static rc_t report_ref_database( const VDBManager *vdb_mgr, VFSManager * vfs_mgr, const char * path, bool extended ) { const VDatabase *db; rc_t rc = VDBManagerOpenDBRead ( vdb_mgr, &db, NULL, "%s", path ); if ( rc != 0 ) { (void)LOGERR( klogErr, rc, "VDBManagerOpenDBRead() failed" ); } else { const ReferenceList * reflist; uint32_t options = ( ereferencelist_usePrimaryIds | ereferencelist_useSecondaryIds | ereferencelist_useEvidenceIds ); rc = ReferenceList_MakeDatabase( &reflist, db, options, 0, NULL, 0 ); if ( rc != 0 ) { (void)LOGERR( klogErr, rc, "ReferenceList_MakeDatabase() failed" ); } else { uint32_t count; rc = ReferenceList_Count( reflist, &count ); if ( rc != 0 ) { (void)LOGERR( klogErr, rc, "ReferenceList_Count() failed" ); } else { rc = KOutMsg( "this object uses %u references\n", count ); if ( rc == 0 ) { uint32_t idx; for ( idx = 0; idx < count && rc == 0; ++idx ) { const ReferenceObj* ref_obj; rc = ReferenceList_Get( reflist, &ref_obj, idx ); if ( rc != 0 ) { (void)LOGERR( klogErr, rc, "ReferenceList_Get() failed" ); } else { rc = report_ref_obj( vdb_mgr, vfs_mgr, path, idx, ref_obj, extended ); ReferenceObj_Release( ref_obj ); } } } } ReferenceList_Release( reflist ); } VDatabaseRelease( db ); } return rc; }
static rc_t CC prepare_region_cb( const char * name, uint32_t start, uint32_t end, void * data ) { prepare_ctx * ctx = ( prepare_ctx * )data; rc_t rc = ReferenceList_Find( ctx->reflist, &ctx->refobj, name, string_size( name ) ); if ( rc != 0 ) { LOGERR( klogInt, rc, "ReferenceList_Find() failed" ); } else { rc = ctx->on_section( ctx, start, end ); if ( rc == 0 ) ReferenceObj_Release( ctx->refobj ); } return rc; }
static rc_t prepare_whole_file( prepare_ctx * ctx ) { rc_t rc = 0; if ( ctx->reflist != NULL ) { uint32_t count; rc = ReferenceList_Count( ctx->reflist, &count ); if ( rc != 0 ) { LOGERR( klogInt, rc, "ReferenceList_Count() failed" ); } else { uint32_t idx; for ( idx = 0; idx < count && rc == 0; ++idx ) { rc = ReferenceList_Get( ctx->reflist, &ctx->refobj, idx ); if ( rc != 0 ) { LOGERR( klogInt, rc, "ReferenceList_Get() failed" ); } else { rc = ctx->on_section( ctx, 0, 0 ); if ( rc == 0 ) ReferenceObj_Release( ctx->refobj ); } } } } else { ctx->refobj = NULL; rc = ctx->on_section( ctx, 0, 0 ); } return rc; }
LIB_EXPORT rc_t CC ReferenceIteratorAddPlacements( ReferenceIterator *self, struct ReferenceObj const *ref_obj, INSDC_coord_zero ref_pos, INSDC_coord_len ref_len, struct VCursor const *ref, struct VCursor const *align, align_id_src ids, const char * spot_group, void * placement_ctx ) { rc_t rc = 0; if ( self == NULL ) rc = RC( rcAlign, rcIterator, rcConstructing, rcSelf, rcNull ); else { if ( ref_obj == NULL ) rc = RC( rcAlign, rcIterator, rcConstructing, rcParam, rcNull ); else { if ( align != NULL ) rc = prepare_align_cursor( align ); if ( rc == 0 ) { PlacementIterator *pi; rc = ReferenceObj_MakePlacementIterator ( ref_obj, &pi, ref_pos, ref_len, self->min_mapq, ref, align, ids, &self->int_func, &self->ext_func, spot_group, placement_ctx ); if ( rc == 0 ) { rc = PlacementSetIteratorAddPlacementIterator ( self->pl_set_iter, pi ); if ( GetRCState( rc ) == rcDone ) { rc = 0; } } } /* if rc != 0 then ref_obj had NO AddRef inside ReferenceObj_MakePlacementIterator() ! */ if ( rc == 0 ) ReferenceObj_Release( ref_obj ); } } return rc; }
