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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

  • #2
    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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