Properly handle RNA aligned to the transcriptome and other fixes
Properly handle RNA aligned to the transcriptome and other fixes

    - The base on the read is being compared to the forward
      genomic strand REF and ALT columns, so the base needs
      to be converted to the forward genomic strand if necessary.

    - Some of the read lengths were negative and based off of
      the insert size.  Now the actual read length is used.

    - The start and stop coordinates on the blat hits can be
      reversed, so check for overlaps in both directions.

    - The previous code was keeping a list of 'other' values,
      and then finding the min or max at the end, but it is much
      easier to just keep the top 'overlapping' value and the
      top 'other' value as each blat hit is processed. The old
      way also had a bug if no 'other' value was set for the
      max overlapping identity.

    - The previous code loaded all of the blat hits into memory
      at the beginning and then looped over the VCF lines to
      process each call.  In order to avoid using a ton of memory
      by loading all the blat hits at once, now the VCF line and
      the corresponding blat hits are loaded into memory one call
      at a time, using python generators.

    - The previous code required the blat alignment length to be
      at least half the read length to set the maxOverlapIdentity,
      but it did not make the same requirement to set the
      maxOverlapEValue. Now both parameters require the blat
      alignment length to be at least half the read length.

    - The transcript name, coordinate, and strand are needed
      for RNA that is aligned to the transcriptome.

    - The RNA secondary alignments flag is needed when the RNA
      is aligned to the transcriptome.

    - Skip the PSL header lines.

    - Changed some parameter names to be consistent with
      other code.

    - Added an order of magnitude flag.

    - Added ability to filter DNA somatic calls by blat.

    - Need to check for empty lines before removing the newline.

aradenbaugh/radia