Request for clearer documentation to explain bitwise FLAG values, ideally with documentation about hts-specs HOT 7 OPEN

I agree the SAM/BAM specification isn't novice-friendly, but maybe it doesn't need to be? It should be a developer centric dry technical document, but supplemented by separate user-facing documentation provided from people using SAM/BAM.

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That would be acceptable, but you would still ideally want to direct people to those more user-friendly sources of documentation from the main SAM documentation.

Most people will come across the current SAM documentation from a Google search for 'SAM format'.

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There is space on SEQwiki for user created format information.
On 25 Nov 2014 21:01, "Keith Bradnam" [email protected] wrote:

That would be acceptable, but you would still ideally want to direct
people to those more user-friendly sources of documentation from the main
SAM documentation.

Most people will come across the current SAM documentation from a Google
search for 'SAM format'.

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#55 (comment).

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FWIW, I've always found http://broadinstitute.github.io/picard/explain-flags.html a very handy calculator for SAM flags.

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The incorporation of these binary flags in an otherwise "readable" format let's me mischievously suspect that they were intended as an obstacle in the first place.

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Bit flag is a succinct way to encapsulate rich information. At the time of the first draft, it was not obvious how to represent multiple info in a readable style without greatly complicating the format. In the lack of an acceptable alternative, we kept the bit flag.

A few years later, I realized that we could use one character for each bit. This was the old samtools view -X output. In this representation, 99=0x63 becomes pP1R. It is more readable while maintaining a simple 1-to-1 translation to the bit flag. Nonetheless, the proposal was rejected by the consensus. Most considered this change too late as SAM was fairly mature.

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Thanks Heng for the comment !
I just found today the, for me, so far best explanation of these flags and some tips on how to deal with them in python and perl scripts here: http://blog.nextgenetics.net/?e=18
I spend a long time searching for this info. For a simple minded biologist a simple letter code has its advantages.

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