[BioC] readGAlignmentPairs perfromace issue

[Phil East [guest]]

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   

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