Align indel variants in alignment view instead of centering

[zachary-foster]

Current behavior when indels are encountered is to center the shorter variants in the gap:

Reference : tctttctatcttcttcctcctcggGTGTCCACCGTGGCCGGTGGACAgTccAcCGTGGCCGGcGttgAgtcctctattgtccctttccctttt  T  t T  accaataggatcgcagcgatgcagttcttttggccaatcagg
      NA1 : ............................................................................................. T294.T292..........................................
      EU1 : .........................----------------------....N.---------.N...N......................... T210.T210..........................................
      EU2 : ................................................G..T.----C----.C...T.........................<C11>.T11 ..........................................
      NA2 : ........................N..........................T.---------.S...W......................... T13 .<G8>..........................................
   oligos : tctttctatcttcttcctcctcggg----------t-----------gtc                                                      gtcctctattgtccctttcccttttCtt             

Would be better to use something like nltk.metrics.distance.edit_distance_align to do a short alignment to the reference or a multiple sequence alignment to make it look like:

Reference : tctttctatcttcttcctcctcggGTGTCCACCGTGGCCGGTGGACAgTccAcCGTGGCCGGcGttgAgtcctctattgtccctttccctttt  T  t T  accaataggatcgcagcgatgcagttcttttggccaatcagg
      NA1 : ............................................................................................. T294.T292..........................................
      EU1 : .........................----------------------....N.---------.N...N......................... T210.T210..........................................
      EU2 : ................................................G..T.C--------.C...T.........................<C11>.T11 ..........................................
      NA2 : ........................N..........................T.---------.S...W......................... T13 .<G8>..........................................
   oligos : tctttctatcttcttcctcctcgggt---------------------gtc                                                      gtcctctattgtccctttcccttttCtt