ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/bioseg/trunk/README.bioseg
(Generate patch)
# Line 57 | Line 57
57   If you have a full installation of PostgreSQL, including the pg_config
58   program, bioseg can be unpacked anywhere and built like:
59  
60 +    make USE_PGXS=t clean
61      make USE_PGXS=t
62      make install USE_PGXS=t
63      (or: sudo make install USE_PGXS=t)
# Line 156 | Line 157
157          you want to use ORDER BY with this type
158  
159  
160 < NOTE: The performance of an R-tree index can largely depend on the
161 < order of input values. It may be very helpful to sort the input table
161 < on the BIOSEG column (see the script sort-segments.pl for an example)
160 > NOTE: The performance of an R-tree index can largely depend on the order of
161 > input values.  It may be helpful to sort the input table on the BIOSEG column.
162  
163  
164   INDEXES
# Line 179 | Line 179
179   based" or "half-open intervals") run the build with INTERBASE_COORDS defined
180   in make, ie.:
181  
182 +    make clean
183      make INTERBASE_COORDS=t
184      make install INTERBASE_COORDS=t
185 +    (or: sudo make install INTERBASE_COORDS=t)
186  
187   This will compile and install the implementation for the "bioseg0" type.
188   The "0" in the name is a mnemonic for "0-based".
# Line 191 | Line 193
193  
194   The bioseg and bioseg0 types can be mixed in the same database.
195  
196 < Note
197 < ----
196 > Notes
197 > -----
198   In the interbase system '1..10'::bioseg0 and '10..20'::bioseg0 don't overlap,
199   whereas in the 1-based system '1..10'::bioseg and '10..20'::bioseg have a one
200   base overlap.  Also note that the length of '1..10'::bioseg0 is 9, whereas the
201   length of '1..10'::bioseg is 10.
202  
203 + Unlike the bioseg type the start and/or end of a bioseg0 can be negative, with
204 + the expected reults.
205 +  eg.   bioseg0_size('-10..10'::bioseg0) == 20
206 +
207   See:
208   http://www.gmod.org/wiki/index.php/Introduction_to_Chado#Interbase_Coordinates
209   for a longer discussion of the differences between the coordinate systems.

Diff Legend

Removed lines
+ Added lines
< Changed lines
> Changed lines