Look into possibility to drop --no-discordant for Bowtie 2 mode to support dovetailing of reads

[FelixKrueger]

Can we explore how easy it would be to disable the Bowtie 2 option --no-discordant since this would allow dovetailing reads to align straight away. This would be very useful for PBAT-type runs that require clipping from their 5'-ends.

[FelixKrueger]

Having looked at this in some detail we decided not to drop --no-discordant because this would then all of a sudden start to report really weird alignments, e.g. reads facing away from each other or reads on different chromosomes. Instead we enabled the new option --dovetail (which will be turned on by default for --pbat libraries) which will now allow dovetailing reads to be reported:

 --dovetail        It is possible, though unusual, for the mates to 'dovetail', with the mates
                   seemingly extending 'past' each other as in this example:

  Mate 1:                 GTCAGCTACGATATTGTTTGGGGTGACACATTACGC
  Mate 2:            TATGAGTCAGCTACGATATTGTTTGGGGTGACACAT
  Reference: GCAGATTATATGAGTCAGCTACGATATTGTTTGGGGTGACACATTACGCGTCTTTGAC

  By default, dovetailing is considered inconsistent with concordant alignment, but setting 
  --dovetail causes Bowtie 2 to consider dovetailing alignments as concordant. This becomes 
  relevant whenever reads are clipped from their 5' end prior to mapping, e.g. because of
  quality or bias issues. --dovetail is set automatically for PBAT libraries.

This new option does indeed seem to work nicely (see this QC Fail article). Added in 395a793 and 8662516.