRIMARY_ALIGNMENT_ID column", seq_row_id, rc);
const uint32_t * p_seq_read_len;
// SEQ:READ_LEN
rc = VCursorCellDataDirect ( seq_cursor, seq_row_id, seq_read_len_idx, NULL, (const void**)&p_seq_read_len, NULL, &data_len );
if ( rc != 0 || p_seq_read_len == NULL )
throw VDB_ROW_ERROR("VCursorCellDataDirect() failed on SEQUENCE table, READ_LEN column", seq_row_id, rc);
if ( seq_pa_id_len != data_len )
{
std::stringstream ss;
ss << "SEQUENCE:" << seq_row_id << " PRIMARY_ALIGNMENT_ID length (" << seq_pa_id_len << ") does not match SEQUENCE:" << seq_row_id << " READ_LEN length (" << data_len << ")";
throw DATA_ERROR(ss.str());
}
uint64_t sum_unaligned_read_len = 0;
for ( uint32_t j = 0; j < seq_pa_id_len; ++j )
{
if ( p_seq_pa_id[j] == 0 )
{
sum_unaligned_read_len += p_seq_read_len[j];
}
}
// SEQ:CMP_READ
rc = VCursorCellDataDirect ( seq_cursor, seq_row_id, seq_cmp_read_idx, NULL, (const void**)&data_ptr, NULL, &data_len );
if ( rc != 0 || data_ptr == NULL )
throw VDB_ROW_ERROR("VCursorCellDataDirect() failed on SEQUENCE table, SEQ:CMP_READ column", seq_row_id, rc);
if ( sum_unaligned_read_len != data_len )
{
std::stringstream ss;
ss << "SEQUENCE:" << seq_row_id << " CMP_READ length (" << data_len << ") does not match sum of unaligned READ_LEN values (" << sum_unaligned_read_len << ")";
throw DATA_ERROR(ss.str());
}
}
if (sa_row_limit < sa_row_count || seq_row_limit < seq_row_count)
PLOGMSG (klogInfo, (klogInfo, "$(ACC) looks good (based on first $(SA_CUTOFF) of SECONDARY_ALIGNMENT and $(SEQ_CUTOFF) SEQUENCE rows)", "ACC=%s,SA_CUTOFF=%lu,SEQ_CUTOFF=%lu", accession, sa_row_limit, seq_row_limit));
else
PLOGMSG (klogInfo, (klogInfo, "$(ACC) looks good", "ACC=%s", accession));
}
/*
function INSDC:coord:zero NCBI:align:ref_pos ( I64 ref_id, INSDC:coord:zero ref_start );
*/
static
rc_t CC align_ref_pos ( void *data, const VXformInfo *info,
int64_t row_id, VRowResult *rslt, uint32_t argc, const VRowData argv[] )
{
rc_t rc = 0;
RefPos const *self = ( void const * )data;
int64_t ref_row_id = 0;
INSDC_coord_zero *ref_pos;
unsigned const ploidy = ( unsigned const )argv[ REF_START ].u.data.elem_count;
unsigned i;
/* get start and length of reference segment */
int64_t const *ref_id = 0;
INSDC_coord_zero const *ref_start;
assert( argv[ REF_ID ].u.data.elem_bits == sizeof( *ref_id ) * 8 );
assert( argv[ REF_START ].u.data.elem_bits == sizeof( *ref_start ) * 8 );
ref_start = argv[ REF_START ].u.data.base;
ref_start += argv[ REF_START ].u.data.first_elem;
if ( self->curs != NULL )
{
char const *name = NULL;
uint32_t name_len;
BSTRowRange *brr;
ref_id = argv[ REF_ID ].u.data.base;
ref_id += argv[ REF_ID ].u.data.first_elem;
brr = ( BSTRowRange * )BSTreeFind( &self->tr_range, &ref_id[ 0 ], row_range_cmp );
if ( brr == NULL )
{
RowRange *new_rr;
SUB_DEBUG( ( "SUB.Rd in 'align-ref-pos.c' at #%lu\n", ref_id[ 0 ] ) );
rc = VCursorCellDataDirect( self->curs, ref_id[ 0 ], self->name_idx, NULL, (void const **)&name, NULL, &name_len );
if ( rc != 0 )
return rc;
rc = VCursorParamsSet( ( struct VCursorParams const * )self->curs, "QUERY_SEQ_NAME", "%.*s", name_len, name );
if ( rc != 0 )
return rc;
rc = VCursorCellDataDirect( self->curs, ref_id[ 0 ], self->name_range_idx, NULL, (void const **)&new_rr, NULL, NULL );
if ( rc != 0 )
return rc;
brr = malloc( sizeof( *brr ) );
if ( brr == NULL )
{
return RC( rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted );
}
else
{
memcpy( &brr->rr, new_rr, sizeof( *new_rr ) );
BSTreeInsert( ( BSTree* )&self->tr_range, ( BSTNode* )brr, row_range_sort );
}
}
ref_row_id = brr->rr.start_id;
}
rc = KDataBufferResize( rslt->data, ploidy );
if ( rc != 0 )
return rc;
ref_pos = rslt->data->base;
for ( i = 0; i != ploidy; ++i )
{
ref_pos[ i ] = ref_start[ i ];
if ( self->curs != NULL )
{
ref_pos[ i ] += ( INSDC_coord_zero )( ( ref_id[ 0 ] - ref_row_id ) * self->max_seq_len );
}
}
rslt->elem_count = ploidy;
rslt->elem_bits = sizeof( ref_pos[ 0 ] ) * 8;
return rc;
}
static rc_t cg_dump_write_spot( cg_dump_opts * opts, cg_dump_ctx * cg_ctx, uint64_t row_id, lane * l )
