Re: [Samtools-devel] picard: header, sortorder

[Alec W. <al...@br...>]

Hi Marian,

Picard is always going to write an @HD record even if one was not 
present in the input.  It will always write an SO tag.  If one was not 
present in the input, it assumes unsorted.  We haven't seen the need to 
suppress the writing of the HD record and SO tag.

-Alec

On 9/20/10 4:21 AM, Marian Thieme wrote:
> Hi,
>
> I want to understand why picard set the sort order in the header to 
> unsorted. my code is taken from the Example class:
>
> ...
> SAMFileHeader outHeader = inputSam.getFileHeader();
> final SAMFileWriter outputSam = new 
> SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader,
>                 true, outputSamOrBamFile);
> ...
>
> The input bamfile I am giving to the class is sorted, though there is 
> no sort order and no @HD defined.
> To avoid setting the @HD tag and/or the sort order would be perfectly 
> fine.
>
>
> Sorry when this question has already been asked. Unfortunatly I havent 
> managed to use the search function of the sourceforege list interface.
> Should it work ? How I can search ?
>
> Thanks,
> Marian
>
>
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