[BioC] Rsamtools: scanBamFlag bug?
Nuno Fonseca
nuno.fonseca at gmail.com
Mon May 21 12:19:07 CEST 2012
Dear all,
I got a unexpected behaviour when I set the isValidVendorRead flag as TRUE.
>library(Rsamtools)
>ScanBamParam(flag=scanBamFlag(isValidVendorRead=TRUE))
class: ScanBamParam
bamFlag (NA unless specified): isValidVendorRead=FALSE
bamSimpleCigar: FALSE
bamReverseComplement: FALSE
bamTag:
bamWhich: 0 elements
bamWhat:
The isValidVendorRead is shown as being FALSE but I would expect it to be TRUE. I started
using Rsamtools recently so I am not sure if I am missing something or if this a bug.
Thanks in advance for your time,
Nuno Fonseca
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rsamtools_1.8.4 Biostrings_2.24.1 GenomicRanges_1.8.5
[4] IRanges_1.14.2 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] bitops_1.0-4.1 stats4_2.15.0 zlibbioc_1.2.0
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