[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
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

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Because I only allowed unique mappings, the ratio is 2. After installing the development package versions, I only got a 10% improvement.

   user  system elapsed 
1681.36   65.79 1752.10
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

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
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

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpages at fhcrc.org
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