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 73 | Line 74
74   integers greater than 0 joined by the range operator ('..' or '...').
75   The first integer must be less than or equal to the second.
76  
77 <  11..22        An interval from 10 to 20 inclusive - length 11 (= 22-11+1)
77 >  11..22        An interval from 11 to 22 inclusive - length 12 (= 22-11+1)
78  
79    1...2         The same as 1..2
80  
# Line 84 | Line 85
85   or can be created with:
86    bioseg_create(start, end)
87  
88 + For the bioseg type <start> must be less than or equal to <end> and <start>
89 + must be 1 or more.
90 +
91   For example:
92    CREATE TABLE test_bioseg (id integer, seg bioseg);
93    insert into test_bioseg values (1, '1000..2000'::bioseg);
# Line 179 | Line 183
183   based" or "half-open intervals") run the build with INTERBASE_COORDS defined
184   in make, ie.:
185  
186 +    make clean
187      make INTERBASE_COORDS=t
188      make install INTERBASE_COORDS=t
189 +    (or: sudo make install INTERBASE_COORDS=t)
190  
191   This will compile and install the implementation for the "bioseg0" type.
192   The "0" in the name is a mnemonic for "0-based".
# Line 191 | Line 197
197  
198   The bioseg and bioseg0 types can be mixed in the same database.
199  
200 < Note
201 < ----
200 > Notes
201 > -----
202   In the interbase system '1..10'::bioseg0 and '10..20'::bioseg0 don't overlap,
203   whereas in the 1-based system '1..10'::bioseg and '10..20'::bioseg have a one
204   base overlap.  Also note that the length of '1..10'::bioseg0 is 9, whereas the
205   length of '1..10'::bioseg is 10.
206  
207 + Unlike the bioseg type the start and/or end of a bioseg0 can be negative, with
208 + the expected reults.
209 +  eg.   bioseg0_size('-10..10'::bioseg0) == 20
210 +
211   See:
212   http://www.gmod.org/wiki/index.php/Introduction_to_Chado#Interbase_Coordinates
213   for a longer discussion of the differences between the coordinate systems.

Diff Legend

Removed lines
+ Added lines
< Changed lines
> Changed lines