ShapeMapper2 version 2.2

• Added DMS mode option
• Fixed bug in MutationParser so that paired (unmerged) reads are now merged
• Provides a temporary fix to STAR mode so that it automatically runs in serial, avoiding the hang that happens in parallel
• Upversioned internal python and thirdparty codes:
  Pipeviewer 1.6.0 > 1.6.20
  Python 3.5.3 > 3.9.12
  numpy 1.11.3 > 1.19.5
  libgcc 5.2.0 > 7.2.0
  java-jdk 8.0.45 > 8.0.112
  perl-threaded 5.22.0 > 5.32.1
  scikit-learn=0.18.1 > 1.1.2
  matplotlib 1.5.1 > 3.6.2
  graphviz 2.38.0 > 7.1.0