CHANGES IN VERSION 1.8.0
-----------------------

NEW FEATURES

    o GmapGenomes can be built from any file supported by rtracklayer
      (so 2bit now works, as well as fasta).

    o Tally BAM files by codon given a set of transcript
      structures. This happens at the read level, i.e., a codon is
      observed within an individual read.

    o Tally BAM files strand by XS tag (inferred strand of
      transcription, instead of strand of alignment).
    
CHANGES IN VERSION 1.6.0
-----------------------

NEW FEATURES

    o Add median distance from nearest end (MDFNE) statistics to output
      of variantSummary.

    o Updated GSNAP, which is orders of magnitude faster than the
      previous version, brings many fixes and offers many new
      features. One new feature is the clip_overlap argument, which
      clips overlapping ends of read pairs (important for variant
      calling).

    o Updated bam_tally, which is faster and includes support for
      counting in soft-clipped regions.
    
USER-VISIBLE CHANGES

    o Changes to tallyVariant statistics: drop the unique read
      position counts; renamed count.pos/count.neg to
      count.plus/count.minus (way better names)

    o tallyVariants does a better job of carrying over the Seqinfo
      from the BAM file.
    
CHANGES IN VERSION 1.4.0
-----------------------

NEW FEATURES

    o Add desired_read_group to BamTallyParam; will limit tallies to
      that specific read group (useful for multi-amplicon sequencing,
      like Fluidigm)

    o Add keep_ref_rows argument to variantSummary() for keeping rows
      for positions where no alt is detected (the rows where ref == alt).

    o gsnap() will now output a GsnapOutputList when there are
      multiple input files

    o Support 'terminal_threshold' and 'gmap_mode' parameters in
      GsnapParam, and use different defaults for DNA vs. RNA. This
      means a big improvement in alignment quality for DNA.

    o GmapGenome now accepts a direct path to the genome as its first argument
    
USER-VISIBLE CHANGES

    o Renamed summarizeVariants to variantSummary

    o The 'which' in GsnapParam is now a GenomicRanges instead of a RangesList

    o Refactor bam_tally, so that bam_tally returns a TallyIIT object,
      which is then summarized via summarizeVariants; this allows computing
      tallies once and summarizing them in different ways (like maybe get
      the coverage). The summarizeVariants function yields a VRanges.

BUG FIXES

    o fix minimum quality cutoff check to >=, instead of >

    o fix asBam,GsnapOutput for when unique_only is TRUE

    o package created by makeGmapGenomePackage now have a GmapGenome with
      the correct name

CHANGES IN VERSION 1.2.0
-----------------------

NEW FEATURES

    o New method getSeq,GmapGenome retrieves sequence from a
      GmapGenome index. This also supports a coercion to DNAStringSet
      and thus easy export to FASTA via rtracklayer.

    o bam_tally gains an ignore_duplicates argument for ignoring BAM
      records flagged as PCR/optical duplicates.

    o Read position mean and variance are now output by bam_tally.

USER-VISIBLE CHANGES

    o GMAP has been updated to the July '12 version (yes, this is old).
    
    o GSTRUCT (bamtally) updated to trunk as of 3/22/13.
    
BUG FIXES

    o asBam,GsnapOutput now actually works.

CHANGES IN VERSION 1.0.0
-----------------------

Initial release

(start date: 12 September, 2012)
