[Bioc-devel] Running Time of readBamGappedAlignmentPairs

[Hervé Pagès]

On 07/29/2013 12:00 AM, Dario Strbenac wrote:
> Because I only allowed unique mappings, the ratio is 2. After installing the development package versions, I only got a 10% improvement.

Mmmh that's disappointing. Can you put the file somewhere so I can have
a look? Thanks.

H.

>
>     user  system elapsed
> 1681.36   65.79 1752.10
>
> ________________________________________
> From: Pages, Herve [hpages at fhcrc.org]
> Sent: Monday, 29 July 2013 3:29 PM
> To: Dario Strbenac
> Cc: bioc-devel at r-project.org
> Subject: Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs
>
> Hi Dario,
>
> The function was optimized in Bioc-devel. Depending on the number
> of records in your BAM file (which is more relevant than its size),
> it should now be between 2x and 5x faster. Please give it a try and
> let us know.
>
> Also keep in mind that the pairing algo will slow down if
> the "average nb of records per unique QNAME" is 3 or more.
> This was discussed here last month:
>    https://stat.ethz.ch/pipermail/bioconductor/2013-June/053390.html
>
> Cheers,
> H.
>
>
> ----- Original Message -----
> From: "Dario Strbenac" <dstr7320 at uni.sydney.edu.au>
> To: bioc-devel at r-project.org
> Sent: Sunday, July 28, 2013 9:00:30 PM
> Subject: [Bioc-devel] Running Time of readBamGappedAlignmentPairs
>
> Hello,
>
> Could readBamGappedAlignmentPairs be optimised ? It's surprising that it takes an extra 29 minutes to calculate the pairing information, for the example below. The BAM file is 4 GB in size.
>
>> system.time(RNAreads <- readBamGappedAlignmentPairs(file))
>     user  system elapsed
> 1852.16   59.00 1939.11
>> system.time(RNAreads <- readBamGappedAlignments(file))
>     user  system elapsed
>   192.80    8.12  214.97
>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
>
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>
>
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>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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