[Bioperl-l] bioperl-db bugs

[Elia Stupka]

Hello there,

I am trying to fix the bugs that Alex reported. 
There is quite a few:

1)There is a strange one, Jason tell me if you seewhat you were trying to
do here:

In Bio/DB/Map/SQL/MarkerAdaptor.pm you write:

my (undef,$chrom) = ( $marker->chrom =~ /(chr)?(X|Y|UL|\d+)/ );

which perl doesn't like. I changed it to:

my ($go,$chrom) = ( $marker->chrom =~ /(chr)?(X|Y|UL|\d+)/ );

2)Also, the marker-db.sql file had lots of commas on the last lines of the
create statements, which made mysql die, I have fixed that.

3)The sql statements in the Adaptor were failing because statements were
made on columns named mapid rather than map_id, name rather than map_name 
as in the sql file

4)The marker schema seems to have changed radically , but not the
MarkerAdaptor.

I am making fixes as we speak, but Jason maybe there is stuff you have not
committed?

Elia



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