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Thread Tools |
07-06-2012, 01:50 AM
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#1 |
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Member
Location: Heidelberg Join Date: Feb 2011
Posts: 69
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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? Thanks |
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07-06-2012, 02:05 AM
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#2 |
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Senior Member
Location: Oxford Join Date: Feb 2012
Posts: 129
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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. Best, dong |
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