BinarySequence |
Base class for a binary 'read'.
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DnaAndQualitySequence |
Binary packed DNA sequence and base calling quality
Notes:
- This is designed for short sequences (such as "short reads")
- Every base is encoded in 8 bits:
- Six bits for the base quality [0 , ..
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DnaAndQualitySequenceWithId |
DnaAndQualitySequence with an ID
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DnaNSequence |
Binary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}
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DnaSequence |
Binary packed DNA sequence
Notes:
- This is designed for short sequences (such as "short reads")
- Every base is encoded in 2 bits {a, c, g, t} <=> {0, 1, 2, 3}
- All bits are stored in an array of 'words' (integers)
- Most significant bits are the first bases in the sequence (makes comparison easier)
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DnaSequenceByte |
Binary packed DNA sequence.
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DnaSequenceId |
Binary packed DNA sequence with an ID (long)
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DnaSequencePe |
Pair end DNA sequence (binary packed)
It consists of 2 DNA sequences separated by a gap.
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GenomicSequences |
This class stores all "relevant" sequences in a genome
This class is able to:
i) Add all regions of interest
ii) Store genomic sequences for those regions of interest
iii) Retrieve genomic sequences by interval
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IdGenerator |
Generates Id
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