Re: [Seqan-dev] mapQ overwritten when writing sam/bam?

[Bernd Jagla <bernd.jagla@pasteur.fr>]

Hi,
sorry, it seems the problem is on my side...
Thanks for looking into it, though,
Cheers,
Bernd

On 5/16/2012 11:18 AM, Holtgrewe, Manuel wrote:
> Hi Bernd,
>
> what do you mean it is changed? Is the wrong value written to the file? Is it changed in the program itself? Are you writing SAM or BAM?
>
> Can you provide a minimal program that shows the problem?
>
> Second, I guess the function signature should be:
>
> template<typename TStream, typename TFormat>
> int writeOutRecordSet(TStream&fp, String<BamAlignmentRecord>  const&  recSet,
>           BamIOContext<StringSet<CharString>  >  &  context, TFormat const&
> tag,
>           ROI&  roi) {
>
> - StringSet<BamAlignmentRecord>  &  recSet ->  String<BamAlignmentRecord>  const&  recSet
>
> Cheers!
> Manuel
> ________________________________________
> From: Bernd Jagla [bernd.jagla@pasteur.fr]
> Sent: Wednesday, May 16, 2012 9:55 AM
> To: seqan-dev@lists.fu-berlin.de
> Subject: [Seqan-dev] mapQ overwritten when writing sam/bam?
>
> Hi,
>
> I am using the sam/bam packages to read and write sam/bam files and I
> noticed that a value for the mapping quality (column 5) has been changed
> from 255 to 0...
> Is this possible? I am using the BamIOContext as in the following example:
>
> template<typename TStream, typename TFormat>
> int writeOutRecordSet(TStream&fp, StringSet<BamAlignmentRecord>  recSet,
>           BamIOContext<StringSet<CharString>  >  &  context, TFormat const&
> tag,
>           ROI&  roi) {
>
>       unsigned maxC = 0;
>       for (unsigned i = 0; i<  length(roi.count); i++) {
>           if (maxC<  roi.count[i])
>               maxC = roi.count[i];
>       }
>       roi.countMax = maxC;
>       for (unsigned i = 0; i<  length(recSet); i++) {
>           BamTagsDict tagDict(recSet[i].tags);
>           setTagValue(tagDict, "rl", roi.len);
>           setTagValue(tagDict, "ri", roi.min);
>           setTagValue(tagDict, "rx", roi.max);
>           setTagValue(tagDict, "ry", maxC);
>           setTagValue(tagDict, "rn", length(recSet), 'i');
>           write2(fp, recSet[i], context, tag);
>       }
>       return maxC;
> }
>
> What do I have to do to keep the value?
>
> Thanks a lot for your kind support.
>
> Best,
>
> Bernd
>
>
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