Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Enable "streaming" bam reads in read.smartseq2.bams #21

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Enable "streaming" bam reads in read.smartseq2.bams #21

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 7 additions & 2 deletions R/momentum_routines.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1377,10 +1377,14 @@ show.velocity.on.embedding.eu <- function(emb,vel,n=30,embedding.knn=TRUE,cell.c
##' @param bam.files list of bam files
##' @param annotation.file refFlat genome annotation file (use gtfToGenePred to generate refFlat file from gtf)
##' @param min.exon.count minimum number of reads (across all cells) for an exon to be considered expressed in the dataset
##' @param stream.bams should the bams be loaded one at a time (slower) or all at once (uses more memory)?
##' @param n.cores
##' @return
##' @export
read.smartseq2.bams <- function(bam.files,annotation.file,min.exon.count=100,n.cores=defaultNCores()) {
read.smartseq2.bams <- function(bam.files,annotation.file,min.exon.count=100,stream.bams=FALSE,n.cores=defaultNCores()) {
if (is.null(names(bam.files))) {
stop("The 'bam.files' vector must be named in order to define cell names")
}
# read in annotation
# TODO: enable direct gtf read
cat("reading gene annotation ... ")
Expand Down Expand Up @@ -1421,7 +1425,7 @@ read.smartseq2.bams <- function(bam.files,annotation.file,min.exon.count=100,n.c
# read in all bam files
cat("reading in",length(bam.files),"bam files ... ")
# annotate individual reads
cdl <- parallel::mclapply(bam.files,t.annotate.bam.reads,genes=genes,exons=exons,margin=1,exon.margin=1,mc.cores=n.cores)
cdl <- parallel::mclapply(bam.files,t.annotate.bam.reads,genes=genes,exons=exons,margin=1,exon.margin=1,mc.cores=n.cores,mc.preschedule=!stream.bams)
cat("done\n")
# get count estimates per gene
cat("estimating gene counts ... ")
Expand Down Expand Up @@ -1564,6 +1568,7 @@ t.annotate.bam.reads <- function(fname, genes, exons, chrl=unique(genes$chr), te
if(use.names) {
bam.data$name <- names(z)
}
rm(z)
bam.data <- bam.data[bam.data$chr %in% chrl,]

chrl <- chrl[chrl %in% unique(bam.data$chr)]
Expand Down