[Bioc-devel] Running Time of readBamGappedAlignmentPairs

Dario Strbenac dstr7320 at uni.sydney.edu.au
Mon Jul 29 09:00:10 CEST 2013

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

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:


----- 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


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

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