[Bioc-sig-seq] different results between Rsamtools and samtools

[Benilton Carvalho]

Hi,

I wonder if you guys could help me out understanding what the problem
may be when reading in some BAM files I have...

When viewing them with samtools, I get reads on chr6 (samtools view
file.bam chr6)

When using scanBam/scanBamHeader, I do not get any reads on chr6
(latest RSamtools on 2.11.1, but same happens with the latest devel
too).

Suggestions on how to proceed in order to understand what may be going
on (or what I may be missing)? My guess is that the files are
corrupted, nothing strange comes up when using samtools...

Thank you,

benilton