[Bioc-devel] Rsamtools: Is extdata/ex1.bam.bai outdated?

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
Hi Henrik -- yes ex1.bam was out of date.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Is the package's index file generated with an outdated version of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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[Bioc-devel] Rsamtools: Is extdata/ex1.bam.bai outdated?

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