Dear list,
There seems to be a problem with the readGAlignmentPairs function:
Querying genomic regions without any alignments using the which
argument results in an error -- see (1) below. Reading in a whole
chromosome takes indefinitely (or at least much longer than in
previous versions) -- see (2) below. I suspect these issues are not
specific to the BAM files I am working with but can provide test data
if required.
Many thanks for your help.
Leonard
--
(1) Attempts to read an empty region results in an error.
> gr <- GRanges("22", IRanges(1000000, 2000000))
>
> param <- ScanBamParam(which = gr)
>
> readGAlignmentPairs(file, param = param)
Error in `elementMetadata<-`(x, ..., value = value) :
replacement 'elementMetadata' value must be a DataTable object or NULL
>
> sessionInfo()
R Under development (unstable) (2013-12-03 r64376)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] GenomicAlignments_0.99.9 Rsamtools_1.15.15 Biostrings_2.31.5
[4] GenomicRanges_1.15.17 XVector_0.3.5 IRanges_1.21.16
[7] BiocGenerics_0.9.2 BiocInstaller_1.13.3
loaded via a namespace (and not attached):
[1] bitops_1.0-6 stats4_3.1.0 tools_3.1.0 zlibbioc_1.9.0
>
... but works fine with previous version
> gr <- GRanges("22", IRanges(1000000, 2000000))
>
> param <- ScanBamParam(which = gr)
>
> readGAlignmentPairs(file, param = param)
GAlignmentPairs with 0 alignment pairs and 0 metadata columns:
seqnames strand : ranges -- ranges
<Rle> <Rle> : <IRanges> -- <IRanges>
---
seqlengths:
1 2 3 ... GL000247.1 GL000248.1 GL000249.1
249250621 243199373 198022430 ... 36422 39786 38502
>
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Rsamtools_1.14.2 Biostrings_2.30.1 GenomicRanges_1.14.4
[4] XVector_0.2.0 IRanges_1.20.6 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 stats4_3.0.0 zlibbioc_1.8.0
(2) Use of the which argument covering chromosome 22 takes under one
minute with an earlier version of readGAlignmentPairs
> gr <- GRanges("22", IRanges(1, 51304566))
>
> param <- ScanBamParam(which = gr)
>
> system.time(gap <- readGAlignmentPairs(file, param = param))
user system elapsed
45.887 0.256 46.168
>
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Rsamtools_1.14.2 Biostrings_2.30.1 GenomicRanges_1.14.4
[4] XVector_0.2.0 IRanges_1.20.6 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 stats4_3.0.0 zlibbioc_1.8.0
>
... but at least twenty times as long with the current version.
> gr <- GRanges("22", IRanges(1, 51304566))
>
> param <- ScanBamParam(which = gr)
>
> system.time(gap <- readGAlignmentPairs(file, param = param))
^C
Timing stopped at: 1108.041 35.998 1144.006
>
> sessionInfo()
R Under development (unstable) (2013-12-03 r64376)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] GenomicAlignments_0.99.9 Rsamtools_1.15.15 Biostrings_2.31.5
[4] GenomicRanges_1.15.17 XVector_0.3.5 IRanges_1.21.16
[7] BiocGenerics_0.9.2
loaded via a namespace (and not attached):
[1] bitops_1.0-6 stats4_3.1.0 zlibbioc_1.9.0
>
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