CHANGES IN VERSION 1.8.0
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
o Add median distance from nearest end (MDFNE) statistics to output
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
o Updated bam_tally, which is faster and includes support for
counting in soft-clipped regions.
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
o Add desired_read_group to BamTallyParam; will limit tallies to
that specific read group (useful for multi-amplicon sequencing,
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
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.
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
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.
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.
o asBam,GsnapOutput now actually works.
CHANGES IN VERSION 1.0.0
(start date: 12 September, 2012)