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Patch rev complement and first implementation of --auto in obicsv

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Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
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Eric Coissac
2023-11-07 09:37:07 +02:00
parent 6a6a6f6f2c
commit 61c30f9b6a
21 changed files with 270 additions and 107 deletions
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Release-notes.md
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@ -2,6 +2,10 @@
## Latest changes
### New feature
- In the obitools language a new `gc` computes the gc fraction of a sequence.
### Enhancement
- A new completely rewritten GO version of the fastq and fasta parser is now used instead of the original C version.
@ -13,6 +17,17 @@
+ If -D is set to 0, the output sequence is the barcode with the priming sites.
+ When -D is set to ### (where ### is an integer), the output sequence is the barcode with the priming sites.
and ### base pairs of flanking sequences.
### Bugs
- in the obitools language, the `composition` function now returns a map indexded by lowercase string "a", "c", "g", "t" and "o" for other instead of being indexed by the ascii codes of the corresponding letters.
- Correction of the reverse-complement operation. Every reverse complement of the DNA sequence follow now the following rules :
+ Nucleotides code are complemented to their lower complementary base
+ `.` and `-` characters are returned without change
+ `[` is complemented to `]` and oppositely
+ all other characters are complemented as `n`
### Becareful
GO 1.21.0 is out, and it includes new functionalities which are used in the OBITools4 code.