Account for gzipped fastq files

## Directories to be created and regex strings for listing files

splitdir=${topDir}"/splits"

donesplitdir=$topDir"/done_splits"

fastqdir=${topDir}"/fastq/*_R*.fastq"

fastqdir=${topDir}"/fastq/*_R*.fastq*"

outputdir=${topDir}"/aligned"

tmpdir=${topDir}"/HIC_tmp"

logdir=${topDir}"/logs"

        name2=\${name}${read2str}

        jname=\$(basename "\$name")\${ext}

        usegzip=0

        if [ "\${ext}" == ".gz" ]

        if [ "\${ext: -3}" == ".gz" ]

        then

            usegzip=1

        fi

        # remove header, add read end indicator to read name

        awk -f ${juiceDir}/scripts/read1_sortproc.awk \${name1}\${ext}_sort.sam > \${name1}\${ext}_sort1.sam

        awk -f ${juiceDir}/scripts/read2_sortproc.awk \${name2}\${ext}_sort.sam > \${name2}\${ext}_sort1.sam

        echo "below is the number of lines in \${name1}\${ext}_sort1.sam"

        cat \${name1}\${ext}_sort1.sam | wc -l

        echo "below is the number of lines in \${name2}\${ext}_sort1.sam"