[med-svn] [r-bioc-genomicalignments] 02/05: New upstream version 1.14.0
Andreas Tille
tille at debian.org
Thu Nov 9 07:56:51 UTC 2017
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tille pushed a commit to branch master
in repository r-bioc-genomicalignments.
commit e421045a63fb3e155bc7414e9d99b9d851c7b3cd
Author: Andreas Tille <tille at debian.org>
Date: Thu Nov 9 08:52:30 2017 +0100
New upstream version 1.14.0
---
DESCRIPTION | 8 ++++----
NAMESPACE | 3 ++-
NEWS | 24 ++++++++++++++++++++++++
R/GAlignmentPairs-class.R | 4 ++--
R/GAlignments-class.R | 7 +++----
R/findOverlaps-methods.R | 18 +++++++++---------
build/vignette.rds | Bin 543 -> 544 bytes
inst/doc/GenomicAlignmentsIntroduction.pdf | Bin 184723 -> 185023 bytes
inst/doc/OverlapEncodings.pdf | Bin 204315 -> 283285 bytes
inst/doc/WorkingWithAlignedNucleotides.pdf | Bin 144152 -> 214717 bytes
inst/doc/summarizeOverlaps.pdf | Bin 166426 -> 204190 bytes
man/findOverlaps-methods.Rd | 4 ++--
12 files changed, 46 insertions(+), 22 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 28d8f8b..a54f378 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -5,15 +5,15 @@ Description: Provides efficient containers for storing and manipulating
to a reference genome). This includes read counting, computing the
coverage, junction detection, and working with the nucleotide content
of the alignments.
-Version: 1.12.2
+Version: 1.14.0
Encoding: UTF-8
Author: Hervé Pagès, Valerie Obenchain, Martin Morgan
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
SNP, Coverage, Alignment
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.15.3), S4Vectors (>=
- 0.13.13), IRanges (>= 2.5.36), GenomeInfoDb (>= 1.11.5),
- GenomicRanges (>= 1.27.19), SummarizedExperiment (>= 1.5.3),
+ 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.13.1),
+ GenomicRanges (>= 1.29.14), SummarizedExperiment (>= 1.5.3),
Biostrings (>= 2.37.1), Rsamtools (>= 1.21.4)
Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel
@@ -37,4 +37,4 @@ Collate: utils.R cigar-utils.R GAlignments-class.R
Video: https://www.youtube.com/watch?v=2KqBSbkfhRo ,
https://www.youtube.com/watch?v=3PK_jx44QTs
NeedsCompilation: yes
-Packaged: 2017-08-17 01:40:15 UTC; biocbuild
+Packaged: 2017-10-30 23:51:14 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index 757ac79..994baf7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -60,6 +60,7 @@ exportMethods(
parallelSlotNames, pcompare,
## Generics defined in IRanges:
+ ranges, rglist,
relistToClass,
narrow,
coverage,
@@ -72,7 +73,7 @@ exportMethods(
seqlevelsInUse,
## Generics defined in GenomicRanges:
- granges, grglist, rglist,
+ granges, grglist,
## Generics defined in Biostrings:
encoding,
diff --git a/NEWS b/NEWS
index dddca88..f54cd34 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,27 @@
+CHANGES IN VERSION 1.14.0
+-------------------------
+
+SIGNIFICANT USER-LEVEL CHANGES
+
+ o makeGAlignmentPairs() no more drops pairs with discordant seqnames.
+
+ o Change 'maxgap' and 'minoverlap' argument defaults in methods of the
+ findOverlaps() so they adhere to the new argument defaults of the generic
+ defined in IRanges 2.12.0. See NEWS file in the IRanges package for more
+ information about this change.
+
+DEPRECATED AND DEFUNCT
+
+ o Remove 'force' argument from seqinfo() and seqlevels() setters (the
+ argument got deprecated in BioC 3.5 in favor of new and more flexible
+ 'pruning.mode' argument).
+
+BUG FIXES
+
+ o Fix bug in pairing code of readGAlignmentPairs() when one mate in a pair
+ is lost because of user-supplied filtering (e.g. mapqFilter=10).
