[Bioc-devel] Running Time of readBamGappedAlignmentPairs

[Dario Strbenac]

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

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Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia