#!/bin/bash

if [ $# -eq 0 ]; then
    echo >&2 ""
    echo >&2 "silentdropduplicatesequences by bcov - a tool to remove duplicate sequence entries from a silent file"
    echo >&2 "Usage:"
    echo >&2 "        silentdropduplicatesequences myfile.silent > uniq.silent"
    exit 1
fi


silent_dir="$(dirname $(type -p "$0"))"

silent=$1


tmp_name=$(head /dev/urandom | tr -dc A-Za-z0-9 | head -c 13)

"$silent_dir"/silentsequence $silent | awk '{print $1,$NF}' > $tmp_name.seq
# merge all columns except last one
#   (Find all columns that have a space before and after 
#    and delete the space before. )
perl -pi -e 's/ ([^ ]+)(?= )/\1/g' $tmp_name.seq

# Get unique lines and slice
sort -k1 $tmp_name.seq | sort -uk1,1 $tmp_name.seq | awk '{print $2}' | "$silent_dir"/silentslice $1

rm $tmp_name.seq


