Taking a stab at the reverse-compliment and k-nucleotide benchmarks from the alioth programming language shootout.
The modified k-nucleotide solution reduced the Elapsed secs metric from 5 minutes to 95.68 seconds and reduced the Memory KB metric from 462,252 to 36,672. At the time of this writing, it's the most memory efficient solution, for any language, and is the fastest JavaScript solution (disregarding my previous attempt which is posted in the "less comparable programs" section).
The modified reverse-compliment solution reduced the Elapsed secs metric from 12.80 seconds to 9.35 seconds and reduced the Memory KB metric from 347,808 to 252,288. At the time of this writing, it's the fastest and most memory efficient JavaScript solution.
The run.sh script validates the output from the modified solutions against the reference output. Then, the reference input is expanded to be much larger (500x and 75,000x). Using the larger input files, the performance of the modified solutions are compared to the performance of the original solutions.
Optionally, the larger files can be deleted when the process is finished (-c option). The full usage information for the script:
Usage: ./run.sh [-hvcskr] [-8 <d8-path>]
Options:
-h help Print this message
-v verbose Print commands as they're executed
-c clean Delete the large input files when finished
-s small Do not run large tests
-k knuc Run only the knucleotide tests
-r rev-comp Run only the reverse-complement tests
-8 v8 Path to v8 binary
Example: ./run.sh -c8 /usr/local/v8/out/native/d8
Output when run on my MacBookPro:
$ ./run.sh -c
Validate output from modified solution:
knucleotide: success
reverse-complement: success
Creating a large knucleotide input file.
This may take a few minutes.
data/knucleotide-input-500.txt
bytes: 127063119
Creating a large reverse-complement input file.
This may take a few minutes.
data/revcomp-input-75k.txt
bytes: 759450119
KNUCLEOTIDE
===========
Improved script processing time:
real 0m27.552s
user 0m27.365s
sys 0m0.167s
Original script processing time:
real 1m39.854s
user 1m39.403s
sys 0m0.360s
REVERSE-COMPLEMENT
==================
Improved script processing time:
real 0m23.252s
user 0m22.159s
sys 0m1.044s
Original script processing time:
real 0m34.330s
user 0m32.162s
sys 0m2.007s