

print <<EOF

create table alignment( 
 queryID text,
 queryLength integer,
 target text,
 strand text,
 targetStart integer,
 targetEnd integer,
 similarity double,
 queryCoverage double,
 evalue text,
 bitScore integer,
 targetSequence text,
 querySequence text,
 alignment text
);


.separator \\t
.import #{ARGV[0]} alignment

create index genome_index on alignment(target, targetStart);
create index query_index on alignment(queryID);

EOF

