Hi Henrik -- yes ex1.bam was out of date. I updated it in devel; was the
staleness causing problems? Thanks for the report. Martin
On 04/18/2014 06:37 PM, Henrik Bengtsson wrote:
When I re-index Rsamtools::extdata/ex1.bam I get a different and
larger index file:
bam <- system.file("extdata", "ex1.bam", package="Rsamtools")
bai <- system.file("extdata", "ex1.bam.bai", package="Rsamtools")
# Reindex
bam2 <- basename(bam)
file.copy(bam, bam2)
bai2 <- Rsamtools::indexBam(bam2)
# New index file is greater
file.info(c(bai, bai2))$size
## [1] 72 176
unname(sapply(c(bai, bai2), function(f) digest::digest(file=f)))
## [1] "f3fa4087d439dad4d404b34dad491747"
## [2] "1888862b9d22ddb8ca663eabc41c78f0"
Is the package's index file generated with an outdated version of
[R]samtools? According to the SVN logs it dates back to 2009-08-08.
Sorry if this is a FAQ.
I get this with Rsamtools 1.16.0 on both Linux and Windows:
sessionInfo()
R version 3.1.0 (2014-04-10)
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] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocGenerics_0.10.0 Biostrings_2.32.0 bitops_1.0-6
[4] digest_0.6.4 GenomeInfoDb_1.0.2 GenomicRanges_1.16.1
[7] IRanges_1.22.3 parallel_3.1.0 Rsamtools_1.16.0
[10] stats4_3.1.0 tools_3.1.0 XVector_0.4.0
[13] zlibbioc_1.10.0
sessionInfo()
R version 3.1.0 Patched (2014-04-10 r65396)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocGenerics_0.10.0 Biostrings_2.32.0 bitops_1.0-6
[4] digest_0.6.4 GenomeInfoDb_1.0.2 GenomicRanges_1.16.1
[7] IRanges_1.22.2 parallel_3.1.0 Rsamtools_1.16.0
[10] stats4_3.1.0 tools_3.1.0 XVector_0.4.0
[13] zlibbioc_1.10.0
/Henrik
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