Lines Matching refs:rgn
73 void rgn_init( regions *rgn ) in rgn_init() argument
75 init_array_file( &rgn->hdf5_regions ); in rgn_init()
77 VectorInit ( &rgn->read_Regions, 0, 5 ); in rgn_init()
78 VectorInit ( &rgn->sort_Regions, 0, 5 ); in rgn_init()
79 VectorInit ( &rgn->stock_Regions, 0, 5 ); in rgn_init()
81 rgn->data_32 = NULL; in rgn_init()
82 rgn->data_32_len = 0; in rgn_init()
83 rgn->data_8 = NULL; in rgn_init()
84 rgn->data_8_len = 0; in rgn_init()
86 rgn->offset = 0; in rgn_init()
87 rgn->spot_id = 0; in rgn_init()
88 rgn->spot_len = 0; in rgn_init()
89 rgn->hq_rgn.start = 0; in rgn_init()
90 rgn->hq_rgn.end = 0; in rgn_init()
92 rgn_stat_init( &( rgn->stat ) ); in rgn_init()
94 rgn->complete_table = NULL; in rgn_init()
95 rgn->table_index = NULL; in rgn_init()
119 void rgn_free( regions *rgn ) in rgn_free() argument
121 free_array_file( &rgn->hdf5_regions ); in rgn_free()
123 VectorWhack ( &rgn->read_Regions, region_whack, NULL ); in rgn_free()
124 VectorWhack ( &rgn->sort_Regions, region_whack, NULL ); in rgn_free()
125 VectorWhack ( &rgn->stock_Regions, region_whack, NULL ); in rgn_free()
127 if ( rgn->data_32 != NULL ) in rgn_free()
128 free( rgn->data_32 ); in rgn_free()
129 if ( rgn->data_8 != NULL ) in rgn_free()
130 free( rgn->data_8 ); in rgn_free()
132 if ( rgn->complete_table != NULL ) in rgn_free()
133 free( rgn->complete_table ); in rgn_free()
134 if ( rgn->table_index != NULL ) in rgn_free()
135 free( rgn->table_index ); in rgn_free()
142 regions *rgn = ( regions * ) data; in rgn_sort_callback() local
145 int32_t spot_id1 = rgn->complete_table[ idx1 * RGN_COLUMN_COUNT ]; in rgn_sort_callback()
146 int32_t spot_id2 = rgn->complete_table[ idx2 * RGN_COLUMN_COUNT ]; in rgn_sort_callback()
154 rc_t rgn_read_complete_table( regions *rgn ) in rgn_read_complete_table() argument
157 uint32_t rowcount = rgn->hdf5_regions.extents[ 0 ]; in rgn_read_complete_table()
160 rgn->complete_table = malloc( rowcount * rowsize ); in rgn_read_complete_table()
161 if ( rgn->complete_table == NULL ) in rgn_read_complete_table()
165 rgn->table_index = malloc( sizeof( uint32_t ) * rowcount ); in rgn_read_complete_table()
166 if ( rgn->table_index == NULL ) in rgn_read_complete_table()
168 free( rgn->complete_table ); in rgn_read_complete_table()
169 rgn->complete_table = NULL; in rgn_read_complete_table()
177 rc = array_file_read_dim2( &(rgn->hdf5_regions), 0, rgn->complete_table, in rgn_read_complete_table()
183 first_spot_id = rgn->complete_table[ pacbio_idx_spot_id ]; in rgn_read_complete_table()
188 … rgn->complete_table[ ( idx * RGN_COLUMN_COUNT ) + pacbio_idx_spot_id ] -= first_spot_id; in rgn_read_complete_table()
193 rgn->table_index[ idx ] = idx; in rgn_read_complete_table()
196 ksort ( rgn->table_index, rowcount, sizeof( uint32_t ), in rgn_read_complete_table()
197 rgn_sort_callback, rgn ); in rgn_read_complete_table()
215 rc_t rgn_open( const KDirectory *hdf5_dir, regions *rgn ) in rgn_open() argument
218 rgn_init( rgn ); in rgn_open()
225 rc = open_element( hdf5_dir, &rgn->hdf5_regions, in rgn_open()
229 rc = rgn_read_complete_table( rgn ); in rgn_open()
232 rgn_free( rgn ); in rgn_open()
662 rc_t rgn_load( regions *rgn, const uint32_t spot_id, in rgn_load() argument
666 uint64_t row_count = rgn->hdf5_regions.extents[ 0 ]; in rgn_load()
669 rgn->hq_rgn.start = 0; in rgn_load()
670 rgn->hq_rgn.end = 0; in rgn_load()
673 rc = rgn_vector_move( &rgn->read_Regions, &rgn->stock_Regions ); in rgn_load()
675 rc = rgn_vector_move( &rgn->sort_Regions, &rgn->stock_Regions ); in rgn_load()
679 if ( !( rgn->spot_id == 0 || rgn->spot_id == ( spot_id - 1 ) ) ) in rgn_load()
689 int32_t idx = rgn->table_index[ rgn->offset ]; in rgn_load()
690 block = &( rgn->complete_table[ idx * RGN_COLUMN_COUNT ] ); in rgn_load()
693 rc = rgn_store_block( &(rgn->stock_Regions), &(rgn->read_Regions), in rgn_load()
694 &(rgn->hq_rgn), block, in rgn_load()
697 rgn->offset++; in rgn_load()
702 rgn->offset < row_count ); in rgn_load()
703 rgn->spot_id = spot_id; in rgn_load()
704 rgn->spot_len = spot_len; in rgn_load()
713 rc = rgn_apply_filter( &(rgn->stock_Regions), &(rgn->read_Regions), in rgn_load()
