Hi Hervé,

Yes the latest version of Rsamtools works fine for both the original and
the new problem.

Many thanks for fixing this bug, and the quick reply.

Best wishes

Leonard


On Fri, Sep 27, 2013 at 4:55 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> Hi Leonard,
>
> Good timing. I was actually going to get back to you today about this
> because yesterday I fixed a bug in findMateAlignment() that I think was
> causing the problem you originally reported on the mailing list. It's
> also probably what is causing this new problem you are reporting below.
> Totally agree with you that even if using a 'which' argument can alter
> the pairing, in any case it should produce an error. More generally the
> intended behavior of readGAlignmentPairs() is to *drop* records that
> don't have a mate and to *dump* ambiguous pairings. Not to choke on
> them. The difference between "drop" and "dump" here is that what's
> dumped can be examined latter with getDumpedAlignments(). See
> ?getDumpedAlignments for the details.
>
> Please let me know if you still run into those issues with the latest
> Rsamtools (1.13.45). Works fine for me on your test.bam file (thanks
> for providing the file).
>
> Cheers,
> H.
>
>
>
> On 09/27/2013 04:23 PM, Leonard Goldstein wrote:
>
>> Hi Hervé
>>
>> Thanks for your and Valerie's comments on using 'which' with
>> readGAlignmentPairs.
>>
>> I actually encountered the same error again without using 'which' (see
>> below). I attached test.bam, which narrows down the problematic
>> alignment(s) to around ~600. If readGAlignmentPairs could drop any
>> unusual alignments rather than generating an error that would be really
>> helpful.
>>
>> Many thanks for your help.
>>
>> Leonard
>>
>>
>>  > readGAlignmentPairs(file = "test.bam")
>> Error in makeGAlignmentPairs(galn, use.names = use.names, use.mcols =
>> use.mcols) :
>>    findMateAlignment() returned an invalid 'mate' vector
>> In addition: Warning message:
>> In findMateAlignment(x) :
>>      2 alignments with ambiguous pairing were dumped.
>>      Use 'getDumpedAlignments()' to retrieve them from the dump
>> environment.
>>  >
>>  > sessionInfo()
>> R version 3.0.0 (2013-04-03)
>> 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=C                 LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] Rsamtools_1.13.44     Biostrings_2.29.19    GenomicRanges_1.13.45
>> [4] XVector_0.1.4         IRanges_1.19.38       BiocGenerics_0.7.5
>>
>> loaded via a namespace (and not attached):
>> [1] bitops_1.0-6   stats4_3.0.0   zlibbioc_1.7.0
>>  >
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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