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  • BAMseek
    Senior Member
    • Apr 2011
    • 124

    #1

    changes to SAM Specs (Sept 7, 2011)

    I recently noticed that the SAM specifications have been updated (September 7, 2011). It would be nice if they listed the differences between versions of the specs and announced changes but I haven't been able to find such a listing. What I ended up doing was converting the pdf to text (via pdftotext) of the recent version and an older version (April 17) and finding the differences that way.

    Two main things I noticed - they changed the term "fragment" to "segment" throughout the file. I think this is great since it will help to cut down on confusion with other meanings of the word fragment. I also noticed they added a Barcode (BC) tag.

    Another minor thing: the flow signal intensities tag (FZ) is now stored as a byte array of uint16_t instead of a byte array in hex format.
  • maubp
    Peter (Biopython etc)
    • Jul 2009
    • 1544

    #2
    You can track the changes to the TEX file used to create the PDf in the samtools SVN repository, but I agree having a human readable summary in the document would be nice.

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    • BAMseek
      Senior Member
      • Apr 2011
      • 124

      #3
      You can track the changes to the TEX file used to create the PDf in the samtools SVN repository
      Thanks, that is good to know. =justin

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