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 [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 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" <dstr7...@uni.sydney.edu.au> To: bioc-devel@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 1939.11system.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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
