gapgenomes可以从rtracklayer支持的任何文件中构建(所以2bit现在可以工作，以及fasta)。o根据密码子对BAM文件进行记录，并给出一组文本结构。这发生在读取级别，即在单个读取中观察到密码子。o通过XS标记标记BAM文件链(推断转录链，而不是比对链)。修改版本1.6.0 -----------------------新功能o添加中位数距离最近的结束(MDFNE)统计输出variantSummary。更新后的GSNAP比以前的版本快了几个数量级，带来了许多修复，并提供了许多新功能。一个新特性是clip_overlap参数，它剪辑读对的重叠结尾(对变量调用很重要)。o更新了bam_tally，这是更快的，包括支持在软剪辑区域计数。更改tallyVariant统计:删除唯一的读位置计数;重命名count.pos /计数。negative 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)