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Old 01-19-2011, 03:23 PM   #1
derobins
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Location: Champaign, Illinois

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Default Is * really a valid value for a SAM FLAG field?

The SAM spec (v1.3-r882, page 3) states that * is a valid value for the SAM FLAG field, yet the table just above it indicates that it is an int in the interval [0, 2^16 - 1] without listing the star (as is done where * is a valid value).

Is the text about * being a valid FLAG value an error? Shouldn't 0 mean that no bits are set, not *?

Thanks,

Dana Robinson
The HDF Group
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Old 01-20-2011, 10:06 AM   #2
maubp
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It does sound like a bug in the spec (especially since there is no way to do anything equivalent in BAM). You might want to ask this on the samtools mailing list.
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