static rc_t ref_walker_add_iterator( struct ref_walker * self, const char * ref_name,
uint64_t start, uint64_t end, const char * src_name, Vector * cur_id_vector,
const VDatabase *db, const ReferenceObj * ref_obj, ReferenceIterator * ref_iter,
const char * table_name, align_id_src id_selector )
{
walker_col_ids * cursor_ids;
rc_t rc = make_cursor_ids( cur_id_vector, &cursor_ids );
if ( rc == 0 )
{
const VTable *tbl;
rc_t rc = VDatabaseOpenTableRead ( db, &tbl, table_name );
if ( rc == 0 )
{
const VCursor *cursor;
rc = add_required_columns( self, tbl, &cursor, cursor_ids );
if ( rc == 0 )
{
rc = ReferenceIteratorAddPlacements ( ref_iter, /* the outer ref-iter */
ref_obj, /* the ref-obj for this chromosome */
start - 1, /* start ( zero-based ) */
( end - start ) + 1, /* length */
NULL, /* ref-cursor */
cursor, /* align-cursor */
id_selector, /* which id's */
self->spot_group, /* what read-group */
cursor_ids /* placement-context */
);
VCursorRelease( cursor );
}
VTableRelease ( tbl );
}
}
return rc;
}
static rc_t test_ref_iterator( trans_ctx *ctx,
const char * ref_name,
INSDC_coord_zero ref_pos,
INSDC_coord_len ref_len,
bool skip_empty,
bool nodebug )
{
rc_t rc;
ReferenceIterator *ref_iter = NULL;
struct VCursor const *ref_cursor = NULL;
struct VCursor const *align_cursor = NULL;
PlacementRecordExtendFuncs ef;
/* (1) make the reference-iterator */
ef.data = ( void * )ctx->almgr;
ef.destroy = NULL; /* ext_rec_destroy; */
ef.populate = ext_rec_populate;
ef.alloc_size = ext_rec_size;
ef.fixed_size = 0;
rc = AlignMgrMakeReferenceIterator ( ctx->almgr, &ref_iter, &ef, 0 /* min_mapq*/ );
if ( rc != 0 )
LOGERR( klogInt, rc, "AlignMgrMakeReferenceIterator() failed" );
/* (2) prepare the alignmnet-cursor (for the needs of the callback...)*/
if ( rc == 0 )
rc = get_prim_align_cursor( ctx->db, &align_cursor );
/* (3) all placements to the ref-iter AND WALK THE REFERENCE-ITERATOR! */
if ( rc == 0 )
{
rc = ReferenceIteratorAddPlacements( ref_iter, ctx->ref_obj, ref_pos, ref_len,
ref_cursor, align_cursor, primary_align_ids, NULL );
if ( rc != 0 )
LOGERR( klogInt, rc, "ReferenceIteratorAddPlacements() failed" );
else
{
/* =============================================== */
rc = walk_ref_iter( ref_iter, skip_empty, nodebug );
/* =============================================== */
}
}
if ( ref_cursor != NULL ) VCursorRelease ( ref_cursor );
if ( align_cursor != NULL ) VCursorRelease ( align_cursor );
if ( ref_iter != NULL ) ReferenceIteratorRelease( ref_iter );
return rc;
}
