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
alignments so
.
__**__
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, Dario Strbenac wrote:
Because I only allowed unique
...@fhcrc.org mailto:hpa...@fhcrc.org]
Sent: Monday, 29 July 2013 3:29 PM
To: Dario Strbenac
Cc: bioc-devel@r-project.org mailto:bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Running Time of
readBamGappedAlignmentPairs
: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
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 function
: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
