Remove multi-mappers and keep uniquely mapped reads in an alignment file. Now support .sam, .bed, and other tab-delimited files.

keepunique.sh

#!/bin/bash

column= type= infile= outfile=
while getopts c:i:o: opt; do
    case $opt in 
    c)
  column=$OPTARG
	;;
    i)
	infile=$OPTARG
        ;;
    o)
	outfile=$OPTARG
	;;
    esac
done

shift $((OPTIND - 1))

if test -z $infile; then
    echo "Remove multi-mappers and keep uniquely mapped reads in an alignment file. Now support .sam, .bed, and other tab-delimited files."
    echo "Usage: $0 [-c] -i infile [-o outfile]"
    echo "       -c Optional. Read name column. Default: 1"
    echo "       -i Manditory. Input file name."
    echo "       -o Optional. Output file name."
    exit 1
fi

if test -z $column; then
    case ${infile##*.} in
	sam)
	    column=1
            echo "Figured out the read name column as column $column by input file extenstion"
	    ;;
	bed)
            column=4
            echo "Figured out the read name column as column $column by input file extenstion"
	    ;;
	*)
	    column=1
	    echo "Could not figure out the read name column by input file extension. Use column $column."
	    ;;
    esac
fi

cut -f $column $infile | uniq -c > count.tmp

if test -z $outfile; then
    join -1 $column -2 2 $infile count.tmp | awk '$NF == 1' |
    awk '{delim = ""; for (i=1;i<=NF-1;i++) {printf delim "%s", $i; delim = OFS}; printf "\n"}'
else
    join -1 $column -2 2 $infile count.tmp | awk '$NF == 1' |
    awk '{delim = ""; for (i=1;i<=NF-1;i++) {printf delim "%s", $i; delim = OFS}; printf "\n"}' > $outfile
fi    
rm count.tmp