NEWS

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deepSNV 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

deepSNV 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()

deepSNV 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

deepSNV 1.99.0 (2013-04-30)

Updates

• New shearwater algorithm
• Including VCF output through summary(deepSNV, value="VCF")

deepSNV 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

deepSNV 1.34.1 (2020-05-27)

Bugfixes

• Partially fixed issue when NM tag is absent

deepSNV 1.33.3

Updates

• Added NM tag mismatch filter in bam2R (max.mismatches=)

deepSNV 1.33.2

Updates

• Add filter for positive filtering of SAM flags (keepflag=)

deepSNV 1.33.1

Bugfixes

• Add error checking to result of sam_itr_next()

deepSNV 1.29.1

Bugfixes

• Added missing #CHROM line to template VCF files

deepSNV 1.27.3

Updates

• Compatibility with VariantAnnotation_1.27.6 and later

deepSNV 1.27.2

Updates

• Added support for overlapping read pairs

deepSNV 1.21.4

Updates

• Added mapping quality filter (mq=)

deepSNV 1.21.3

Updates

• Added SAM flag mask filter (mask=)

deepSNV 1.21.1

Updates

• Rearranged code to hopefully improve speed of BAM access

deepSNV 1.15.1

Updates

• Adapt to VariantAnnotation's VCF class changing to extend the RangedSummarizedExperiment class rather than SummarizedExperiment

deepSNV 1.14.2 (2015-06-07)

Bugfixes

• Fix memory leak

deepSNV 1.14.1 (2015-05-27)

Bugfixes

• Corrected linking to betabinom.o

deepSNV 1.13.8

Updates

• Shearwater ML (Inigo Marticorena)
• Rhtslib support (David Jones)

deepSNV 1.11.1

Bugfixes

• Report correct table in summary(..., value="VCF"); Thanks to David Gacquer.

deepSNV 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 :)

deepSNV 1.3.3 (2012-09-14)

Updates

• Changed CITATION
• Updated documentation
• Updated biocViews
• Using roxygen2 for generating man pages

deepSNV 1.3.2 (2012-04-10)

Updates

• New devel version, identical to release 1.2.3

deepSNV 1.2.3 (2012-04-10)

Bugfixes

• Fixed Vignette
• Jumped a few numbers due to automated bioc version numbering

deepSNV 1.0.0 (2012-03-29)

Updates

• Added CITATION file
• Made NEWS (this file) R-readable
• Changed Vignette

deepSNV 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

deepSNV 0.99.2 (2012-01-20)

Updates

• Changed plot to S3 method (to avoid warning in R-devel)

deepSNV 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.

deepSNV 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

deepSNV 0.9.5

Updates

• "summary" now reports additional columns from regions slot.

Bugfixes

• drop=FALSE in subsetting and summary.

deepSNV 0.9.4

Updates

• Directly link to static samtools library provided by Rsamtools
• Load example .bam files over http

deepSNV 0.9.3

• Added beta-binomial model
• Extended documentation
• Use summary instead of significantSNV

deepSNV 0.9.2

• Minor bugfixes

deepSNV 0.9.1

• Minor bugfixes

deepSNV 0.9.0

• Pre-release