Many changes including how the coordinate ranges are selected, performance improvements, bug fixes, and some new options
Many changes including how the coordinate ranges are selected, performance improvements, bug fixes, and some new options

 - Completely changed the selection and processing of coordinates:
    - If only a chromosome is specified, then selection is done on the
      whole chromosome
    - If a chromosome, start and stop are specified, then the selection
      is done only on the region on the chromosome for the start and
      stop
    - If a coordinatesFilename is specified, then selection is done on
      each (chrom, start, stop) specified

 - Added ability to input a coordinates file that specifies single
   coordinates or coordinate ranges to query (3 column tab delimited
   (chr, start, stop))

 - The -c or -—chromSizesFilename has been deprecated
    - The user has to specify at least one fasta file with the fasta
      index file that contains the lengths of the chromosome sizes,
      so this parameter is not needed
    - Instead, the -c or -—coordinatesFilename are now used to specify
      single coordinates or coordinate ranges to query (3 column tab
      delimited (chr, start, stop))

 - Fixed problem with user specifying .mpileup files as input. The
   .mpileup files were ignored and instead the .bam files were queried

 - If we find a variant, make sure the possible parent allele count is
   above the previous aMinAltNumBases

 - To improve performance, added new processing of raw reads that
   significantly reduces runtime

 - Added a break for the case when no more data is available

 - Added the modification filters 'MF' and modification filter types
   'MFT' to the header

 - Added an option to suppress the outputting of the header

 - Added an option to output all data at a position, no matter if a
   variant is present or not

 - Added some flags for outputting VCF lines when debugging

 - Added ability to query one single position

 - Added ability to include RNA secondary alignments

 - Added analyte to the SAMPLE tag in the header

 - The AD format field should be an Integer instead of a Float

aradenbaugh/radia