Score and strand inversion.

gff_merge_transcripts.sh

@@ -46,7 +46,7 @@ merge_bedtools()
     # -g 1,4,5,6 assumes that for a given name,
     # chromosome, score and strand are always the same
     trap '' PIPE && exec \
-    bedtools groupby -g 1,4,6,5 -c 2,3 -o min,max -i "stdin" \
+    bedtools groupby -g 1,4,5,6 -c 2,3 -o min,max -i "stdin" \
         | mawk -v OFS="\t" '{print $1,$5,$6,$2,$3,$4}' \
         | sort-bed - \
         || error_exit "merge_bedtools failed"