Addition of the strandMode parameter to readGAlignmentsList()

DESCRIPTION

@@ -10,7 +10,7 @@ biocViews: Infrastructure, DataImport, Genetics, Sequencing, RNASeq, SNP,
 URL: https://bioconductor.org/packages/GenomicAlignments
 Video: https://www.youtube.com/watch?v=2KqBSbkfhRo , https://www.youtube.com/watch?v=3PK_jx44QTs
 BugReports: https://github.com/Bioconductor/GenomicAlignments/issues
-Version: 1.35.0
+Version: 1.35.1
 License: Artistic-2.0
 Encoding: UTF-8
 Authors@R: c(

R/readGAlignments.R

@@ -290,20 +290,54 @@ setMethod("readGAlignmentPairs", "character",
 
 setGeneric("readGAlignmentsList", signature="file",
     function(file, index=file, use.names=FALSE, param=ScanBamParam(),
-                   with.which_label=FALSE)
+                   with.which_label=FALSE, strandMode=NA)
         standardGeneric("readGAlignmentsList")
 )
 
-.matesFromBam <- function(file, use.names, param, what0, with.which_label)
+.setRealStrand <- function(gal, param, strandMode) {
+    if (strandMode == 0L)
+        strand(gal) <- Rle(strand("*"), length(gal))
+    else {
+        gal_mcols <- mcols(gal, use.names=FALSE)
+        if (is.null(gal_mcols$flag))
+            warning("Flag information missing in GAlignmentsList object. Strand information might not be accurate.")
+        else {
+            mask_first_mate <- bamFlagTest(gal_mcols$flag, "isFirstMateRead")
+            if (strandMode == 1L)
+                strand(gal[!mask_first_mate]) <-
+                    invertStrand(strand(gal[!mask_first_mate]))
+            else if (strandMode == 2L)
+                strand(gal[mask_first_mate]) <-
+                    invertStrand(strand(gal[mask_first_mate]))
+            else
+                stop("strandMode should be either 0, 1 or 2.")
+        }
+    }
+    ## if the user didn't request the 'flag' info
+    ## then remove it to reduce memory footprint
+    if (!"flag" %in% bamWhat(param))
+        mcols(gal)$flag <- NULL
+    gal
+}
+.matesFromBam <- function(file, use.names, param, what0, with.which_label,
+                          strandMode)
 {
     bamcols <- .load_bamcols_from_BamFile(file, param, what0,
                                           with.which_label=with.which_label)
     seqlengths <- .load_seqlengths_from_BamFile(file, levels(bamcols$rname))
     gal <- GAlignments(seqnames=bamcols$rname, pos=bamcols$pos,
                        cigar=bamcols$cigar, strand=bamcols$strand,
                        seqlengths=seqlengths)
-    gal <- .bindExtraData(gal, use.names=FALSE, param, bamcols,
-                          with.which_label=with.which_label)
+    if (!is.na(strandMode)) {
+        flag0 <- scanBamFlag()
+        what0 <- "flag"
+        param2 <- .normargParam(param, flag0, what0)
+        gal <- .bindExtraData(gal, use.names=FALSE, param2, bamcols,
+                              with.which_label=with.which_label)
+        gal <- .setRealStrand(gal, param, strandMode)
+    } else
+        gal <- .bindExtraData(gal, use.names=FALSE, param, bamcols,
+                              with.which_label=with.which_label)
     if (asMates(file)) {
         f <- factor(bamcols$groupid)
         gal <- unname(split(gal, f))
@@ -320,30 +354,34 @@ setGeneric("readGAlignmentsList", signature="file",
 
 .readGAlignmentsList.BamFile <- function(file, index=file,
                                          use.names=FALSE, param=ScanBamParam(),
-                                         with.which_label=FALSE)
+                                         with.which_label=FALSE,
+                                         strandMode=NA)
 {
     if (!isTRUEorFALSE(use.names))
         stop("'use.names' must be TRUE or FALSE")
     if (!asMates(file))
         bamWhat(param) <- setdiff(bamWhat(param), 
                                   c("groupid", "mate_status"))
     what0 <- c("rname", "strand", "pos", "cigar", "groupid", "mate_status")
+    if (!is.na(strandMode))
+        what0 <- c(what0, "flag")
     if (use.names)
         what0 <- c(what0, "qname")
-    .matesFromBam(file, use.names, param, what0, with.which_label)
+    .matesFromBam(file, use.names, param, what0, with.which_label, strandMode)
 }
 
 setMethod("readGAlignmentsList", "BamFile", .readGAlignmentsList.BamFile)
 
