Documentation
¶
Overview ¶
Package bio is a library representing Bioinformatics solutions.
This library defines biological data types abstractly by their functionality (interfaces) and how these abstract types relate to one another (functions) while not requiring any set structure. The advantage of this approach is that concrete data can be restructured for efficiency while still providing a compile-time check that it is still a functional representation of its abstract type.
Source Files
Directories
¶
| Path | Synopsis |
|---|---|
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Package alphabet defines the abstract interface for a biological alphabet.
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Package alphabet defines the abstract interface for a biological alphabet. |
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hashmap
Package hashmap is a collection of defined biological alphabets such as DNA, RNA, and Protein
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Package hashmap is a collection of defined biological alphabets such as DNA, RNA, and Protein |
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Package data is commonly referenced data such as lookup tables
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Package data is commonly referenced data such as lookup tables |
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codon
Package codon contains 31 DNA to Protein translation tables.
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Package codon contains 31 DNA to Protein translation tables. |
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quality
Package quality handles scores used to encode quality of a sequence
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Package quality handles scores used to encode quality of a sequence |
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Package io is a collection of IO operations with a focus on common standard formats
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Package io is a collection of IO operations with a focus on common standard formats |
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fasta
Package fasta handles reading, writing, and utilizing FASTA format
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Package fasta handles reading, writing, and utilizing FASTA format |
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fasta/base
Package base is a basic implementation of FASTA reading
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Package base is a basic implementation of FASTA reading |
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fastq
Package fastq handles reading, writing, and utilizing FASTQ format
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Package fastq handles reading, writing, and utilizing FASTQ format |
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Package sequence defines the abstract interface for a biological sequence.
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Package sequence defines the abstract interface for a biological sequence. |
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immutable
Package immutable is an implementation of biological sequences that have immutability.
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Package immutable is an implementation of biological sequences that have immutability. |
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mutable
Package mutable is an implementation of biological sequences that mutate internally.
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Package mutable is an implementation of biological sequences that mutate internally. |
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Package test defines any testing constants or functions used to validate assumptions.
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Package test defines any testing constants or functions used to validate assumptions. |
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Package utils is a collection of helpful utilities
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Package utils is a collection of helpful utilities |
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