Hi Valerie, Thank you for getting back to me. Here are the times for readGAlignmentPairs, readGAlignmentsList, and scanBam using the code you sent. $readGAlignmentsList user system elapsed 2529.510 57.487 2589.144 $scanBam user system elapsed 2465.353 49.404 2516.275 $readGAlignmentPairs user system elapsed 2560.754 56.612 2619.769 Best wishes Phil On Fri, 2014-05-16 at 12:55 -0700, Valerie Obenchain wrote: > Hi Phil, > > We have several functions that call the same C code in the background. > To help isolate the problem can you please run your code with scanBam() > and readGAlignmentsList()? > > bf <- BamFile(fl, asMates=TRUE) > readGAlignmentsList(bf, param=param0) > scanBam(bf, param=param0) > > readGAlignmentsList() and readGAlignementPairs() should be very close in > time. scanBam() will be faster but not by a huge amount. > > Thanks. > Valerie > > > On 05/13/2014 07:23 AM, Maintainer wrote: > > Hi Guys, > > > > I'm experiencing some performance issues with readGAlignmentPairs from the latest version of Bioconductor (GenomicAlignments_1.0.1, BioC 2.14, R 3.1.0) > > > > Reading RNASeq paired reads aligned to chr19 (mm9) from a BAM file containing 108,592,829 paired reads takes 3118s. The same code run in R-3.0.2, BioC 2.13, Rsamtools_1.14.3 takes 208s. The results are identical across the two versions. > > > > Here's the code: > > > > library(GenomicAlignments) > > library(Rsamtools) > > > > param0 <- ScanBamParam(which=GRanges(seqnames="chr19", > > ranges=IRanges(start=1, end=chr19Length)) > > rd <- readGAlignmentPairs(bamFile, param=param0) > > > > Any ideas as to why this might be? > > > > Thanks in advance > > > > Phil East > > > > > > > > -- output of sessionInfo(): > > > > R version 3.1.0 (2014-04-10) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB > > [4] LC_COLLATE=en_GB LC_MONETARY=en_GB LC_MESSAGES=en_GB > > [7] LC_PAPER=en_GB LC_NAME=C LC_ADDRESS=C > > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C > > > > attached base packages: > > [1] grDevices datasets parallel stats graphics utils methods > > [8] base > > > > other attached packages: > > [1] GenomicAlignments_1.0.1 BSgenome_1.32.0 Rsamtools_1.16.0 > > [4] Biostrings_2.32.0 XVector_0.4.0 GenomicRanges_1.16.3 > > [7] GenomeInfoDb_1.0.2 IRanges_1.22.6 Biobase_2.24.0 > > [10] BiocGenerics_0.10.0 > > > > loaded via a namespace (and not attached): > > [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 bitops_1.0-6 > > [5] brew_1.0-6 codetools_0.2-8 DBI_0.2-7 digest_0.6.4 > > [9] fail_1.2 foreach_1.4.2 iterators_1.0.7 plyr_1.8.1 > > [13] Rcpp_0.11.1 RSQLite_0.11.4 sendmailR_1.1-2 stats4_3.1.0 > > [17] stringr_0.6.2 tools_3.1.0 zlibbioc_1.10.0 > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > __________________________________________________________________ ______ > > devteam-bioc mailing list > > To unsubscribe from this mailing list send a blank email to > > devteam-bioc-leave at lists.fhcrc.org > > You can also unsubscribe or change your personal options at > > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc > > > > NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for ...{{dropped:8}}