fix symlinks

# Pipeline to run UMI-seq analysis from fastq to read count tables.

# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann

# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se

vers=3.0beta

vers=2.5.5

currentv=`curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/master/zUMIs-master.sh | grep '^vers=' | cut -f2 -d "="`

if [ "$currentv" != "$vers" ]; then echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------"; fi

  echo "Filtering..."

  f=`cut -d' ' -f1 <(echo $fqfiles)` # the first fastq file to determine gzip status

  fullsize=`stat --printf="%s" $f`

  fullsize=`stat -L --printf="%s" $f`

  tmpMerge=$outdir/zUMIs_output/.tmpMerge/

then

  if [[ "$isstats" == "yes" ]]; then

    echo "Descriptive statistics..."

    echo "... are currently not implemented"

      #$Rexc $zumisdir/zUMIs-stats2.R $yaml

      $Rexc $zumisdir/zUMIs-stats2.R $yaml

  fi

  date

fi