[med-svn] r19397 - in trunk/packages/R/r-bioc-genomicalignments/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Sat Jun 27 17:02:05 UTC 2015
Author: tille
Date: 2015-06-27 17:02:05 +0000 (Sat, 27 Jun 2015)
New Revision: 19397
Modified:
trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog
trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control
trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/disable-testing-pasillaBamSubset.patch
trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/series
Log:
New upstream version
Modified: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog 2015-06-27 15:29:03 UTC (rev 19396)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog 2015-06-27 17:02:05 UTC (rev 19397)
@@ -1,10 +1,11 @@
-r-bioc-genomicalignments (1.4.1-1) UNRELEASED; urgency=medium
+r-bioc-genomicalignments (1.4.1-1) unstable; urgency=medium
* New upstream version
* Disable patch
* Citation
+ * New versioned dependency r-bioc-rsamtools (>= 1.20.4)
- -- Andreas Tille <tille at debian.org> Mon, 11 May 2015 14:37:31 +0200
+ -- Andreas Tille <tille at debian.org> Thu, 25 Jun 2015 23:04:53 +0200
r-bioc-genomicalignments (1.2.0-1) experimental; urgency=medium
Modified: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control 2015-06-27 15:29:03 UTC (rev 19396)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control 2015-06-27 17:02:05 UTC (rev 19397)
@@ -6,7 +6,7 @@
Build-Depends: debhelper (>= 9),
cdbs,
r-base-dev,
- r-bioc-rsamtools (>= 1.20.0),
+ r-bioc-rsamtools (>= 1.20.4),
r-bioc-biocparallel (>= 1.0.0)
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genomicalignments/trunk/
@@ -18,7 +18,7 @@
Depends: ${R:Depends},
${misc:Depends},
${shlibs:Depends},
- r-bioc-rsamtools (>= 1.18.0),
+ r-bioc-rsamtools (>= 1.20.4),
r-bioc-biocparallel (>= 1.0.0)
Recommends: r-bioc-shortread
Description: BioConductor representation and manipulation of short genomic alignments
Modified: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/disable-testing-pasillaBamSubset.patch
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/disable-testing-pasillaBamSubset.patch 2015-06-27 15:29:03 UTC (rev 19396)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/disable-testing-pasillaBamSubset.patch 2015-06-27 17:02:05 UTC (rev 19397)
@@ -6,25 +6,25 @@
which is not packaged for Debian.
See README.test for more information.
---- a/inst/unitTests/test_readGAlignmentsListFromBam.R
+--- a/inst/unitTests/test_readGAlignmentsList.R
+++ /dev/null
-@@ -1,180 +0,0 @@
+@@ -1,189 +0,0 @@
-library(pasillaBamSubset)
-chr4 <- untreated3_chr4()
-
--test_readGAlignmentsListFromBam_construction <- function()
+-test_readGAlignmentsList_construction <- function()
-{
- fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
- bf <- BamFile(fl, asMates=TRUE)
-- galist <- readGAlignmentsListFromBam(fl)
+- galist <- readGAlignmentsList(fl)
- checkTrue(is.null(names(galist)))
-- galist <- readGAlignmentsListFromBam(fl, use.names=TRUE)
+- galist <- readGAlignmentsList(fl, use.names=TRUE)
- target <- c("EAS54_61:4:143:69:578", "EAS219_FC30151:7:51:1429:1043")
- checkIdentical(names(galist)[1:2], target)
-
- ## first segment first
- param <- ScanBamParam(what="flag")
-- galist <- readGAlignmentsListFromBam(fl, param=param)
+- galist <- readGAlignmentsList(fl, param=param)
- mates <- galist[mcols(galist)$mate_status == "mated"]
- flagBit <- bamFlagAsBitMatrix(mcols(unlist(mates))$flag,
- bitnames="isFirstMateRead")
@@ -32,15 +32,15 @@
- checkIdentical(c(1572L, 0), rowSums(m))
-}
-
--test_readGAlignmentsListFromBam_noYieldSize <- function()
+-test_readGAlignmentsList_noYieldSize <- function()
-{
- fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
- bf <- BamFile(fl, asMates=TRUE)
-- galist <- readGAlignmentsListFromBam(fl)
+- galist <- readGAlignmentsList(fl)
- checkTrue(validObject(galist))
-}
-
--test_readGAlignmentsListFromBam_yieldSize <- function()
+-test_readGAlignmentsList_yieldSize <- function()
-{
- bf <- BamFile(chr4, asMates=TRUE, yieldSize=1)
- scn1 <- scanBam(bf)
@@ -57,34 +57,43 @@
- checkTrue(length(unique(scn2[[1]]$qname)) == length(galist2))
-}
-
--test_readGAlignmentsListFromBam_mcols <- function()
+-test_readGAlignmentsList_mcols <- function()
-{
- bf <- BamFile(chr4, asMates=TRUE, yieldSize=100)
- param <- ScanBamParam(tag=("NM"))
-- galist <- readGAlignmentsListFromBam(bf, param=param)
+- galist <- readGAlignmentsList(bf, param=param)
- checkIdentical(colnames(mcols(unlist(galist))), "NM")
- checkTrue(names(mcols(galist)) == "mate_status")
-
- param <- ScanBamParam(tag=("FO"))
