<commit_before># Call tRNA peaks using annotation
input="$1"
output="$2"
annotation="$project_data_dir/$(read_conf trna-call-peaks annotation)"

# Read individual parts and reconstruct line in order to get rid of excess
# whitespace.
while read chr trna type from to rest; do
    line="$chr	$trna	$type	$from	$to	$rest"
    if [ $from -gt $to ]; then
        tmp=$from
        from=$to
        to=$tmp<commit_msg>Update to match format of tRNA annotation<commit_after># Call tRNA peaks using annotation
input="$1"
output="$2"
annotation="$project_data_dir/$(read_conf trna-call-peaks annotation)"

# Read individual parts and reconstruct line in order to get rid of excess
# whitespace.

# OLD FORMAT:
# chr1	 .trna1000	AspGTC 	172995560	172995489	  Asp 	GTC	 72 bp  Sc: 72.92
# NEW FORMAT (tRNAScan-SE native):
# 1	284	78297795	78297866	Pro	AGG	0	0	48.57	Bo
while read chr trna from to rest; do
    line="$chr	$trna	$from	$to	$rest"
    if [ $from -gt $to ]; then
        tmp=$from
        from=$to
        to=$tmp
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