# Annotate BED-file with gene and strand

cat $BEDFILE |
awk -F '\t' '{printf("select DISTINCT \"%s\",\"%s\",\"%s\", G.name2,G.strand from refGene as G  where chrom=\"%s\" \
and  (%s<txEnd and %s>txStart);\n",$1,$2,$3,$1,$2,$3);}'  |\
mysql --user=genome --host=genome-mysql.cse.ucsc.edu  -A  -N -D hg19