Version: 1.8.0
Category: NEW FEATURES
Text: GmapGenomes can be built from any file supported by rtracklayer
        (so 2bit now works, as well as fasta).

Version: 1.8.0
Category: NEW FEATURES
Text: 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.

Version: 1.8.0
Category: NEW FEATURES
Text: Tally BAM files strand by XS tag (inferred strand of
        transcription, instead of strand of alignment).

Version: 1.6.0
Category: NEW FEATURES
Text: Add median distance from nearest end (MDFNE) statistics to output
        of variantSummary.

Version: 1.6.0
Category: NEW FEATURES
Text: 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).

Version: 1.6.0
Category: NEW FEATURES
Text: Updated bam_tally, which is faster and includes support for
        counting in soft-clipped regions.

Version: 1.6.0
Category: USER-VISIBLE CHANGES
Text: Changes to tallyVariant statistics: drop the unique read position
        counts; renamed count.pos/count.neg to count.plus/count.minus
        (way better names)

Version: 1.6.0
Category: USER-VISIBLE CHANGES
Text: tallyVariants does a better job of carrying over the Seqinfo from
        the BAM file.

Version: 1.4.0
Category: NEW FEATURES
Text: Add desired_read_group to BamTallyParam; will limit tallies to
        that specific read group (useful for multi-amplicon sequencing,
        like Fluidigm)

Version: 1.4.0
Category: NEW FEATURES
Text: Add keep_ref_rows argument to variantSummary() for keeping rows
        for positions where no alt is detected (the rows where ref ==
        alt).

Version: 1.4.0
Category: NEW FEATURES
Text: gsnap() will now output a GsnapOutputList when there are multiple
        input files

Version: 1.4.0
Category: NEW FEATURES
Text: 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.

Version: 1.4.0
Category: NEW FEATURES
Text: GmapGenome now accepts a direct path to the genome as its first
        argument

Version: 1.4.0
Category: USER-VISIBLE CHANGES
Text: Renamed summarizeVariants to variantSummary

Version: 1.4.0
Category: USER-VISIBLE CHANGES
Text: The 'which' in GsnapParam is now a GenomicRanges instead of a
        RangesList

Version: 1.4.0
Category: USER-VISIBLE CHANGES
Text: 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.

Version: 1.4.0
Category: BUG FIXES
Text: fix minimum quality cutoff check to >=, instead of >

Version: 1.4.0
Category: BUG FIXES
Text: fix asBam,GsnapOutput for when unique_only is TRUE

Version: 1.4.0
Category: BUG FIXES
Text: package created by makeGmapGenomePackage now have a GmapGenome
        with the correct name

Version: 1.2.0
Category: NEW FEATURES
Text: 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.

Version: 1.2.0
Category: NEW FEATURES
Text: bam_tally gains an ignore_duplicates argument for ignoring BAM
        records flagged as PCR/optical duplicates.

Version: 1.2.0
Category: NEW FEATURES
Text: Read position mean and variance are now output by bam_tally.

Version: 1.2.0
Category: USER-VISIBLE CHANGES
Text: GMAP has been updated to the July '12 version (yes, this is old).

Version: 1.2.0
Category: USER-VISIBLE CHANGES
Text: GSTRUCT (bamtally) updated to trunk as of 3/22/13.

Version: 1.2.0
Category: BUG FIXES
Text: asBam,GsnapOutput now actually works.

Version: 1.0.0
Category: Initial release
Text: (start date: 12 September, 2012)