[Bioc-devel] Rsamtools: Is extdata/ex1.bam.bai outdated?

[Martin Morgan]

Hi Henrik -- yes ex1.bam was out of date.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 Is the package's index file generated with an outdated version of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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