[Bioc-devel] Rsamtools: Is extdata/ex1.bam.bai outdated?

[Henrik Bengtsson]

Thanks Martin,

I just happen to notice it because I got:

>samtools idxstats ex1.bam
seq1    1575    0       0
seq2    1584    0       0
*       0       0       0

whereas with ex1.bam.bai in Rsamtools 1.17.6:
>samtools idxstats ex1.bam
seq1    1575    1482    19
seq2    1584    1789    17
*       0       0       0

For others, it's 'ex1.bam.bai' and not 'ex1.bam' that has been updated.

/Henrik

On Mon, Apr 21, 2014 at 10:44 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>
> Hi Henrik -- yes ex1.bam was out of date.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 Is the package's index file generated with an outdated version of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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>>
>
>
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