NEWS
818929e9
 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).
     
c42aaf5e
 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.
     
084199c0
 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
 
d6a37798
 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)