https://github.com/alexpreynolds/kmer-counter-abseil
Count canonical kmers with Abseil C++ `absl::flat_hash_map`
Science Score: 13.0%
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Low similarity (6.9%) to scientific vocabulary
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Repository
Count canonical kmers with Abseil C++ `absl::flat_hash_map`
Basic Info
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- Stars: 1
- Watchers: 2
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- Open Issues: 0
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Metadata Files
README.md
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.
Owner
- Name: Alex Reynolds
- Login: alexpreynolds
- Kind: user
- Location: Seattle, WA USA
- Company: Altius Institute for Biomedical Sciences
- Website: bitsumma.com
- Repositories: 92
- Profile: https://github.com/alexpreynolds
Pug caregiver, curler, cyclist, gardener, beginning French scholar
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Top Committers
| Name | Commits | |
|---|---|---|
| Alex Reynolds | a****s@g****m | 3 |
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