rc_t prepare_ref_iter( prepare_ctx *ctx,
const VDBManager *vdb_mgr,
VSchema *vdb_schema,
const char * path,
BSTree * regions )
{
rc_t rc = prepare_db_table( ctx, vdb_mgr, vdb_schema, path );
if ( rc == 0 )
{
rc = prepare_reflist( ctx );
if( rc == 0 )
{
if ( ctx->reflist == NULL || count_ref_regions( regions ) == 0 )
{
/* the user has not specified a reference-range : use the whole file... */
rc = prepare_whole_file( ctx );
}
else
{
/* pick only the requested ranges... */
rc = foreach_ref_region( regions, prepare_region_cb, ctx );
}
}
if ( ctx->reflist != NULL )
{
ReferenceList_Release( ctx->reflist );
}
}
VTableRelease ( ctx->seq_tab );
VDatabaseRelease ( ctx->db );
return rc;
}
static rc_t ref_walker_prepare( struct ref_walker * self )
{
rc_t rc = 0;
if ( self == NULL )
rc = RC( rcApp, rcNoTarg, rcConstructing, rcParam, rcNull );
else
{
uint32_t s_count = 0;
rc = VNameListCount ( self->sources, &s_count );
if ( rc == 0 && s_count > 0 )
{
uint32_t r_count = count_ref_regions( &self->regions );
if ( r_count == 0 )
{
uint32_t idx;
for ( idx = 0; idx < s_count && rc == 0; ++idx )
{
const char * name = NULL;
rc = VNameListGet ( self->sources, idx, &name );
if ( rc == 0 && name != NULL )
rc = ref_walker_prepare_1_src( self, name );
}
}
}
check_ref_regions( &self->regions );
self->prepared = ( rc == 0 );
}
return rc;
}
static rc_t gather_region_options( Args * args, samdump_opts * opts )
{
uint32_t count;
rc_t rc = ArgsOptionCount( args, OPT_REGION, &count );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error counting comandline option '$(t)'", "t=%s", OPT_REGION ) );
}
else if ( count > 0 )
{
uint32_t i;
BSTreeInit( &opts->regions );
for ( i = 0; i < count && rc == 0; ++i )
{
const char * s;
rc = ArgsOptionValue( args, OPT_REGION, i, &s );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error retrieving comandline option '$(t)'", "t=%s", OPT_REGION ) );
}
else
rc = parse_and_add_region( &opts->regions, s );
}
if ( rc == 0 )
{
check_ref_regions( &opts->regions );
opts->region_count = count_ref_regions( &opts->regions );
}
}
return rc;
}
