版本1.8.0的变化- - - - - - - - - - - - - - - - - - - - - - - - o GmapGenomes新特性可以由任何文件支持rtracklayer(2位现在的作品,以及fasta)。o统计文件的密码子的BAM给定一组记录结构。这种情况发生在阅读层面,即。,一个密码子中观察到一个人阅读。o统计BAM x标记链的文件(推断的转录,而不是链对齐)。版本1.6.0变化- - - - - - - - - - - - - - - - - - - - - - - - o添加新特性值距离最近的结束(MDFNE)统计variantSummary的输出。o GSNAP更新,这是数量级的速度比以前的版本,带来了许多补丁和提供了许多新特性。一个新特性是clip_overlap论点,剪辑重叠结束阅读对变量调用(重要)。o bam_tally更新,更快,包括支持计数soft-clipped地区。用户可见的变化改变阿tallyVariant统计:独特的阅读位置下降; 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)