 setMethod("readGAlignmentsList", "character",
     function(file, index=file, use.names=FALSE, param=ScanBamParam(),
-                   with.which_label=FALSE)
+                   with.which_label=FALSE, strandMode=NA)
     {
         bam <- .open_BamFile(file, index=index, asMates=TRUE, param=param)
         on.exit(close(bam))
         readGAlignmentsList(bam, character(0),
                             use.names=use.names, param=param,
-                            with.which_label=with.which_label)
+                            with.which_label=with.which_label,
+                            strandMode=strandMode)
     }
 )
 

inst/unitTests/test_readGAlignmentsList.R

@@ -182,3 +182,18 @@ test_readGAlignmentsList_which <- function()
     rng2 <- as.vector(mcols(unlist(target1[2]))$which_label)
     checkTrue(all(rng2 %in% my_ROI_labels[4]))
 }
+
+text_readGAlignmentsList_findOverlaps <- function()
+{
+    fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
+    bf <- BamFile(fl, asMates=TRUE)
+    galist <- readGAlignmentsList(bf, strandMode=1L)
+    f <- GRanges(seqnames="seq1", IRanges(30, 250), strand="-")
+    ov <- findOverlaps(galist[1], f, ignore.strand=FALSE)
+    checkIdentical(0L, length(ov))
+
+    galist <- readGAlignmentsList(bf, strandMode=2L)
+    f <- GRanges(seqnames="seq1", IRanges(30, 250), strand="-")
+    ov <- findOverlaps(galist[1], f, ignore.strand=FALSE)
+    checkIdentical(1L, length(ov))
+}

man/readGAlignments.Rd

@@ -34,7 +34,8 @@ readGAlignmentPairs(file, index=file, use.names=FALSE, param=NULL,
                           with.which_label=FALSE, strandMode=1)
 
 readGAlignmentsList(file, index=file, use.names=FALSE,
-                          param=ScanBamParam(), with.which_label=FALSE)
+                          param=ScanBamParam(), with.which_label=FALSE,
+                          strandMode=NA)
 
 readGappedReads(file, index=file, use.names=FALSE, param=NULL,
                       with.which_label=FALSE)
@@ -103,8 +104,12 @@ readGappedReads(file, index=file, use.names=FALSE, param=NULL,
     represented as a factor-\link[S4Vectors]{Rle}.
   }
   \item{strandMode}{
-    Strand mode to set on the returned \link{GAlignmentPairs} object.
-    See \code{?\link{strandMode}} for more information.
+    Strand mode to set on the returned \link{GAlignmentPairs} or
+    \link{GAlignmentsList} object. Note that the default value for
+    this parameter is different for \code{readGAlignmentPairs()} and
+    \code{readGAlignmentsList()}.
+    See details below on \code{readGAlignmentsList()} and
+    \code{?\link{strandMode}} for more information.
   }
 }
 
@@ -155,6 +160,12 @@ readGappedReads(file, index=file, use.names=FALSE, param=NULL,
           See the \sQuote{asMates} section of \code{?\link[Rsamtools]{BamFile}}
           in the \pkg{Rsamtools} package for details. 
 
+          Note that, by default, \code{strandMode=NA}, which is different to
+          the default value in \code{readGAlignmentPairs()} and which implies
+          that, by default, the strand values in the returned
+          \code{GAlignmentsList} object correspond to the original strand of
+          the reads.
+
     \item \code{readGappedReads} reads a file containing aligned reads as a
           \link{GappedReads} object. See \code{?\link{GappedReads}} for a
           description of \link{GappedReads} objects.
@@ -398,7 +409,19 @@ readGAlignmentsList(bamfile)
 ## Use a 'param' to fine tune the results.
 param <- ScanBamParam(flag=scanBamFlag(isProperPair=TRUE))
 galist2 <- readGAlignmentsList(bam, param=param)
+galist2[1:3]
 length(galist2)
+table(elementNROWS(galist2))
+
+## For paired-end data, we can set the 'strandMode' parameter to
+## infer the strand of a pair from the strand of the first and
+## last alignments in the pair
+galist3 <- readGAlignmentsList(bam, param=param, strandMode=0)
+galist3[1:3]
+galist4 <- readGAlignmentsList(bam, param=param, strandMode=1)
+galist4[1:3]
+galist5 <- readGAlignmentsList(bam, param=param, strandMode=2)
+galist5[1:3]
 
 ## ---------------------------------------------------------------------
 ## D. COMPARING 4 STRATEGIES FOR LOADING THE ALIGNMENTS THAT OVERLAP