-- galist <- readGAlignmentsListFromBam(bf, param=param)
+- galist <- readGAlignmentsList(bf, param=param)
- checkIdentical(rep.int(NA, length(unlist(galist))),
- mcols(unlist(galist))[["FO"]])
-}
-
--test_readGAlignmentsListFromBam_compare_pairs <- function()
+-test_readGAlignmentsList_compare_pairs <- function()
-{
- bamfile <- BamFile(untreated3_chr4(), asMates=TRUE)
-- galist <- readGAlignmentsListFromBam(bamfile)
+- galist <- readGAlignmentsList(bamfile)
- mates <- galist[mcols(galist)$mate_status == "mated"]
-- galp <- readGAlignmentPairsFromBam(bamfile)
-- checkIdentical(length(galp), length(mates))
+- galp <- readGAlignmentPairs(bamfile)
+- checkIdentical(length(galp), 75346L)
+- tbl <- table(mcols(galist))
+- checkIdentical(tbl[["mated"]], 75409L)
+- checkIdentical(tbl[["ambiguous"]], 0L)
+- checkIdentical(tbl[["unmated"]], 21227L)
+-
+- ## GAlignmentPairs holds concordant (opposite strand) pairs
+- samestrand <- galist[elementLengths(runValue(strand(galist))) == 1L]
+- samestrandp <- sum(mcols(samestrand)$mate_status == "mated")
+- checkIdentical(tbl[["mated"]] - samestrandp, length(galp))
-}
-
--test_readGAlignmentsListFromBam_flags <- function()
+-test_readGAlignmentsList_flags <- function()
-{
- bamfile <- BamFile(untreated3_chr4(), asMates=TRUE)
- param <- ScanBamParam(flag=scanBamFlag(isProperPair=TRUE))
-- galist <- readGAlignmentsListFromBam(bamfile, param=param)
+- galist <- readGAlignmentsList(bamfile, param=param)
- status <- table(mcols(galist)$mate_status)
- checkIdentical(status[["mated"]], 45828L)
- checkIdentical(status[["ambiguous"]], 0L)
@@ -122,15 +131,15 @@
-## 1 secondary proper + 1 secondary non proper
-## p009: 3 pairs mapped to the same position:
-## 1 primary proper + 2 secondary proper.
--source(system.file("unitTests", "test_readGAlignmentPairsFromBam.R",
+-source(system.file("unitTests", "test_readGAlignmentPairs.R",
- package="GenomicAlignments"))
-bf <- BamFile(toy_bamfile, asMates=TRUE)
-
--test_readGAlignmentsListFromBam_toybamfile <- function()
+-test_readGAlignmentsList_toybamfile <- function()
-{
- param <- ScanBamParam(tag="pi")
-- galp <- readGAlignmentPairsFromBam(toy_bamfile, use.names=TRUE, param=param)
-- galist <- readGAlignmentsListFromBam(bf, use.names=TRUE, param=param)
+- galp <- readGAlignmentPairs(toy_bamfile, use.names=TRUE, param=param)
+- galist <- readGAlignmentsList(bf, use.names=TRUE, param=param)
-
- ## 'mated'
- mated_galist <- unlist(galist[mcols(galist)$mate_status == "mated"])
@@ -157,21 +166,21 @@
- unmated <- na.omit(unique(mcols(unmated_galist)$pi))
- checkTrue(all(unmated %in% pi_target))
-
-- ## Reads of this type cannot be filtered out wrt
-- ## readGAlignmentsList. They are always returned by
-- ## readGAlignmentsList but never returned by readGAlignmentPairs.
+- ## Reads of this type cannot be filtered out wrt readGAlignmentsList.
+- ## They are always returned by readGAlignmentsList but never returned by
+- ## readGAlignmentPairs.
- bamFlag(param) <- scanBamFlag(isProperPair=TRUE,
- hasUnmappedMate=FALSE,
- isUnmappedQuery=FALSE,
- isPaired=TRUE)
-- galist <- readGAlignmentsListFromBam(bf, use.names=TRUE, param=param)
+- galist <- readGAlignmentsList(bf, use.names=TRUE, param=param)
- unmated_galist <- unlist(galist[mcols(galist)$mate_status == "unmated"])
- unmated <- names(unmated_galist)[is.na(mcols(unmated_galist)$pi)]
- name_target <- c("m001", "m002", "p991")
- checkTrue(all(unmated %in% name_target))
-}
-
--test_readGAlignmentsListFromBam_which <- function()
+-test_readGAlignmentsList_which <- function()
-{
- ## 4 non-overlapping regions of interest: first two regions only overlap
- ## with first p001 mate and last two regions only with last p001 mate.
@@ -179,8 +188,8 @@
- my_ROI_labels <- c("chr2:10-10", "chr2:15-15",
- "chr2:110-110", "chr2:115-115")
- param <- ScanBamParam(tag="pi", which=my_ROI[c(1, 4)])
-- target1 <- readGAlignmentsListFromBam(toy_bamfile, use.names=TRUE,
-- param=param, with.which_label=TRUE)
+- target1 <- readGAlignmentsList(toy_bamfile, use.names=TRUE,
+- param=param, with.which_label=TRUE)
- ## Duplicate results with distinct 'which_label'
- checkIdentical(2L, length(target1))
- checkIdentical(as.vector(mcols(target1)$mate_status), c("mated", "mated"))
Modified: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/series 2015-06-27 15:29:03 UTC (rev 19396)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/series 2015-06-27 17:02:05 UTC (rev 19397)
@@ -1 +1 @@
-# disable-testing-pasillaBamSubset.patch
+disable-testing-pasillaBamSubset.patch
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