# roughAli.sql was originally generated by the autoSql program, which also 
# generated roughAli.c and roughAli.h.  This creates the database representation of
# an object which can be loaded and saved from RAM in a fairly 
# automatic way.

#A rough alignment - not detailed
CREATE TABLE roughAli (
    chrom varchar(255) not null,	# Human chromosome or FPC contig
    chromStart int unsigned not null,	# Start position in chromosome
    chromEnd int unsigned not null,	# End position in chromosome
    name varchar(255) not null,	# Name of other sequence
    score int unsigned not null,	# Score from 0 to 1000
    strand char(1) not null,	# + or -
    otherStart int unsigned not null,	# Start in other sequence
    otherEnd int unsigned not null,	# End in other sequence
              #Indices
    INDEX(chrom(12),chromStart),
    INDEX(name(12))
);
