注意:由于空间限制,java源代码并没有包含在这个包中。如果你想获得这段代码,请通过ccabansk@dom.wustl.edu联系包维护者克里斯Cabanski 1.9.1 ReQON版本的变化- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -轻微变化的故事。2012年9月4日- - - - - - - - - - - - - - - - - -我们的手稿描述ReQON已经发表在BMC生物信息学。请参考本文进一步ReQON算法的描述和比较与其他质量分数调整算法。如果您使用我们的包,请引用本文。Cabanski CR et al。(2012) ReQON: Bioconductor包调整质量分数从下一代测序数据。BMC生物信息学13 (221)。doi: 10.1186 / 1471-2105-13-221。1.5.0 ReQON版本的变化- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - BUG修复一些用户接受错误hist.default(),这取决于指定的训练区域。这是固定的。 CHANGES in ReQON VERSION 1.3.4 ------------------------------- NEW FEATURES - An additional option has been added to ReadPosErrorPlot.R. The option "startpos" now allows users to designate the starting read position to be plotted. The default start position is 1. BUG FIXES - The required version of R has increased to 2.15. Major changes to the ReQON package were made in version 1.2.0, and older versions of R would download ReQON v. 1.0.0, which is incompatible with the current documentation. - There were minor inconsistencies between the FWSE reported in the output plots and FWSE calculated from the recalibrated BAM file, which has now been fixed. CHANGES in ReQON VERSION 1.3.2 ------------------------------- NEW FEATURES - ReQON no longer recalibrates 'N' bases. It returns the original quality score for these bases in the output BAM file. - Minor modifications have been made to FWSEplot.R. Points are now shaded according to the relative frequency of bases assigned that quality score. See the reference manual for more details. CHANGES in ReQON VERSION 1.2.0 ------------------------------- NEW FEATURES - Output BAM file keeps input header and adds header line: "@CO Quality scores were recalibrated with ReQON." - Allow threshold options (nerr and nrf) to remove positions from the training set that are likely to contain incorrect error calls. (e.g., novel variants and systematic mapping errors) - diagnostic output now outputs flagged read positions ($FlagPos) and regression coefficients ($coeff)