kmer-counter-abseil

The kfs program reads in multiline FASTA records, counts canonical kmers using the Abseil C++ container:flat_hash_map.

Abseil C++

Integration of the Abseil C++ kit requires use of bazel, e.g., on OS X:

$ brew cask install homebrew/cask-versions/java8
$ brew install bazel

Clone the Abseil C++ Github repository:

$ make abseil-cpp

Edit the WORKSPACE file in this directory to specify the correct path for the Abseil C++ installation.

Then complete the build:

$ make abseil-cpp-build

This can take a few minutes.

Usage

Compilation

$ make kfs
$ make msl
$ make generate_fasta

These targets build binaries bazel-bin/src/kfs, bazel-bin/src/msl, and bazel-bin/src/generate_fasta, respectively.

Test data

$ bazel-bin/src/generate_fasta > test.fa

(Or build the generate_test_data target.)

Performance testing

Specify variables K (integer) and FASTA (path to FASTA sequences), before running tests with those variables, e.g.:

$ export K=29
$ export FASTA=test.fa
$ /usr/bin/time -l bazel-bin/src/kfs -k ${K} -i ${FASTA}
...

Etc.