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

[Julian Gehring]

Hi Martin,

thanks for fixing these issues so quickly - the reports are now built 
without problems.


Best
Julian


On 05/24/2012 05:30 PM, Martin Morgan wrote:
> 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>