Pagès
Cc: Dario Strbenac; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs
On 07/31/2013 04:05 PM, Hervé Pagès wrote:
> Hi Dario,
>
> Thanks for providing the file.
>
> The file has 55780092 records in it and yes it only contains primary
me of readBamGappedAlignmentPairs() (11 min / 15
>> min
>> with BioC devel on my Linux server). This is a little bit
>> surprising
>> to me and that's something I'd like to investigate.
>>
>> Cheers,
>> H.
>>
>
<https://stat.ethz.ch/pipermail/bioconductor/2013-June/053390.html>
Cheers,
H.
----- Original Message -
From: "Dario Strbenac" mailto:dstr7...@uni.sydney.edu.au>>
To: bioc-devel@r-projec
ppedAlignments() takes more than 70%
>> of the total time of readBamGappedAlignmentPairs() (11 min / 15 min
>> with BioC devel on my Linux server). This is a little bit surprising
>> to me and that's something I'd like to investigate.
>>
>> Cheers,
>> H.
>
gate the granges coercion function
? It also took half an hour.
________
From: Hervé Pagès [hpa...@fhcrc.org]
Sent: Tuesday, 30 July 2013 3:29 AM
To: Dario Strbenac
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs
On 07/29/
n function ?
It also took half an hour.
____
From: Hervé Pagès [hpa...@fhcrc.org]
Sent: Tuesday, 30 July 2013 3:29 AM
To: Dario Strbenac
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs
On 07/29/2013 12:00 AM, Dari
user system elapsed
1681.36 65.79 1752.10
From: Pages, Herve [hpa...@fhcrc.org]
Sent: Monday, 29 July 2013 3:29 PM
To: Dario Strbenac
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs
Hi Dario,
The functio
:29 PM
To: Dario Strbenac
Cc: bioc-devel@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
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
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
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