Merge pull request #22 from eastgenomics/fix_intersect_bug

fix bug on intersecting

bin/annotate_bed.sh

@@ -63,7 +63,7 @@ outfile=$(basename $bp_coverage)
 outfile=${outfile/.per-base.bed.gz/_annotated.bed}
 
 # add gene and exon annotation to panel bed file from exons nirvana tsv
-bedtools intersect -a $input_bed -b $gene_file -wa -wb | awk 'OFS="\t" {if ($4 == $9) print}' | cut -f 1,2,3,8,9,10 > ${tmp}.txt
+bedtools intersect -f 1.0 -r -a $input_bed -b $gene_file -wa -wb | awk 'OFS="\t" {if ($4 == $9) print}' | cut -f 1,2,3,8,9,10 > ${tmp}.txt
 
 # add coverage annotation from per base coverage bed file
 bedtools intersect -wa -wb -a $tmp.txt -b $bp_coverage | cut -f 1,2,3,4,5,6,8,9,10 > $outfile