static rc_t ref_walker_walk_ref_range( struct ref_walker * self, ref_walker_data * rwd ) { ReferenceIterator * ref_iter; rc_t rc = AlignMgrMakeReferenceIterator ( self->amgr, &ref_iter, &self->cb_block, self->min_mapq ); /* align/iterator.h */ if ( rc == 0 ) { /* construct the reference iterator */ uint32_t idx, count; uint32_t reflist_options = ref_walker_make_reflist_options( self ); /* above */ Vector cur_id_vector; VectorInit ( &cur_id_vector, 0, 12 ); rc = VNameListCount ( self->sources, &count ); for ( idx = 0; idx < count && rc == 0; ++idx ) { const char * src_name = NULL; rc = VNameListGet ( self->sources, idx, &src_name ); if ( rc == 0 && src_name != NULL ) { const VDatabase *db; rc = VDBManagerOpenDBRead ( self->vmgr, &db, self->vschema, "%s", src_name ); if ( rc == 0 ) { const ReferenceList * ref_list; rc = ReferenceList_MakeDatabase( &ref_list, db, reflist_options, 0, NULL, 0 ); if ( rc == 0 ) { const ReferenceObj * ref_obj; rc = ReferenceList_Find( ref_list, &ref_obj, rwd->ref_name, string_size( rwd->ref_name ) ); if ( rc == 0 ) { INSDC_coord_len len; rc = ReferenceObj_SeqLength( ref_obj, &len ); if ( rc == 0 ) { if ( rwd->ref_start == 0 ) rwd->ref_start = 1; if ( ( rwd->ref_end == 0 )||( rwd->ref_end > len + 1 ) ) rwd->ref_end = ( len - rwd->ref_start ) + 1; if ( self->primary_alignments ) rc = ref_walker_add_iterator( self, rwd->ref_name, rwd->ref_start, rwd->ref_end, src_name, &cur_id_vector, db, ref_obj, ref_iter, TBL_PRIM, primary_align_ids ); if ( rc == 0 && self->secondary_alignments ) rc = ref_walker_add_iterator( self, rwd->ref_name, rwd->ref_start, rwd->ref_end, src_name, &cur_id_vector, db, ref_obj, ref_iter, TBL_SEC, secondary_align_ids ); if ( rc == 0 && self->evidence_alignments ) rc = ref_walker_add_iterator( self, rwd->ref_name, rwd->ref_start, rwd->ref_end, src_name, &cur_id_vector, db, ref_obj, ref_iter, TBL_EV, evidence_align_ids ); } ReferenceObj_Release( ref_obj ); } ReferenceList_Release( ref_list ); } VDatabaseRelease( db ); } } } if ( rc == 0 ) { /* walk the reference iterator */ struct ReferenceObj const * ref_obj; rc = ReferenceIteratorNextReference( ref_iter, NULL, NULL, &ref_obj ); if ( rc == 0 && ref_obj != NULL ) { if ( self->use_seq_name ) rc = ReferenceObj_Name( ref_obj, &rwd->ref_name ); else rc = ReferenceObj_SeqId( ref_obj, &rwd->ref_name ); if ( rc == 0 ) { INSDC_coord_zero first_pos; INSDC_coord_len len; rc_t rc_w = ReferenceIteratorNextWindow ( ref_iter, &first_pos, &len ); while ( rc == 0 && rc_w == 0 ) { rc_t rc_p = ReferenceIteratorNextPos ( ref_iter, !self->no_skip ); if ( rc_p == 0 ) { rc = ReferenceIteratorPosition ( ref_iter, &rwd->pos, &rwd->depth, &rwd->bin_ref_base ); if ( rwd->depth > 0 && rc == 0 ) { rc_t rc_sg = 0; rwd->ascii_ref_base = _4na_to_ascii( rwd->bin_ref_base, false ); if ( self->on_enter_ref_pos != NULL ) rc = self->on_enter_ref_pos( rwd ); while ( rc_sg == 0 && rc == 0 ) { rc_sg = ReferenceIteratorNextSpotGroup ( ref_iter, &rwd->spot_group, &rwd->spot_group_len ); if ( rc_sg == 0 ) { rc_t rc_pr = 0; if ( self->on_enter_spot_group != NULL ) rc = self->on_enter_spot_group( rwd ); while ( rc == 0 && rc_pr == 0 ) { const PlacementRecord * rec; rc_pr = ReferenceIteratorNextPlacement ( ref_iter, &rec ); if ( rc_pr == 0 && self->on_alignment != NULL ) rc = ref_walker_walk_alignment( self, ref_iter, rec, rwd ); } if ( self->on_exit_spot_group != NULL ) rc = self->on_exit_spot_group( rwd ); } } if ( self->on_exit_ref_pos != NULL ) rc = self->on_exit_ref_pos( rwd ); } rc = Quitting(); } } } } } /* free cur_id_vector */ ReferenceIteratorRelease ( ref_iter ); } return rc; }
static rc_t ref_walker_prepare_1_src( struct ref_walker * self, const char * name ) { VPath * path = NULL; const VPath * local_cache = NULL; const KFile * remote_file = NULL; rc_t rc = VFSManagerResolveSpec ( self->vfs_mgr, name, &path, &remote_file, &local_cache, true ); if ( rc != 0 ) { PLOGERR( klogErr, ( klogErr, rc, "cannot resolve '$(n)' via VFSManager", "n=%s", name ) ); } else { char buffer[ 4096 ]; size_t num_read; rc = VPathReadPath ( path, buffer, sizeof buffer, &num_read ); if ( rc != 0 ) { PLOGERR( klogErr, ( klogErr, rc, "cannot read path from vpath for '$(n)'", "n=%s", name ) ); } else { if ( rc == 0 ) { int path_type = ( VDBManagerPathType ( self->vmgr, "%s", buffer ) & ~ kptAlias ); if ( path_type == kptDatabase ) { const ReferenceList * reflist; uint32_t options = ( ereferencelist_usePrimaryIds | ereferencelist_useSecondaryIds | ereferencelist_useEvidenceIds ); rc = ReferenceList_MakePath( &reflist, self->vmgr, name, options, 0, NULL, 0 ); if ( rc != 0 ) { PLOGERR( klogErr, ( klogErr, rc, "cannot create ReferenceList for '$(n)'", "n=%s", name ) ); } else { uint32_t count; rc = ReferenceList_Count( reflist, &count ); if ( rc != 0 ) { PLOGERR( klogErr, ( klogErr, rc, "ReferenceList_Count() for '$(n)' failed", "n=%s", name ) ); } else { uint32_t idx; for ( idx = 0; idx < count && rc == 0; ++idx ) { const ReferenceObj * refobj; rc = ReferenceList_Get( reflist, &refobj, idx ); if ( rc != 0 ) { LOGERR( klogInt, rc, "ReferenceList_Get() failed" ); } else { const char * seqid; rc = ReferenceObj_SeqId( refobj, &seqid ); if ( rc == 0 ) { INSDC_coord_len seqlen; rc = ReferenceObj_SeqLength( refobj, &seqlen ); if ( rc == 0 ) { rc = add_region( &self->regions, seqid, 0, seqlen - 1 ); } } ReferenceObj_Release( refobj ); } } } ReferenceList_Release( reflist ); } } } } KFileRelease( remote_file ); VPathRelease ( local_cache ); VPathRelease ( path ); } return rc; }