[med-svn] r17424 - in trunk/packages/R/r-bioc-genomicalignments/trunk/debian: . patches

Andreas Tille tille at moszumanska.debian.org
Tue Jul 8 09:07:11 UTC 2014


Author: tille
Date: 2014-07-08 09:07:11 +0000 (Tue, 08 Jul 2014)
New Revision: 17424

Added:
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/disable-testing-pasillaBamSubset.patch
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/series
Modified:
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/README.test
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog
Log:
Skip test requiring pasillaBamSubset since this is not (yet) packaged.


Modified: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/README.test	2014-07-08 08:44:46 UTC (rev 17423)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/README.test	2014-07-08 09:07:11 UTC (rev 17424)
@@ -8,3 +8,16 @@
 EOT
 
 in order to confirm its integrity.
+
+Attention:
+
+The original source package contains a test suite which depends from a dataset provided at
+
+  http://bioconductor.org/packages/release/data/experiment/html/pasillaBamSubset.html
+
+This test is skipped inside the Debian package.  If you want to run the full
+test suite you can also create a Debian package from this data.  The packaging code is
+available in the Debian Med repository at
+
+  svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-pasillabamsubset/trunk/
+

Modified: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog	2014-07-08 08:44:46 UTC (rev 17423)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog	2014-07-08 09:07:11 UTC (rev 17424)
@@ -2,4 +2,4 @@
 
   * Initial release (closes: #?)
 
- -- Andreas Tille <tille at debian.org>  Sun, 08 Jun 2014 18:33:04 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 08 Jul 2014 10:55:48 +0200

