Comments (1)
Basic implementation done. Further improvements will be handled in new issues.
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Related Issues (20)
- Choose error tolerance for self-alignment such that all relevant repeats will be detected HOT 1
- Alignment coverage for detection of "bad" loci HOT 2
- Option to output the set of filtered reads HOT 1
- Select only proper reads as candidates
- Weakly anchored alignment chains should not be used for pile ups HOT 1
- `getComplementaryOrder` should not combine all local alignments into one
- Favor direct sequential output
- Move loop structure out of the main algorithm
- Make main algorithm one-pass-only HOT 1
- Initialize repeat mask with user input
- Is the self-alignment essential?
- Filtering for `isValid` discard good reads
- Require a minimum coverage in pile ups before consensus
- Take complementary alignment into account when assembling contigs HOT 1
- Add option to enable extensions
- Users must provide initial alignment
- User may select a block of the reference DB HOT 1
- Testing: insert real Illumina gaps into PacBio assembly HOT 1
- Concise logging rules
- Reduce number of consensus computations
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from djunctor.