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)