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# Line 30 | Line 30
30      make install
31  
32   The user running "make install" may need root access; depending on the
33 < configuration of PostgreSQL.
33 > configuration of PostgreSQL.  If so this may work:
34 >
35 >    sudo make install
36  
37   This only installs the type implementation and documentation.  To make the
38   type available in any particular database, do
# Line 51 | Line 53
53   If you have a full installation of PostgreSQL, including the pg_config
54   program, bioseg can be unpacked anywhere and built like:
55  
56 <     make USE_PGXS=t
57 <     make install USE_PGXS=t
56 >    make USE_PGXS=t
57 >    make install USE_PGXS=t
58  
59   and the type can then be installed in a particular database by any user with:
60  
# Line 62 | Line 64
64   SYNTAX
65   ======
66  
67 < The external representation of an interval is formed using one or two
67 > The user visible representation of an interval is formed using one or two
68   integers greater than 0 joined by the range operator ('..' or '...').
69   The first integer must be less than or equal to the second.
70  
71 < 11..22        An interval from 10 to 20 inclusive - length 11 (= 22-11+1)
71 >  11..22        An interval from 10 to 20 inclusive - length 11 (= 22-11+1)
72 >
73 >  1...2         The same as 1..2
74  
75 < 1...2         The same as 1..2
75 >  50            The same as 50..50
76  
77 < 50            The same as 50..50
77 > In a statement, bioseg values have the form:
78 >  '<start>..<end>'::bioseg
79 > or can be created with:
80 >  bioseg_create(start, end)
81 >
82 > For example:
83 >  CREATE TABLE test_bioseg (id integer, seg bioseg);
84 >  insert into test_bioseg values (1, '1000..2000'::bioseg);
85 > or, equivalently
86 >  insert into test_bioseg values (1, bioseg_create(1000, 2000));
87  
88  
89   USAGE
90   =====
91  
92 < Available operators include:
92 > See http://www.bioinformatics.org/bioseg/wiki/Main/BiosegUsage for usage
93 > examples.
94 >
95 > The following is a list of the available operators.  The [a, b] should be
96 > replaced in a statement with 'a..b'::bioseg or bioseg_create(a, b).
97  
98   [a, b] && [c, d]        Overlaps
99  
# Line 161 | Line 178
178      make install INTERBASE_COORDS=t
179  
180   This will compile and install the implementation for the "bioseg0" type.
181 < The "0" in the name being a mnemonic for "0-based".
181 > The "0" in the name is a mnemonic for "0-based".
182  
183 < Then restart PostgreSQL and run:
184 <    psql -d databasename < bioseg.sql
185 < as usual to install the type in the database.
183 > Then read "bioseg0.sql" into your database:
184 >    psql -d databasename < bioseg0.sql
185 > to install the type.
186 >
187 > The bioseg and bioseg0 types can be mixed in the same database.
188  
189   Note
190   ----
# Line 192 | Line 211
211  
212   Note from the author: Most of the code and all of the hard work needed to
213   implement BIOSEG was by Gene Selkov, Jr, author of the SEG type (contrib/seg
214 < in the PostgreSQL source).  All bugs are due to me.
214 > in the PostgreSQL source).  All bugs are due to me (kmr).
215  
216  
217   AUTHOR
218   ======
219  
220   Kim Rutherford <kmr@flymine.org>
221 +
222 + SEG code by Gene Selkov, Jr.
223 +

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