Added: 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	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/disable-testing-pasillaBamSubset.patch	2014-07-08 09:07:11 UTC (rev 17424)
@@ -0,0 +1,191 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 08 Jul 2014 10:55:48 +0200
+Description: Skip test requiring pasillaBamSubset
+ This package contains a test suite which depends from a dataset provided at
+  http://bioconductor.org/packages/release/data/experiment/html/pasillaBamSubset.html
+ which is not packaged for Debian.
+ See README.test for more information.
+
+--- a/inst/unitTests/test_readGAlignmentsListFromBam.R
++++ /dev/null
+@@ -1,180 +0,0 @@
+-library(pasillaBamSubset)
+-chr4 <- untreated3_chr4()
+-
+-test_readGAlignmentsListFromBam_construction <- function()
+-{
+-    fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
+-    bf <- BamFile(fl, asMates=TRUE)
+-    galist <- readGAlignmentsListFromBam(fl)
+-    checkTrue(is.null(names(galist)))
+-    galist <- readGAlignmentsListFromBam(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)
+-    mates <- galist[mcols(galist)$mate_status == "mated"]
+-    flagBit <- bamFlagAsBitMatrix(mcols(unlist(mates))$flag,
+-                                  bitnames="isFirstMateRead") 
+-    m <- matrix(flagBit, nrow=2)
+-    checkIdentical(c(1572L, 0), rowSums(m))
+-}
+-
+-test_readGAlignmentsListFromBam_noYieldSize <- function()
+-{
+-    fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
+-    bf <- BamFile(fl, asMates=TRUE)
+-    galist <- readGAlignmentsListFromBam(fl)
+-    checkTrue(validObject(galist))
+-}
+-
+-test_readGAlignmentsListFromBam_yieldSize <- function()
+-{
+-    bf <- BamFile(chr4, asMates=TRUE, yieldSize=1)
+-    scn1 <- scanBam(bf)
+-    galist1 <- readGAlignmentsList(bf)
+-    checkTrue(length(scn1[[1]]$qname) == 2)
+-    checkTrue(length(unique(scn1[[1]]$qname)) == 1)
+-    checkTrue(length(unique(scn1[[1]]$qname)) == length(galist1))
+-
+-    bf <- BamFile(chr4, asMates=TRUE, yieldSize=2)
+-    scn2 <- scanBam(bf)
+-    galist2 <- readGAlignmentsList(bf)
+-    checkTrue(length(scn2[[1]]$qname) == 4)
+-    checkTrue(length(unique(scn2[[1]]$qname)) == 2)
+-    checkTrue(length(unique(scn2[[1]]$qname)) == length(galist2))
+-}
+-
+-test_readGAlignmentsListFromBam_mcols <- function()
+-{
+-    bf <- BamFile(chr4, asMates=TRUE, yieldSize=100)
+-    param <- ScanBamParam(tag=("NM"))
+-    galist <- readGAlignmentsListFromBam(bf, param=param)
+-    checkIdentical(colnames(mcols(unlist(galist))), "NM")
+-    checkTrue(names(mcols(galist)) == "mate_status")
+-
+-    param <- ScanBamParam(tag=("FO"))
+-    galist <- readGAlignmentsListFromBam(bf, param=param)
+-    checkIdentical(rep.int(NA, length(unlist(galist))), 
+-                   mcols(unlist(galist))[["FO"]])
+-}
+-
+-test_readGAlignmentsListFromBam_compare_pairs <- function()
+-{
+-    bamfile <- BamFile(untreated3_chr4(), asMates=TRUE)
+-    galist <- readGAlignmentsListFromBam(bamfile)
+-    mates <- galist[mcols(galist)$mate_status == "mated"]
+-    galp <- readGAlignmentPairsFromBam(bamfile)
+-    checkIdentical(length(galp), length(mates)) 
+-}
+-
+-test_readGAlignmentsListFromBam_flags <- function()
+-{
+-    bamfile <- BamFile(untreated3_chr4(), asMates=TRUE)
+-    param <- ScanBamParam(flag=scanBamFlag(isProperPair=TRUE))
+-    galist <- readGAlignmentsListFromBam(bamfile, param=param)
+-    status <- table(mcols(galist)$mate_status)
+-    checkIdentical(status[["mated"]], 45828L)
+-    checkIdentical(status[["ambiguous"]], 0L)
+-    checkIdentical(status[["unmated"]], 0L)
+-}
+-
+-## toy_bamfile read summary: 
+-## --------------------------
+-
+-## single-end
+-## s001: 1 primary alignment
+-## s002: 1 primary alignment + 3 secondary alignments
+-## s003: unmapped
+-
+-## paired-end
+-## p991: 1 pair with a missing mate (can happen if file was subsetted)
+-## p992: 1 pair with 1st mate unmapped and 2nd mate mapped
+-## p993: 1 pair with both mates unmapped
+-
+-## multi-segments
+-## m001: 3 segments in the template (index of each segment is known)
+-## m002: 3 segments in the template (index of each segment was lost) 
+-
+-## mapped pairs ('pi' tag only exists for these mapped pairs)
+-## p001: 1 primary proper pair
+-## p002: 1 primary non proper pair
+-## p003: 2 proper pairs: 1 primary + 1 secondary
+-## p004: 2 non proper pairs: 1 primary + 1 secondary
+-## p005: 2 primary pairs
+-## p006: 3 pairs: 1 primary proper + 1 secondary proper + 
+-##                1 secondary non proper
+-## p007: 2 pairs mapped to the same position: 
+-##       1 primary proper + 1 secondary proper
+-## p008: 3 pairs mapped to the same position: 1 primary proper + 
+-##       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", 
+-                   package="GenomicAlignments"))
+-bf <- BamFile(toy_bamfile, asMates=TRUE)
+-
+-test_readGAlignmentsListFromBam_toybamfile <- function()
+-{
+-    param <- ScanBamParam(tag="pi")
+-    galp <- readGAlignmentPairsFromBam(toy_bamfile, use.names=TRUE, param=param)
+-    galist <- readGAlignmentsListFromBam(bf, use.names=TRUE, param=param)
+-
+-    ## 'mated' 
+-    mated_galist <- unlist(galist[mcols(galist)$mate_status == "mated"]) 
+-    pi_target <- c("p001", "p002", "p003a", "p003b", "p004a", "p004b",
+-                   "p005a", "p005b", "p006a", "p006b", "p006c",
+-                   "p007a", "p007b", "p008a", "p008b", "p008c", "p009a")
+-    checkTrue(all(mcols(mated_galist)$pi %in% pi_target))
+-
+-    ## 'ambiguous' GAList match 'dumped' GAPairs
+-    ambig_galist <- unlist(galist[mcols(galist)$mate_status == "ambiguous"]) 
+-    dumped_galp <- getDumpedAlignments()
+-    pi_target <- rep(c("p009b", "p009c"), each=2)
+-    checkIdentical(pi_target, sort(mcols(dumped_galp)$pi))
+-    checkIdentical(pi_target, sort(mcols(ambig_galist)$pi))
+-
+-    ## 'unmated':
+-    unmated_galist <- unlist(galist[mcols(galist)$mate_status == "unmated"]) 
+-    ## unmated single-end, paired-end or multi-segment (no pi tags) 
+-    name_target <- c("m001", "m002", "p991", "p992", "s001", "s002")
+-    unmated <- names(unmated_galist)[is.na(mcols(unmated_galist)$pi)] 
+-    checkTrue(all(unmated %in% name_target)) 
+-    ## non-proper mapped-pairs (have pi tags) 
+-    pi_target <- c("p002", "p004a", "p004b", "p006c", "p008c")
+-    unmated <- na.omit(unique(mcols(unmated_galist)$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.
+-    bamFlag(param) <- scanBamFlag(isProperPair=TRUE,
+-                                  hasUnmappedMate=FALSE,
+-                                  isUnmappedQuery=FALSE,
+-                                  isPaired=TRUE)
+-    galist <- readGAlignmentsListFromBam(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()
+-{
+-    ## 4 non-overlapping regions of interest: first two regions only overlap
+-    ## with first p001 mate and last two regions only with last p001 mate.
+-    my_ROI <- GRanges("chr2", IRanges(c(10, 15, 110, 115), width=1))
+-    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)
+-    ## Duplicate results with distinct 'which_label'
+-    checkIdentical(2L, length(target1))
+-    checkIdentical(as.vector(mcols(target1)$mate_status), c("mated", "mated"))
+-    rng1 <- as.vector(mcols(unlist(target1[1]))$which_label)
+-    checkTrue(all(rng1 %in% my_ROI_labels[1]))
+-    rng2 <- as.vector(mcols(unlist(target1[2]))$which_label)
+-    checkTrue(all(rng2 %in% my_ROI_labels[4]))
+-}

Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/series	2014-07-08 09:07:11 UTC (rev 17424)
@@ -0,0 +1 @@
+disable-testing-pasillaBamSubset.patch




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