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 version 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
