deepSNV -- an R package for subclonal variant calling. Changes in version 1.42.1 (2022-05-31) Bugfixes * Fully adjust VCF creation to use VariantAnnotation 1.27.6 and later's API (fixes broken VCF output like `##fileformat=<ID=fileformat,Value=VCFv4.1>`) * Fix crash when encountering reads that don't have an NM field * Fix crash when compiled with CentOS 8's GCC 8.3.1-4 * Correct the template VCF files' `#CHROM` header lines Changes in version 1.34.1 (2020-05-27) Bugfixes * Partially fixed issue when NM tag is absent Changes in version 1.33.3 Updates * Added NM tag mismatch filter in bam2R (max.mismatches=) Changes in version 1.33.2 Updates * Add filter for positive filtering of SAM flags (keepflag=) Changes in version 1.33.1 Bugfixes * Add error checking to result of sam_itr_next() Changes in version 1.29.1 Bugfixes * Added missing #CHROM line to template VCF files Changes in version 1.27.3 Updates * Compatibility with VariantAnnotation_1.27.6 and later Changes in version 1.27.2 Updates * Added support for overlapping read pairs Changes in version 1.21.4 Updates * Added mapping quality filter (mq=) Changes in version 1.21.3 Updates * Added SAM flag mask filter (mask=) Changes in version 1.21.1 Updates * Rearranged code to hopefully improve speed of BAM access Changes in version 1.15.1 Updates * 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 * Fix memory leak Changes in version 1.14.1 (2015-05-27) Bugfixes * Corrected linking to betabinom.o Changes in 1.13.8 Updates * Shearwater ML (Inigo Marticorena) * Rhtslib support (David Jones) Changes in version 1.11.1 Bugfixes * Report correct table in summary(..., value="VCF"); Thanks to David Gacquer. Changes in version 1.7.4 (2013-09-28) Updates * Only using the Dirichlet prior for control * Change back version numbers from 1.99.x to 1.7.x (2.0 not quite there :) Changes in version 1.99.3 (2013-07-25) Updates * A few changes to shearwater vignette * Renamed arguments pi.gene and pi.backgr in makePrior() Bugfixes * Fixed bug in bf2Vcf() when no variant is called Changes in version 1.99.2 (2013-07-11) Updates * Updated CITATION * Added verbose option to bam2R to suppress output * Changed mode() to "integer" for value of loadAllData() Bugfixes * Fixed bug when only one variant is called in bf2Vcf() Changes in version 1.99.1 (2013-06-25) Updates * Using knitr for prettier vignettes * Including shearwater vignette Bugfixes * fixed issues with deletions in bf2Vcf() * makePrior() adds background on all sites Changes in version 1.99.0 (2013-04-30) Updates * New shearwater algorithm * Including VCF output through summary(deepSNV, value="VCF") Changes in version 1.3.3 (2012-09-14) Updates * Changed CITATION * Updated documentation * Updated biocViews * Using roxygen2 for generating man pages Changes in version 1.3.2 (2012-04-10) Updates * New devel version, identical to release 1.2.3 Changes in version 1.2.3 (2012-04-10) Bugfixes * Fixed Vignette * Jumped a few numbers due to automated bioc version numbering Changes in version 1.0.0 (2012-03-29) Updates * Added CITATION file * Made NEWS (this file) R-readable * Changed Vignette Changes in version 0.99.3 Bugfixes * Fixed error in summary() when there were no significant SNVs. * Some fixes if only a single column of the alignment is selected Changes in version 0.99.2 (2012-01-20) Updates * Changed plot to S3 method (to avoid warning in R-devel) Changes in version 0.99.1 (2012-01-06) Updates * Added small .bam example files test.bam, control.bam with 100 positions. * Modified man pages for bam2R() * Modified man page for coordinates() * Corrected example of consensusSequence() * Compressed .RData files with tools::resaveRdaFiles * Changed vignette to attach data, rather than load remotely. * Argument "regions" of deepSNV can be a GRanges object. Changes in version 0.99.0 (2011-12-21) Updates * Added BiocViews field * Added HIVmix data * Added new examples * Registered bam2R with R_registerRoutines * New accessor functions "test", "control", "p.val", and "coordinates" * Updated vignette Changes in version 0.9.5 Updates * "summary" now reports additional columns from regions slot. Bugfixes * drop=FALSE in subsetting and summary. Changes in version 0.9.4 Updates * Directly link to static samtools library provided by Rsamtools * Load example .bam files over http Changes in version 0.9.3 * Added beta-binomial model * Extended documentation * Use summary instead of significantSNV Changes in version 0.9.2 * Minor bugfixes Changes in version 0.9.1 Minor bugfixes Changes in version 0.9.0 Pre-release