now using samtools 0.1.19
added SSW library: Complete-Striped-Smith-Waterman-Library by Mengyao Zhao
changed options parsing (-longopt to --longopt)
added --realign option with optional SW parameters
  with explicit support of ambiguous bases in the reference file
  using SSW library
  added logic for removing and appending softclipping
added ambiguity matches when considering placement (using MD field)
a few bugfixes and brought 0.1.19 version of bam_fillmd1_core into samtools_helper
brought 0.1.19 version of bam_fillmd1_core into samtools_helper
attempt to fix assertion bombing on files with multiple primary placements
added --SNPreport option
added tests for --realign and --SNPreport options
restored error messages when input files could not be opened
added --minQual option to ignore, for Z-normalization calculations, quality
   scores below 2.  This was leading to extremely high Z-normalization numbers
   when Illumina classifies a string of bases with quality 2 but the read is
   largely correct
bugfix in --minQual help and implementation
fixed a comment
fixed a segfault with --SNPreport and fixed --pl to actually work
added clean and gitignore files