[Ssrformat] Status of SRF?

[Asim Siddiqui]

James,
 
I realized that I hadn't responded to your comment about concatenating srf files.
I agree with your suggestion of a dedicated srf_cat tool to create a single index.
 
I spotted a error in the name of a field in the index. The first "bytesToDBH" field should be named "bytesToContainer". This is a naming error only - the actual structure of the index is correct.
 
Asim

________________________________

From: ssrformat-bounces at mail.bcgsc.ca on behalf of James Bonfield
Sent: Thu 24/01/2008 5:37 AM
To: ssrformat at bcgsc.ca
Subject: [Ssrformat] Status of SRF?



Hello all,

Can I get a quick feeling for how people consider SRF now please? I
think the format should be solid now and unlikely to be changing
much. Do others agree or are there tweaks we feel are necessary? [1]

The reason I ask is simply that we, the Sanger Institute, are getting
to the stage of producing lots of data and in conjunction with EBI
would like to start archiving it in public repositories, so naturally
SRF is the storage of choice.

I believe the 1000 genomes project are also discussing how to archive
data and it would be a good message to send out if we can sign off the
standard and declare it as non draft.

James

[1] The only tweak I can personally think of involves indexing and
isn't really a critical issue anyway. If we concatenate multiple
indexed SRF files together then the only thing stopping us from being
able to query each index serially in turn is knowing the distance from
an index to the previous one. However realistically this isn't a
common case and it's trivially worked around by using a dedicated
srf_cat tool instead of unix cat and one single index record is more
efficient than several small ones.

--
James Bonfield (jkb at sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
                                  | Plurima gyrabant gymbolitare vabo;
  A Staden Package developer:     | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi.


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