anchor.diff:  // cuffmerge
   deftask cuffmerge( merged( File ) : <transcript( File )> geneanno( File ) [fa( File ) fai( File )] )in bash *{
     merged=merged_asm/merged.gtf
  -  if ! [ -f genome.fa ]
  -  then
  -    ln -s $fa genome.fa
  -  fi
  -  if ! [ -f genome.fa.fai ]
  -  then
  -    ln -s $fai genome.fa.fai
  -  fi
  +  ln -sf $fa genome.fa
  +  ln -sf $fai genome.fa.fai
     printf "%s\n" ${transcript[@]} > assemblies.txt
     cuffmerge -g $geneanno -s genome.fa -p 4 assemblies.txt
   }*
  
positive.code:   b2=`printf ",%s" ${bam2[@]}`
    b2=${b2:1}
  
    if ! [ -f genome.fa ]
    then
      ln -s $fa genome.fa
    fi
    if ! [ -f genome.fa.fai ]
    then
      ln -s $fai genome.fa.fai
    fi
  
    cuffdiff --no-update-check -p 4 \
    -o diff_out \
  
negative.code: 
  deftask samtools-idxstats( idxstats( File ) : bam( File ) bai( File ) )in bash *{
  
    ln -sf $bam alignment.bam
    ln -sf $bai alignment.bam.bai
  
    samtools idxstats alignment.bam > $idxstats
  }*
  