NEWS

gmapR 1.8.0

GmapGenomes can be built from any file supported by rtracklayer (so 2bit now works, as well as fasta).
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.
Tally BAM files strand by XS tag (inferred strand of transcription, instead of strand of alignment).

Add median distance from nearest end (MDFNE) statistics to output of variantSummary.
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).
Updated bam_tally, which is faster and includes support for counting in soft-clipped regions.

Changes to tallyVariant statistics: drop the unique read position counts; renamed count.pos/count.neg to count.plus/count.minus (way better names)
tallyVariants does a better job of carrying over the Seqinfo from the BAM file.

Add desired_read_group to BamTallyParam; will limit tallies to that specific read group (useful for multi-amplicon sequencing, like Fluidigm)
Add keep_ref_rows argument to variantSummary() for keeping rows for positions where no alt is detected (the rows where ref == alt).
gsnap() will now output a GsnapOutputList when there are multiple input files
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.
GmapGenome now accepts a direct path to the genome as its first argument

Renamed summarizeVariants to variantSummary
The 'which' in GsnapParam is now a GenomicRanges instead of a RangesList
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.

fix minimum quality cutoff check to >=, instead of >
fix asBam,GsnapOutput for when unique_only is TRUE
package created by makeGmapGenomePackage now have a GmapGenome with the correct name

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.
bam_tally gains an ignore_duplicates argument for ignoring BAM records flagged as PCR/optical duplicates.
Read position mean and variance are now output by bam_tally.