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 n
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
