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 [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 1939.11 > 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@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
