版本1.8.0的更改----------------------------------新功能o Gmapgenomes可以根据Rtracklayer支持的任何文件构建（因此2bit现在也有效作为fasta）。o tally bam by by密码子给定了一组成绩单结构。这发生在读取级别，即在单个读取中观察到密码子。o tally bam files strand通过XS标签（推断的转录线，而不是对齐的线）。版本1.6.0的更改----------------------------------------新功能o将最近端（MDFNE）统计信息的中值距离添加到Variantsummary的输出。o更新的GSNAP（比以前的版本都要快数量级）带来了许多修复程序并提供了许多新功能。一个新功能是clip_overlap参数，该参数剪辑了读取对的重叠末端（对于变体调用很重要）。o更新的BAM_TALLY，它更快，包括在软剪裁区域中计数的支持。用户可见的更改o对tallyvariant统计信息的更改：删除唯一的读取位置计数； 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)