+
+
CHANGES IN VERSION 1.12.0
-------------------------
diff --git a/R/GAlignmentPairs-class.R b/R/GAlignmentPairs-class.R
index f0eef86..5bd4648 100644
--- a/R/GAlignmentPairs-class.R
+++ b/R/GAlignmentPairs-class.R
@@ -222,14 +222,14 @@ setMethod("seqlevelsInUse", "GAlignmentPairs",
)
setReplaceMethod("seqinfo", "GAlignmentPairs",
- function(x, new2old=NULL, force=FALSE,
+ function(x, new2old=NULL,
pruning.mode=c("error", "coarse", "fine", "tidy"),
value)
{
if (!is(value, "Seqinfo"))
stop("the supplied 'seqinfo' must be a Seqinfo object")
dangling_seqlevels <- GenomeInfoDb:::getDanglingSeqlevels(x,
- new2old=new2old, force=force,
+ new2old=new2old,
pruning.mode=pruning.mode,
seqlevels(value))
if (length(dangling_seqlevels) != 0L) {
diff --git a/R/GAlignments-class.R b/R/GAlignments-class.R
index 6ebbfa2..58c7c57 100644
--- a/R/GAlignments-class.R
+++ b/R/GAlignments-class.R
@@ -134,8 +134,7 @@ setReplaceMethod("rname", "GAlignments",
setReplaceMethod("strand", "GAlignments",
function(x, value)
{
- x at strand <-
- GenomicRanges:::normargGenomicRangesStrand(value, length(x))
+ x at strand <- GenomicRanges:::normalize_strand_replacement_value(value, x)
x
}
)
@@ -145,7 +144,7 @@ setReplaceMethod("strand", "GAlignments",
### FIXME: This repeats most of the code in
### GenomicRanges:::set_GenomicRanges_seqinfo!
set_GAlignments_seqinfo <-
- function(x, new2old=NULL, force=FALSE,
+ function(x, new2old=NULL,
pruning.mode=c("error", "coarse", "fine", "tidy"),
value)
{
@@ -156,7 +155,7 @@ set_GAlignments_seqinfo <-
if (!is(value, "Seqinfo"))
stop("the supplied 'seqinfo' must be a Seqinfo object")
dangling_seqlevels <- GenomeInfoDb:::getDanglingSeqlevels(x,
- new2old=new2old, force=force,
+ new2old=new2old,
pruning.mode=pruning.mode,
seqlevels(value))
if (length(dangling_seqlevels) != 0L) {
diff --git a/R/findOverlaps-methods.R b/R/findOverlaps-methods.R
index cafe0ef..96dd850 100644
--- a/R/findOverlaps-methods.R
+++ b/R/findOverlaps-methods.R
@@ -4,7 +4,7 @@
setMethod("findOverlaps", c("GAlignments", "Vector"),
- function(query, subject, maxgap = 0L, minoverlap = 1L,
+ function(query, subject, maxgap = -1L, minoverlap = 0L,
type = c("any", "start", "end", "within"),
select = c("all", "first", "last", "arbitrary"),
ignore.strand = FALSE)
@@ -17,7 +17,7 @@ setMethod("findOverlaps", c("GAlignments", "Vector"),
)
setMethod("findOverlaps", c("Vector", "GAlignments"),
- function(query, subject, maxgap = 0L, minoverlap = 1L,
+ function(query, subject, maxgap = -1L, minoverlap = 0L,
type = c("any", "start", "end", "within"),
select = c("all", "first", "last", "arbitrary"),
ignore.strand = FALSE)
