# patch_59_60_c.sql
#
# Title:
#   A patch to fix a couple of inconsistencies in the schema.
#
# Description:
#   QC turned up issues with the signedness of a number of fields in
#   the Ensembl Core schema.  This patch fixes these.  The fields
#   are: karyotype.seq_region_start, karyotype.seq_region_end and
#   seq_region.length (should all be UNSIGNED).

to find.

#
# Title:
#   A patch to fix a couple of inconsistencies in the schema.
#
# Description:
#   A couple of fixes to the schema to do with inconsistencies found
#   during QC.

get_all_DBEntries().  From Michael S.

unneccesarily in add_Attributes().  Transcript attributes do not affect
exon sequences.  Also, the code tried to fiddle with the internals of
the exon object, which is a no-no (especially since those particular
internals did not exist!).

While at it, I changed a few of "$hash->{'key'} = undef" into
"delete($hash->{'key'})".

conditional operator.

In fetch_all_by_Transcript():  Be absolutely sure not to add the
exon_transcript table twice.  Should solve a bug reported by Jan.

In translation_id(): Update for this method.

All from Michael S.

throw() has the correct message (but leave it commented out since it
would stop circular genomes working).

In overlap_size(): Correct documentation.


All from Michael S.

Michael S.

Also, reformat method.

Michael S.

Michael S.

Also, reformat method.

message.  From Michael S.

Also, reformat method.

mentioning of return values as none are returned (and the rest of the
API is not expecting anything).  From Michael S.


Also, reformat method.

transcript's translation.

translation's transcript.

of the two slices into account.  From Michael S.

transcripts.

In get_all_DBEntries(): Document undocumented arguments.


From Michael S.

slice was given.  Noticed by Michael S.

From Michael S.

external DB type strings contains '%' and use "LIKE" or "=" accordingly.
Document this behaviour in the POD of the method.  Also, safely quote
strings inserted into SQL.

In _type_by_external_db_id(): Fix documentation for method.

Both pointed out by Michael S.

  Fix misspelt "Exmaple".

  In AUTOLOAD(): warning() before throw(), otherwise not much joy.

Also get rid of inconsistency pointed out by Michael S.

  Fix documentation for register_assembled(), register_component(),
  _register_chained_special().

  Remove unused variable in _build_combined_mapper().

  Initialise $mid_cs_id in _register_chained_special() properly.

  Use splice() to remove a list element in register_all_chained() rather
  than setting the list length (say what?!).