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;
}
static rc_t consensus_loader( ld_context *lctx, const char * table_name,
bool cache_content )
{
uint32_t col_idx[ consensus_tab_count ];
rc_t rc = add_columns( lctx->cursor, consensus_tab_count, -1,
col_idx, consensus_tab_names );
if ( rc == 0 )
{
rc = VCursorOpen( lctx->cursor );
if ( rc != 0 )
LOGERR( klogErr, rc, "cannot open cursor on consensus-table" );
else
{
BaseCalls_cmn ConsensusTab;
const INSDC_SRA_platform_id platform = SRA_PLATFORM_PACBIO_SMRT;
rc = VCursorDefault ( lctx->cursor, col_idx[ consensus_tab_PLATFORM ],
sizeof platform * 8, &platform, 0, 1 );
if ( rc != 0 )
LOGERR( klogErr, rc, "cannot set cursor-default on consensus-table for platform-column" );
else
{
const INSDC_SRA_read_filter filter = SRA_READ_FILTER_PASS;
rc = VCursorDefault ( lctx->cursor, col_idx[ consensus_tab_READ_FILTER ],
sizeof filter * 8, &filter, 0, 1 );
if ( rc != 0 )
LOGERR( klogErr, rc, "cannot set cursor-default on consensus-table for read-filter-column" );
}
if ( rc == 0 )
rc = open_BaseCalls_cmn( lctx->hdf5_dir, &ConsensusTab, true,
"PulseData/ConsensusBaseCalls", 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 = zmw_for_each( &ConsensusTab.zmw, lctx, col_idx, NULL,
true, consensus_load_spot, &ConsensusTab );
else
rc = RC( rcExe, rcNoTarg, rcAllocating, rcParam, rcInvalid );
close_BaseCalls_cmn( &ConsensusTab );
}
}
}
return rc;
}
static rc_t open_BaseCalls( const KDirectory *hdf5_dir, BaseCalls *tab,
const char * path, bool cache_content, bool * rgn_present )
{
rc_t rc;
init_BaseCalls( tab );
rc = open_BaseCalls_cmn( hdf5_dir, &tab->cmn, false, path, cache_content, false );
if ( rc == 0 )
{
rc_t rc1 = rgn_open( hdf5_dir, &tab->rgn );
if ( rgn_present != NULL )
*rgn_present = ( rc1 == 0 );
open_element( hdf5_dir, &tab->PreBaseFrames, path, "PreBaseFrames",
PRE_BASE_FRAMES_BITSIZE, PRE_BASE_FRAMES_COLS,
true, cache_content, true );
if ( rc == 0 )
{
rc = open_element( hdf5_dir, &tab->PulseIndex, path, "PulseIndex",
PULSE_INDEX_BITSIZE_16, PULSE_INDEX_COLS,
false, cache_content, false );
/* try again if it is not 16 bit! */
if ( rc != 0 )
rc = open_element( hdf5_dir, &tab->PulseIndex, path, "PulseIndex",
PULSE_INDEX_BITSIZE_32, PULSE_INDEX_COLS,
true, cache_content, false );
}
open_element( hdf5_dir, &tab->WidthInFrames, path, "WidthInFrames",
WIDTH_IN_FRAMES_BITSIZE, WIDTH_IN_FRAMES_COLS,
true, cache_content, true );
if ( rc != 0 )
close_BaseCalls( tab ); /* releases only initialized elements */
}
return rc;
}
