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Old 01-19-2011, 03:23 PM   #1
Junior Member
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 *?


Dana Robinson
The HDF Group
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Old 01-20-2011, 10:06 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

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.
maubp is offline   Reply With Quote

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