Changes in version 1.99.3 (2013-07-25) Updates o A few changes to shearwater vignette o Renamed arguments pi.gene and pi.backgr in makePrior() Bugfixes o Fixed bug in bf2Vcf() when no variant is called Changes in version 1.99.2 (2013-07-11) Updates o Updated CITATION o Added verbose option to bam2R to suppress output o Changed mode() to "integer" for value of loadAllData() Bugfixes o Fixed bug when only one variant is called in bf2Vcf() Changes in version 1.99.1 (2013-06-25) Updates o Using knitr for prettier vignettes o Including shearwater vignette Bugfixes o fixed issues with deletions in bf2Vcf() o makePrior() adds background on all sites Changes in version 1.99.0 (2013-04-30) Updates o New shearwater algorithm o Including VCF output through summary(deepSNV, value="VCF") Changes in version 1.42.1 (2022-05-31) Bugfixes o Fully adjust VCF creation to use VariantAnnotation 1.27.6 and later's API (fixes broken VCF output like `##fileformat=`) o Fix crash when encountering reads that don't have an NM field o Fix crash when compiled with CentOS 8's GCC 8.3.1-4 o Correct the template VCF files' `#CHROM` header lines Changes in version 1.34.1 (2020-05-27) Bugfixes o Partially fixed issue when NM tag is absent Changes in version 1.33.3 Updates o Added NM tag mismatch filter in bam2R (max.mismatches=) Changes in version 1.33.2 Updates o Add filter for positive filtering of SAM flags (keepflag=) Changes in version 1.33.1 Bugfixes o Add error checking to result of sam_itr_next() Changes in version 1.29.1 Bugfixes o Added missing #CHROM line to template VCF files Changes in version 1.27.3 Updates o Compatibility with VariantAnnotation_1.27.6 and later Changes in version 1.27.2 Updates o Added support for overlapping read pairs Changes in version 1.21.4 Updates o Added mapping quality filter (mq=) Changes in version 1.21.3 Updates o Added SAM flag mask filter (mask=) Changes in version 1.21.1 Updates o Rearranged code to hopefully improve speed of BAM access Changes in version 1.15.1 Updates o Adapt to VariantAnnotation's VCF class changing to extend the RangedSummarizedExperiment class rather than SummarizedExperiment Changes in version 1.14.2 (2015-06-07) Bugfixes o Fix memory leak Changes in version 1.14.1 (2015-05-27) Bugfixes o Corrected linking to betabinom.o Changes in version 1.13.8 Updates o Shearwater ML (Inigo Marticorena) o Rhtslib support (David Jones) Changes in version 1.11.1 Bugfixes o Report correct table in summary(..., value="VCF"); Thanks to David Gacquer. Changes in version 1.7.4 (2013-09-28) Updates o Only using the Dirichlet prior for control o Change back version numbers from 1.99.x to 1.7.x (2.0 not quite there :) Changes in version 1.3.3 (2012-09-14) Updates o Changed CITATION o Updated documentation o Updated biocViews o Using roxygen2 for generating man pages Changes in version 1.3.2 (2012-04-10) Updates o New devel version, identical to release 1.2.3 Changes in version 1.2.3 (2012-04-10) Bugfixes o Fixed Vignette o Jumped a few numbers due to automated bioc version numbering Changes in version 1.0.0 (2012-03-29) Updates o Added CITATION file o Made NEWS (this file) R-readable o Changed Vignette Changes in version 0.99.3 Bugfixes o Fixed error in summary() when there were no significant SNVs. o Some fixes if only a single column of the alignment is selected Changes in version 0.99.2 (2012-01-20) Updates o Changed plot to S3 method (to avoid warning in R-devel) Changes in version 0.99.1 (2012-01-06) Updates o Added small .bam example files test.bam, control.bam with 100 positions. o Modified man pages for bam2R() o Modified man page for coordinates() o Corrected example of consensusSequence() o Compressed .RData files with tools::resaveRdaFiles o Changed vignette to attach data, rather than load remotely. o Argument "regions" of deepSNV can be a GRanges object. Changes in version 0.99.0 (2011-12-21) Updates o Added BiocViews field o Added HIVmix data o Added new examples o Registered bam2R with R_registerRoutines o New accessor functions "test", "control", "p.val", and "coordinates" o Updated vignette Changes in version 0.9.5 Updates o "summary" now reports additional columns from regions slot. Bugfixes o drop=FALSE in subsetting and summary. Changes in version 0.9.4 Updates o Directly link to static samtools library provided by Rsamtools o Load example .bam files over http Changes in version 0.9.3 o Added beta-binomial model o Extended documentation o Use summary instead of significantSNV Changes in version 0.9.2 o Minor bugfixes Changes in version 0.9.1 o Minor bugfixes Changes in version 0.9.0 o Pre-release