rc_t load_consensus_src( con_ctx * sctx, KDirectory * hdf5_src )
{
BaseCalls_cmn ConsensusTab;
rc_t rc = 0;
if ( sctx->lctx->check_src_obj )
rc = check_src_objects( hdf5_src, consensus_groups_to_check,
consensus_tables_to_check, false );
if ( rc == 0 )
rc = open_BaseCalls_cmn( hdf5_src, &ConsensusTab, true,
"PulseData/ConsensusBaseCalls", sctx->lctx->cache_content, true );
if ( rc == 0 )
{
uint64_t total_bases = zmw_total( &ConsensusTab.zmw );
uint64_t total_spots = ConsensusTab.zmw.NumEvent.extents[ 0 ];
KLogLevel tmp_lvl = KLogLevelGet();
KLogLevelSet( klogInfo );
PLOGMSG( klogInfo, ( klogInfo,
"loading consensus-table ( $(bases) bases / $(spots) spots ):",
"bases=%lu,spots=%lu", total_bases, total_spots ));
KLogLevelSet( tmp_lvl );
if ( !check_Consensus_totalcount( &ConsensusTab, total_bases ) )
rc = RC( rcExe, rcNoTarg, rcAllocating, rcParam, rcInvalid );
else
rc = zmw_for_each( &ConsensusTab.zmw, &sctx->lctx->xml_progress, sctx->cursor,
sctx->lctx->with_progress, sctx->col_idx, NULL,
true, consensus_load_spot, &ConsensusTab );
close_BaseCalls_cmn( &ConsensusTab );
}
return rc;
}
rc_t load_passes( VDatabase * database, KDirectory * hdf5_src, ld_context *lctx )
{
rc_t rc = 0;
if ( lctx->check_src_obj )
rc = check_src_objects( hdf5_src, passes_groups_to_check,
passes_tables_to_check, false );
if ( rc == 0 )
rc = load_table( database, hdf5_src, lctx, passes_schema_template,
passes_table_to_create, passes_loader );
return rc;
}
rc_t load_consensus( ld_context *lctx, bool cache_content, bool check_src_obj )
{
rc_t rc = 0;
if ( check_src_obj )
rc = check_src_objects( lctx->hdf5_dir, consensus_groups_to_check,
consensus_tables_to_check, false );
if ( rc == 0 )
rc = load_table( lctx, consensus_schema_template,
consensus_table_to_create, consensus_loader, cache_content );
return rc;
}
rc_t load_seq( VDatabase * database, KDirectory * hdf5_src, ld_context *lctx )
{
rc_t rc = 0;
if ( lctx->check_src_obj )
rc = check_src_objects( hdf5_src, seq_groups_to_check, seq_tables_to_check, true );
if ( rc == 0 )
/* in pl-tools.c */
rc = load_table( database, hdf5_src, lctx, seq_schema_template,
seq_table_to_create, seq_loader );
return rc;
}
rc_t rgn_open( const KDirectory *hdf5_dir, regions *rgn )
{
rc_t rc;
rgn_init( rgn );
/* check if the necessary groups/tables are there */
rc = check_src_objects( hdf5_dir, region_groups_to_check,
region_tables_to_check, false );
if ( rc == 0 )
{
/* open the region-table... */
rc = open_element( hdf5_dir, &rgn->hdf5_regions,
region_groups_to_check[ 0 ], "Regions",
REGIONS_BITSIZE, REGIONS_COLS, true, false, true );
if ( rc == 0 )
rc = rgn_read_complete_table( rgn );
}
if ( rc != 0 )
rgn_free( rgn );
return rc;
}
rc_t load_passes_src( pas_ctx * sctx, KDirectory * hdf5_src )
{
Passes_src Passes;
rc_t rc = 0;
if ( sctx->lctx->check_src_obj )
rc = check_src_objects( hdf5_src, passes_groups_to_check,
passes_tables_to_check, false );
if ( rc == 0 )
rc = open_Passes_src( hdf5_src, &Passes, "PulseData/ConsensusBaseCalls/Passes",
sctx->lctx->cache_content );
if ( rc == 0 )
{
if ( check_Passes_extents( &Passes ) )
rc = passes_load_loop( sctx->lctx, sctx->cursor, &Passes, sctx->col_idx );
else
rc = RC( rcExe, rcNoTarg, rcAllocating, rcParam, rcInvalid );
close_Passes_src( &Passes );
}
return rc;
}
rc_t load_seq_src( seq_ctx * sctx, KDirectory * hdf5_src )
{
rc_t rc = 0;
if ( sctx->lctx->check_src_obj )
rc = check_src_objects( hdf5_src, seq_groups_to_check, seq_tables_to_check, true );
if ( rc == 0 && !sctx->src_open )
rc = open_BaseCalls( hdf5_src, &sctx->BaseCallsTab, "PulseData/BaseCalls", sctx->lctx->cache_content, &sctx->rgn_present );
if ( rc == 0 )
{
/* calculates the total number of bases, according to the zmw-table */
uint64_t total_bases = zmw_total( &sctx->BaseCallsTab.cmn.zmw );
/* calculates the total number of spots, according to the zmw-table */
uint64_t total_spots = sctx->BaseCallsTab.cmn.zmw.NumEvent.extents[ 0 ];
KLogLevel tmp_lvl = KLogLevelGet();
KLogLevelSet( klogInfo );
PLOGMSG( klogInfo, ( klogInfo,
"loading sequence-table ( $(bases) bases / $(spots) spots ):",
"bases=%lu,spots=%lu", total_bases, total_spots ));
KLogLevelSet( tmp_lvl );
/* checks that all tables, which are loaded do have the correct
number of values (the number that the zmw-table requests) */
if ( !check_BaseCall_totalcount( &sctx->BaseCallsTab, total_bases ) )
rc = RC( rcExe, rcNoTarg, rcAllocating, rcParam, rcInvalid );
else
{
region_type_mapping mapping;
if ( sctx->rgn_present )
{
const KNamelist *region_types;
/* read the meta-data-entry "RegionTypes" of the hdf5-regions-table
into a KNamelist */
rc = KArrayFileGetMeta ( sctx->BaseCallsTab.rgn.hdf5_regions.af, "RegionTypes", ®ion_types );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "cannot read Regions.RegionTypes" );
}
else
{
/* extract the region-type-mapping out of the read KNamelist */
rc = rgn_extract_type_mappings( region_types, &mapping, false );
KNamelistRelease ( region_types );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "cannot map regions-types" );
}
}
}
if ( rc == 0 )
{
region_type_mapping *mapping_ptr = NULL;
if ( sctx->rgn_present )
mapping_ptr = &mapping;
/* call for every spot the function >seq_load_spot< */
rc = zmw_for_each( &sctx->BaseCallsTab.cmn.zmw, &sctx->lctx->xml_progress, sctx->cursor,
sctx->lctx->with_progress, sctx->col_idx, mapping_ptr, false,
seq_load_spot, &sctx->BaseCallsTab );
}
if ( sctx->rgn_present )
seq_load_info( &sctx->BaseCallsTab.rgn.stat );
sctx->lctx->total_seq_bases += total_bases;
sctx->lctx->total_seq_spots += total_spots;
}
close_BaseCalls( &sctx->BaseCallsTab );
sctx->src_open = false;
}
return rc;
}
