[Bioc-devel] ShortRead: 'qa' fails for single read alignments

[Martin Morgan]

Thanks Julian -- these were separate issues (3 was from a recent change 
in Rsamtools, the other is more long-standing). Corrected in svn and 
1.14.4 / 1.15.6 when these become available.

Martin

On 05/24/2012 05:32 AM, Julian Gehring wrote:
> Hi,
>
> while using the 'ShortRead' package for some quality assessment of
> aligned reads (see example below), I observed the following behavior:
>
> ## Example code ##
>
> library(ShortRead)
> qa1 <- qa(dirPath="tmp/", pattern="*sub.bam", type="BAM")
> report_html(qa1, dest="out")
>
> ##
>
> 1. For R-2.14.0, the report is built as expected (see
> http://www.ebi.ac.uk/~jgehring/share/shortRead-pkg/perCycleBaseCall-R-2.14.0.pdf
> for a comparison).
>
> 2. For R-2.15.0, the cycle-specific base calls and read quality plot
> looks mixed up (see
> http://www.ebi.ac.uk/~jgehring/share/shortRead-pkg/perCycleBaseCall-R-2.15.0.pdf).
>
>
> 3. For R-2.16.0devel (2012-05-24 r59439), the 'qa' command fails with
> the error message:
> ""
> Error: ValueUnavailable
> 0 elements returned; expected >=1
> In addition: Warning message:
> UnspecifiedWarning
> elements: 1 2 3 4
> UnspecifiedError: bamFlagTest(flag, "isValidVendorRead")
> 'is' must be character(1) in 'isPaired' 'isProperPair' 'isUnmappedQuery'
> 'hasUnmappedMate' 'isMinusStrand' 'isMateMinusStrand' 'isFirstMateRead'
> 'isSecondMateRead' 'isNotPrimaryRead' 'isNotPassingQualityControls'
> 'isDuplicate'
> UnspecifiedError: bamFlagTest(flag, "isValidVendorRead")
> 'is' must be character(1) in 'isPaired' 'isProperPair' 'isUnmappedQuery'
> 'hasUnmappedMate' 'isMinusStrand' 'isMateMinusStrand' 'isFirstMateRead'
> 'isSecondMateRead' 'isNotPrimaryRead' 'isNotPassingQualityControls'
> 'isDuplicate'
> UnspecifiedError: bamFlagTest(flag, "isValidVendorRead")
> 'is' must be character(1) in 'isPaired' 'isProperPair' 'isUnmappedQuery'
> 'hasUnmappedMate' 'isMinusStrand' 'isMateMinusStrand' 'isFirstMateRead'
> 'isSecondMateRead' 'isNotPrimaryRead' 'isNotPassingQualityControls'
> 'isDuplicate'
> UnspecifiedError: bamFlagTest(flag, "isValidVendorRead")
> 'is' must be character(1) in 'isPaired' [... truncated]
> ""
>
> See also
> - http://www.ebi.ac.uk/~jgehring/share/shortRead-pkg/session-info-2.14.txt
> - http://www.ebi.ac.uk/~jgehring/share/shortRead-pkg/session-info-2.15.txt
> - http://www.ebi.ac.uk/~jgehring/share/shortRead-pkg/session-info-2.16.txt
> for the corresponding session infos.
>
> Can this be caused by having BAM files with single-read alignments?
> Also, I'm not sure if the different behavior for R-2.15 and R-2.16 is
> directly related.
>
>
> Best
> Julian
>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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