When I ran BiScan_null.R for chr22, it took a little over 9.5 hours to complete. I profiled the code and found a few bottlenecks to optimize. When I ran the new version, it took a little over 4.5 hours to process chr22.
I compared the results and they were essentially identical. sd1_chr22.txt and sd2_chr22.txt were literally identical between the two runs. Of the total 45,000 lines across all of the Qmax output files for chr22, there were only 36 lines that differed (when running diff in the terminal). I did a manual inspection of these 36 lines to confirm the differences were only ever in the 12th or 13th decimal place.
When I ran BiScan_null.R for chr22, it took a little over 9.5 hours to complete. I profiled the code and found a few bottlenecks to optimize. When I ran the new version, it took a little over 4.5 hours to process chr22.
I compared the results and they were essentially identical.
sd1_chr22.txtandsd2_chr22.txtwere literally identical between the two runs. Of the total 45,000 lines across all of the Qmax output files for chr22, there were only 36 lines that differed (when runningdiffin the terminal). I did a manual inspection of these 36 lines to confirm the differences were only ever in the 12th or 13th decimal place.