docs: def alignmentbed2dalignedfasta(cfg):
      """
      Get sequences in FASTA format from BED file
      step#5
  
      :param cfg: configuration dict
      """    
      datatmpd=cfg['datatmpd']
      alignmentbedp=cfg['alignmentbedp']    
      dalignedfastap=cfg['dalignedfastap']
      logging.info(basename(dalignedfastap))
      if not exists(dalignedfastap) or cfg['force']:
          alignedfastap='{}/05_alignment.fa'.format(datatmpd)
          if not exists(alignedfastap) or cfg['force']:
              cmd=f"{cfg['bedtools']} getfasta -s -name -fi {cfg['genomep']} -bed {alignmentbedp} -fo {alignedfastap}"
              runbashcmd(cmd)
  
          dalignedfasta=fa2df(alignedfastap)
          dalignedfasta.columns=['aligned sequence']
          dalignedfasta=dalignedfasta.loc[(dalignedfasta.apply(lambda x: not 'N' in x['aligned sequence'],axis=1)),:] #FIXME bwa aligns to NNNNNs
          dalignedfasta.index=[i.split('(')[0] for i in dalignedfasta.index] # for bedtools 2.27, the fasta header now has hanging (+) or (-)
          dalignedfasta.index.name='id'
          dalignedfasta.to_csv(dalignedfastap,sep='\t')
      return cfg