{
uint32_t elem_bits, boff, read_len;
const char * read;
rc_t rc = VCursorCellDataDirect( cg_ctx->seq_cur, row_id, cg_ctx->seq_read_idx, &elem_bits, (const void**)&read, &boff, &read_len );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot read READ in row #$(row_id)", "row_id=%lu", row_id ) );
}
else
{
uint32_t qual_len;
const char * qual;
rc = VCursorCellDataDirect( cg_ctx->seq_cur, row_id, cg_ctx->seq_qual_idx, &elem_bits, (const void**)&qual, &boff, &qual_len );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot read QUALITY in row #$(row_id)", "row_id=%lu", row_id ) );
}
else
{
if ( ( read_len != 70 ) && ( qual_len != 70 ) )
{
rc = RC( rcExe, rcDatabase, rcReading, rcRange, rcInvalid );
(void)LOGERR( klogErr, rc, "len of read/quality columns do not match cg-length of 2 x 35" );
}
else
{
char buffer[ 1024 ];
size_t num_writ_buf;
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf,
"%lu\t0\t%.35s\t%.35s\n%lu\t1\t%.35s\t%.35s\n",
row_id, read, qual, row_id, &(read[35]), &(qual[35]) );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot generate output in row #$(row_id)", "row_id=%lu", row_id ) );
}
else
{
if ( opts->comp != oc_null )
{
if ( l->spot_count >= opts->cutoff )
{
KFileRelease( l->reads );
l->chunk++;
l->spot_count = 0;
l->write_pos = 0;
rc = make_read_file( opts, cg_ctx->lookup, cg_ctx->out_dir, l );
}
if ( rc == 0 )
{
size_t num_writ_file;
rc = KFileWrite ( l->reads, l->write_pos, buffer, num_writ_buf, &num_writ_file );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot write output in row #$(row_id)", "row_id=%lu", row_id ) );
}
else
{
l->write_pos += num_writ_file;
l->spot_count ++;
}
}
}
}
}
}
}
return rc;
}
rc_t initialize_ref_pos (
PileupIteratorState* pileup_state,
VCursor const* cursor_ref, VCursor const* cursor_pa,
char const* const* column_names_ref, uint32_t* column_index_ref, size_t column_count_ref,
char const* const* column_names_pa, uint32_t* column_index_pa, size_t column_count_pa,
char* error_buf,
size_t error_buf_size
)
{
int64_t row_id;
uint64_t row_count;
uint32_t max_seq_len, row_len;
rc_t rc = VCursorIdRange ( cursor_ref, 0, & row_id, & row_count );
/*printf ("REFERENCE table: row_id=%lld, row_count=%llu\n", row_id, row_count);*/
if ( row_count < 1 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"There is no rows in REFERENCE table");
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return (rc_t)(-1);
}
pileup_state->total_row_count = row_count;
/* We don't know the reference end id use its name to notice the moment when it changes - this will be the end */
rc = VCursorReadDirect ( cursor_ref, pileup_state->reference_start_id, column_index_ref [COL_NAME],
sizeof (pileup_state->ref_name[0]) * 8, pileup_state->ref_name, countof(pileup_state->ref_name), & row_len );
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: VCursorReadDirect(ref) failed with error: 0x%08x (%u) [%R]", rc, rc, rc);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return rc;
}
pileup_state->ref_name[ min ( countof(pileup_state->ref_name) - 1, row_len) ] = '\0';
/* Read MAX_SEQ_LEN from the start_row_id and assume that it's the same for all the rest */
rc = VCursorReadDirect ( cursor_ref, pileup_state->reference_start_id, column_index_ref [COL_MAX_SEQ_LEN],
sizeof (max_seq_len) * 8, & max_seq_len, 1, & row_len );
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: VCursorReadDirect(ref) failed with error: 0x%08x (%u) [%R]", rc, rc, rc);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return rc;
}
pileup_state->max_seq_len = max_seq_len;
if ( row_len < 1 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"There is no MAX_SEQ_LEN column for row_id=%lld in REFERENCE table", row_id);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return (rc_t)(-1);
}
printf ("MAX_SEQ_LEN=%lu\n", max_seq_len);
pileup_state->slice_start_id = pileup_state->reference_start_id + pileup_state->slice_start/max_seq_len;
pileup_state->slice_end_id = pileup_state->slice_length != 0 ?
