[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.

class: ScanBamParam
bamFlag (NA unless specified): isValidVendorRead=FALSE
bamSimpleCigar: FALSE
bamReverseComplement: FALSE
bamWhich: 0 elements

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

R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-linux-gnu (64-bit)

  [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

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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