benchmarking SmartSeq perl script

            # match indexes to R1

            fastq_pair  ${convR1}.umi.fastq ${convI1}

            fastq_pair  ${convR1}.umi.fastq ${convI2}

end2=$(date +%s.%N)

runtime=$(python -c "print(${end2} - ${start2})")

echo "Runtime for trimming with bbduk.sh was $runtime"

runtime=$(python -c "print(${end2} - ${start1})")

echo "Runtime for trimming and filtering with bbduk.sh was $runtime"

            #replace original files

             mv ${convI1}.fastq.paired.fq ${convI1}

             mv ${convI2}.fastq.paired.fq ${convI2}

             mv $crIN/trimmed_R1.fq ${convR1}

             mv $crIN/trimmed_R2.fq ${convR2}

             rm $crIN/*fastq.paired.fq $crIN/*fastq.single.fq $crIN/clean_R1.fq $crIN/clean_R2.fq $crIN/fail_R1.fq $crIN/fail_R2.fq $crIN/pass_singletons.fq ${convR1}.umi.fastq

end2=$(date +%s.%N)

runtime=$(python -c "print(${end2} - ${start2})")

echo "Runtime for trimming with bbduk.sh was $runtime"

runtime=$(python -c "print(${end2} - ${start1})")

echo "Runtime for trimming and filtering with bbduk.sh was $runtime"

start=$(date +%s.%N)

            perl sub/FilterSmartSeqReadUMI.pl --r1=${convR1}--r2=${convR2} --i1=${convI1} --i2=${convI2} --out .

end=$(date +%s.%N)

runtime=$(python -c "print(${end} - ${start})")

echo "Runtime for trimming and filtering with custom perl was $runtime"

        done

    fi

exit 0