pileup_state->reference_start_id + (pileup_state->slice_start + (int64_t)pileup_state->slice_length)/max_seq_len :
(int64_t)pileup_state->total_row_count;
printf ("slice position range: [%lld, %llu]\n", pileup_state->slice_start, pileup_state->slice_start + pileup_state->slice_length);
/*printf ("slice id range: [%lld, %lld]\n", slice_start_id, slice_end_id);*/
/* Read reference slice_start_id,
read OVERLAP_*_POS to find out how
many rows we need to read ahead of slice_start_id
TODO: this is not implemented yet, insted we read just 10 rows ahead
*/
/* Set cursor to <read_ahead_rows> rows ahead of slice_start_id
and cache corresponding PRIMARY_ALIGNMENTS
*/
{
int64_t current_id = max (pileup_state->reference_start_id, pileup_state->slice_start_id - 10);
int64_t stop_id = pileup_state->slice_start_id;
uint32_t seq_start;
uint32_t dummy;
#if USE_SINGLE_BLOB_FOR_ALIGNMENT_IDS != 1
int64_t const* alignment_ids;
#endif
for (; ; ++current_id)
{
/* We don't know the current reference end_id
read it's name and break when it changes
*/
char ref_name[ countof (pileup_state->ref_name) ];
rc = VCursorReadDirect ( cursor_ref, current_id, column_index_ref [COL_NAME],
sizeof (ref_name[0]) * 8, ref_name, countof(ref_name), & row_len );
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: VCursorReadDirect(ref) failed with error: 0x%08x (%u) [%R]", rc, rc, rc);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return rc;
}
ref_name[ min ( countof(ref_name) - 1, row_len) ] = '\0';
if ( current_id > stop_id || strcmp (ref_name, pileup_state->ref_name) )
break;
#if USE_SINGLE_BLOB_FOR_ALIGNMENT_IDS == 1
rc = open_blob_for_current_id ( current_id,
cursor_ref, & pileup_state->blob_alignment_ids,
column_index_ref [COL_PRIMARY_ALIGNMENT_IDS],
error_buf, error_buf_size );
if (rc != 0)
return rc;
#endif
/* Read REFERENCE row's SEQ_START column to know the offset */
rc = VCursorReadDirect ( cursor_ref, current_id,
column_index_ref [COL_SEQ_START],
sizeof (seq_start) * 8, & seq_start, 1, & row_len );
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: VCursorReadDirect(ref-seq_start) failed with error: 0x%08x (%u) [%R]",
rc, rc, rc);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return rc;
}
pileup_state->current_seq_start = seq_start;
/* Read REFERENCE row's PRIMARY_ALIGNMENT_IDS column to iterate through them */
/* elem_bits = sizeof (*pileup_state->alignment_ids) * 8;*/
#if USE_SINGLE_BLOB_FOR_ALIGNMENT_IDS == 1
rc = VBlobCellData ( pileup_state->blob_alignment_ids, current_id,
& dummy, & pileup_state->alignment_ids, NULL, & row_len );
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: VBlobCellData(ref-pa_ids) failed with error: 0x%08x (%u) [%R], row_len=%u",
rc, rc, rc, row_len);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return rc;
}
pileup_state -> size_alignment_ids = row_len;
#else
rc = VCursorCellDataDirect ( cursor_ref, current_id,
column_index_ref [COL_PRIMARY_ALIGNMENT_IDS],
NULL,
(void const**)(& alignment_ids), 0, & row_len );
/*rc = VCursorReadDirect ( cursor_ref, current_id,
column_index_ref [COL_PRIMARY_ALIGNMENT_IDS],
sizeof (*pileup_state->alignment_ids) * 8,
pileup_state->alignment_ids,
countof (pileup_state->alignment_ids), & row_len );*/
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: VCursorCellDataDirect(ref-pa_ids) failed with error: 0x%08x (%u) [%R], row_len=%u",
rc, rc, rc, row_len);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return rc;
}
rc = PileupIteratorState_SetAlignmentIds ( pileup_state, alignment_ids, row_len );
if ( rc != 0 )
{
rc_t res = string_printf ( error_buf, error_buf_size, NULL,
"ERROR: PileupIteratorState_SetAlignmentIds failed with error: 0x%08x (%u), row_len=%u",
rc, rc, row_len);
if (res == rcBuffer || res == rcInsufficient)
error_buf [ error_buf_size - 1 ] = '\0';
return rc;
}
#endif
pileup_state->next_alignment_idx = 0;
/*pileup_state->size_alignment_ids = row_len;*/
/*printf ("Read %lu PRIMARY_ALIGNMENT_IDS for REFERENCE row_id=%lld:", row_len, current_id);*/
{
/*size_t i = 0;
for (; i < row_len; ++i)
printf(" %lld", pa_ids [i]);*/
/*printf ("\n");*/
}
/* For each PRIMARY_ALIGNMENT_ID in alignment_ids: read its start, length and
cache it if it intersects the starting position
*/
rc = add_ref_row_to_cache ( pileup_state, cursor_pa, seq_start,
pileup_state->slice_start,
pileup_state->alignment_ids, row_len,
column_names_pa, column_index_pa, column_count_pa,
error_buf, error_buf_size );
if ( rc != 0 )
return rc;
}
}
return rc;
}