714 &(rgn->hq_rgn), rgn->spot_id, rgn->spot_len ); in rgn_load()
721 rc = rgn_correct( &(rgn->stock_Regions), in rgn_load()
722 &(rgn->read_Regions), &(rgn->sort_Regions), in rgn_load()
723 rgn->spot_id, rgn->spot_len, &(rgn->stat) ); in rgn_load()
728 rc = rgn_merge_consecutive_regions( &(rgn->stock_Regions), in rgn_load()
729 &(rgn->sort_Regions), in rgn_load()
730 &(rgn->read_Regions) ); in rgn_load()
737 rc = rgn_check( &(rgn->read_Regions), rgn->spot_len ); in rgn_load()
744 static rc_t rgn_resize_data_32( regions *rgn ) in rgn_resize_data_32() argument
749 needed_len = ( sizeof( *rgn->data_32 ) * VectorLength( &rgn->read_Regions ) ); in rgn_resize_data_32()
750 if ( rgn->data_32 == NULL ) in rgn_resize_data_32()
752 rgn->data_32 = malloc( needed_len ); in rgn_resize_data_32()
754 else if ( rgn->data_32_len < VectorLength( &rgn->read_Regions ) ) in rgn_resize_data_32()
756 rgn->data_32 = realloc ( rgn->data_32, needed_len ); in rgn_resize_data_32()
758 if ( rgn->data_32 == NULL ) in rgn_resize_data_32()
761 rgn->data_32_len = VectorLength( &rgn->read_Regions ); in rgn_resize_data_32()
766 void rgn_set_filter_value_for_all( regions *rgn, const uint32_t filter_value ) in rgn_set_filter_value_for_all() argument
768 uint32_t i, n = VectorLength( &rgn->read_Regions ); in rgn_set_filter_value_for_all()
771 region * a_region = VectorGet ( &rgn->read_Regions, i ); in rgn_set_filter_value_for_all()
778 static rc_t rgn_resize_data_8( regions *rgn ) in rgn_resize_data_8() argument
783 needed_len = ( sizeof( *rgn->data_8 ) * VectorLength( &rgn->read_Regions ) ); in rgn_resize_data_8()
785 if ( rgn->data_8 == NULL ) in rgn_resize_data_8()
787 rgn->data_8 = malloc( needed_len ); in rgn_resize_data_8()
789 else if ( rgn->data_8_len < VectorLength( &rgn->read_Regions ) ) in rgn_resize_data_8()
791 rgn->data_8 = realloc ( rgn->data_8, needed_len ); in rgn_resize_data_8()
793 if ( rgn->data_8 == NULL ) in rgn_resize_data_8()
796 rgn->data_8_len = VectorLength( &rgn->read_Regions ); in rgn_resize_data_8()
801 rc_t rgn_start_data( regions *rgn, uint32_t *count ) in rgn_start_data() argument
803 rc_t rc = rgn_resize_data_32( rgn ); in rgn_start_data()
807 uint32_t *ptr = rgn->data_32; in rgn_start_data()
808 *count = VectorLength( &rgn->read_Regions ); in rgn_start_data()
811 region * a_region = VectorGet ( &rgn->read_Regions, i ); in rgn_start_data()
820 rc_t rgn_len_data( regions *rgn, uint32_t *count ) in rgn_len_data() argument
822 rc_t rc = rgn_resize_data_32( rgn ); in rgn_len_data()
826 uint32_t *ptr = rgn->data_32; in rgn_len_data()
827 *count = VectorLength( &rgn->read_Regions ); in rgn_len_data()
830 region * a_region = VectorGet ( &rgn->read_Regions, i ); in rgn_len_data()
839 rc_t rgn_type_data( regions *rgn, uint32_t *count ) in rgn_type_data() argument
841 rc_t rc = rgn_resize_data_8( rgn ); in rgn_type_data()
845 uint8_t *ptr = rgn->data_8; in rgn_type_data()
847 *count = VectorLength( &rgn->read_Regions ); in rgn_type_data()
850 region * a_region = VectorGet ( &rgn->read_Regions, i ); in rgn_type_data()
859 rc_t rgn_filter_data( regions *rgn, uint32_t *count ) in rgn_filter_data() argument
861 rc_t rc = rgn_resize_data_8( rgn ); in rgn_filter_data()
865 uint8_t *ptr = rgn->data_8; in rgn_filter_data()
867 *count = VectorLength( &rgn->read_Regions ); in rgn_filter_data()
870 region * a_region = VectorGet ( &rgn->read_Regions, i ); in rgn_filter_data()
879 rc_t rgn_label_start_data( regions *rgn, uint32_t *count ) in rgn_label_start_data() argument
881 rc_t rc = rgn_resize_data_32( rgn ); in rgn_label_start_data()
885 uint32_t *ptr = rgn->data_32; in rgn_label_start_data()
888 *count = VectorLength( &rgn->read_Regions ); in rgn_label_start_data()
891 region * a_region = VectorGet ( &rgn->read_Regions, i ); in rgn_label_start_data()
916 rc_t rgn_label_len_data( regions *rgn, uint32_t *count ) in rgn_label_len_data() argument
918 rc_t rc = rgn_resize_data_32( rgn ); in rgn_label_len_data()
922 uint32_t *ptr = rgn->data_32; in rgn_label_len_data()
925 *count = VectorLength( &rgn->read_Regions ); in rgn_label_len_data()
928 region * a_region = VectorGet ( &rgn->read_Regions, i ); in rgn_label_len_data()