[med-svn] [r-bioc-variantannotation] 01/05: New upstream version 1.24.2

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-bioc-variantannotation.

commit 7599f4c801158e680719ead364ccd10bfbb28f79
Author: Andreas Tille <tille at debian.org>
Date:   Mon Dec 4 18:06:31 2017 +0100

    New upstream version 1.24.2
---
 DESCRIPTION                    |   4 ++--
 inst/doc/VariantAnnotation.pdf | Bin 203854 -> 203857 bytes
 inst/doc/filterVcf.pdf         | Bin 176665 -> 176665 bytes
 man/VCF-class.Rd               |  14 +++++++-------
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 015df7d..025bd23 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Annotation of Genetic Variants
 Description: Annotate variants, compute amino acid coding changes,
         predict coding outcomes.
-Version: 1.24.1
+Version: 1.24.2
 Authors at R: c(person("Valerie", "Obenchain", role=c("aut", "cre"),
         email="maintainer at bioconductor.org"),
     person("Martin", "Morgan", role="aut"),
@@ -29,7 +29,7 @@ biocViews: DataImport, Sequencing, SNP, Annotation, Genetics,
 Video:
         https://www.youtube.com/watch?v=Ro0lHQ_J--I&list=UUqaMSQd_h-2EDGsU6WDiX0Q
 NeedsCompilation: yes
-Packaged: 2017-11-07 23:55:06 UTC; biocbuild
+Packaged: 2017-11-23 00:02:16 UTC; biocbuild
 Author: Valerie Obenchain [aut, cre],
   Martin Morgan [aut],
   Michael Lawrence [aut],
diff --git a/inst/doc/VariantAnnotation.pdf b/inst/doc/VariantAnnotation.pdf
index c17ebe3..a36ea30 100644
Binary files a/inst/doc/VariantAnnotation.pdf and b/inst/doc/VariantAnnotation.pdf differ
diff --git a/inst/doc/filterVcf.pdf b/inst/doc/filterVcf.pdf
index e453e35..7e25bd1 100644
Binary files a/inst/doc/filterVcf.pdf and b/inst/doc/filterVcf.pdf differ
diff --git a/man/VCF-class.Rd b/man/VCF-class.Rd
index e12c259..e6f5fef 100644
--- a/man/VCF-class.Rd
+++ b/man/VCF-class.Rd
@@ -101,12 +101,7 @@
 \section{Constructors}{
   \describe{
     \item{}{
-      \code{readVcf(rowRanges = GRanges(), colData = DataFrame(), 
-                exptData = list(), fixed = DataFrame(), 
-                info = DataFrame(), geno = SimpleList(), 
-                ..., collapsed=TRUE, verbose = FALSE)}
-      Creates a CollapsedVCF class from data in a Variant Call
-      Format file on disk. 
+      \code{readVcf(file, genome, param, ..., row.names=TRUE)}
     }
     \item{}{
       \code{VCF(rowRanges = GRanges(), colData = DataFrame(), 
@@ -116,6 +111,9 @@
                 verbose = FALSE)}
       Creates CollapsedVCF when \code{collapsed = TRUE} and an
       ExpandedVCF when \code{collapsed = FALSE}.
+
+      This is a low-level constructor used internally. Most instances
+      of the \code{VCF} are created with \code{readVcf}.
     }
   }
 }
@@ -143,7 +141,7 @@
       specified in the \code{ScanVcfParam} and distinguishes which records
       match each range.
 
-      The metadata columns can be accessed with the following:
+      The metadata columns of a VCF object are accessed with the following:
       \itemize{
         \item{\code{ref(x)}, \code{ref(x) <- value}:
           Gets or sets the reference allele (REF). \code{value} must 
@@ -412,6 +410,8 @@
 }
 
 \examples{
+## readVcf() parses data into a VCF object:
+
 fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
 vcf <- readVcf(fl, genome="hg19")
 

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