Re: [Bio-bwa-help] A question about BWA

[Chaolin Z. <cz...@ma...>]

Hi Nils,

Thanks for the information.  We made substantial changes on top of bwa, so that at this point it will be difficult for us to switch to a new version.  Your notes are a bit suprising for me though, since I expect the speed to retrieval of the suffix array elements will be doubled if we set OCC_INTERVAL to half.

Looks like I need to change quite a few places.  I made some notes about the arrangement in the BWT string, but apparently now I need a lot of efforts to recall…

Chaolin




On Feb 14, 2012, at 10:19 PM, Nils Homer wrote:

I tried this (changing the compression) in a fork of BWA and did not observe a significant speedup.  Note that there were a few bugs beyond the below.

The best speedup I have seen is this branch of BWA: http://github.com/RoelKluin/bwa

Nils

On Tue, Feb 14, 2012 at 9:35 PM, Heng Li <he...@br...<mailto:he...@br...>> wrote:
Yes, it is possible to make bwa faster by decrease OCC_INTERVAL. However, I am not sure if bwa still works when you only change OCC_INTERVAL only. If you want to give a try, you should try on the latest 0.6.1. You should also change bwt_bwt() and bwt_occ_intv() which are hard coded to OCC_INTERVAL==128. You can find the generic form in the comment of bwt.h.

You can ignore OCC_INTERVAL in bwt_gen.h. bwt_gen has a separate code base.

Heng

On Feb 14, 2012, at 9:25 PM, Chaolin Zhang wrote:

> Dear Heng,
>
> This is Chaolin Zhang from Rockefeller.  I am wondering if I can make BWA even faster at the cost of using more memory (which are quite affordable now).  I guess one quick way is to change the OCC_INTERVAL value in BWA, but I am having a question.  I noticed that OCC_INTERVAL is defined in both bwt.h and bwt_gen/bwt_gen.h and interestingly the values are different (128 and 256 respectively).  Any explanation for this?  Thanks!
>
> Chaolin
>


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