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Old 07-06-2012, 01:50 AM   #1
Location: Heidelberg

Join Date: Feb 2011
Posts: 69
Default when does BWA writes the outpu .sai

This might be a dumb question, but I can't find the answer anywhere and also don't have to possibility to test it right now.
When does BWA wrirte the output to the *.sai file?
Is it happening on the fly read by read or in small parts or all at the end. I think it is on the fly whenever a read gets mapped, is this correct?

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Old 07-06-2012, 02:05 AM   #2
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Location: Oxford

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If you run BWA ALN, you will see:

[bwa_aln_core] calculate SA coordinate... 0.69 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 0.67 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 524288 sequences have been processed.

So it's batch read, batch write.


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