@@ -37,7 +37,7 @@ setMethod("findOverlaps", c("Vector", "GAlignments"),
### "GAlignments#GAlignments".
### "ANY#GAlignments" would also be valid
setMethod("findOverlaps", c("GAlignments", "GAlignments"),
- function(query, subject, maxgap = 0L, minoverlap = 1L,
+ function(query, subject, maxgap = -1L, minoverlap = 0L,
type = c("any", "start", "end", "within"),
select = c("all", "first", "last", "arbitrary"),
ignore.strand = FALSE)
@@ -50,7 +50,7 @@ setMethod("findOverlaps", c("GAlignments", "GAlignments"),
)
setMethod("findOverlaps", c("GAlignmentPairs", "Vector"),
- function(query, subject, maxgap = 0L, minoverlap = 1L,
+ function(query, subject, maxgap = -1L, minoverlap = 0L,
type = c("any", "start", "end", "within"),
select = c("all", "first", "last", "arbitrary"),
ignore.strand = FALSE)
@@ -63,7 +63,7 @@ setMethod("findOverlaps", c("GAlignmentPairs", "Vector"),
)
setMethod("findOverlaps", c("Vector", "GAlignmentPairs"),
- function(query, subject, maxgap = 0L, minoverlap = 1L,
+ function(query, subject, maxgap = -1L, minoverlap = 0L,
type = c("any", "start", "end", "within"),
select = c("all", "first", "last", "arbitrary"),
ignore.strand = FALSE)
@@ -76,7 +76,7 @@ setMethod("findOverlaps", c("Vector", "GAlignmentPairs"),
)
setMethod("findOverlaps", c("GAlignmentPairs", "GAlignmentPairs"),
- function(query, subject, maxgap = 0L, minoverlap = 1L,
+ function(query, subject, maxgap = -1L, minoverlap = 0L,
type = c("any", "start", "end", "within"),
select = c("all", "first", "last", "arbitrary"),
ignore.strand = FALSE)
@@ -89,7 +89,7 @@ setMethod("findOverlaps", c("GAlignmentPairs", "GAlignmentPairs"),
)
setMethod("findOverlaps", c("GAlignmentsList", "Vector"),
- function(query, subject, maxgap = 0L, minoverlap = 1L,
+ function(query, subject, maxgap = -1L, minoverlap = 0L,
type = c("any", "start", "end", "within"),
select = c("all", "first", "last", "arbitrary"),
ignore.strand = FALSE)
@@ -107,7 +107,7 @@ setMethod("findOverlaps", c("GAlignmentsList", "Vector"),
)
setMethod("findOverlaps", c("Vector", "GAlignmentsList"),
- function(query, subject, maxgap = 0L, minoverlap = 1L,
+ function(query, subject, maxgap = -1L, minoverlap = 0L,
type = c("any", "start", "end", "within"),
select = c("all", "first", "last", "arbitrary"),
ignore.strand = FALSE)
@@ -125,7 +125,7 @@ setMethod("findOverlaps", c("Vector", "GAlignmentsList"),
)
setMethod("findOverlaps", c("GAlignmentsList", "GAlignmentsList"),
- function(query, subject, maxgap = 0L, minoverlap = 1L,
+ function(query, subject, maxgap = -1L, minoverlap = 0L,
type = c("any", "start", "end", "within"),
select = c("all", "first", "last", "arbitrary"),
ignore.strand = FALSE)
diff --git a/build/vignette.rds b/build/vignette.rds
index 5f2e311..cbc2cb1 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/GenomicAlignmentsIntroduction.pdf b/inst/doc/GenomicAlignmentsIntroduction.pdf
index 4885317..d5e099b 100644
Binary files a/inst/doc/GenomicAlignmentsIntroduction.pdf and b/inst/doc/GenomicAlignmentsIntroduction.pdf differ
diff --git a/inst/doc/OverlapEncodings.pdf b/inst/doc/OverlapEncodings.pdf
index d8bd91c..a97cf43 100644
Binary files a/inst/doc/OverlapEncodings.pdf and b/inst/doc/OverlapEncodings.pdf differ
diff --git a/inst/doc/WorkingWithAlignedNucleotides.pdf b/inst/doc/WorkingWithAlignedNucleotides.pdf
index 92c3ac1..e8ad1e6 100644
Binary files a/inst/doc/WorkingWithAlignedNucleotides.pdf and b/inst/doc/WorkingWithAlignedNucleotides.pdf differ
diff --git a/inst/doc/summarizeOverlaps.pdf b/inst/doc/summarizeOverlaps.pdf
index 7460bbf..453fb4c 100644
Binary files a/inst/doc/summarizeOverlaps.pdf and b/inst/doc/summarizeOverlaps.pdf differ
diff --git a/man/findOverlaps-methods.Rd b/man/findOverlaps-methods.Rd
index 3acd19a..9feb107 100644
--- a/man/findOverlaps-methods.Rd
+++ b/man/findOverlaps-methods.Rd
@@ -35,7 +35,7 @@
\usage{
\S4method{findOverlaps}{GAlignments,GAlignments}(query, subject,
- maxgap=0L, minoverlap=1L,
+ maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
@@ -48,7 +48,7 @@
A vector-like object containing ranges for the other one.
}
\item{maxgap, minoverlap, type, select}{
- See \code{\link[IRanges]{findOverlaps}} in the \pkg{IRanges} package
+ See \code{?\link[IRanges]{findOverlaps}} in the \pkg{IRanges} package
for a description of these arguments.
}
\item{ignore.strand}{
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