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Former-commit-id: 1fee30445f03ff627dab1c335e75c3f278621f6e
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Eric Coissac
2023-11-07 21:20:45 +02:00
parent aa0443e484
commit 8f96517f3c
2 changed files with 6 additions and 6 deletions
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10
Release-notes.md
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@ -4,18 +4,18 @@
### New feature ### New feature
- In the obitools language a new `gc` computes the gc fraction of a sequence. - In the OBITools language a new `gc` computes the GC fraction of a sequence.
### Enhancement ### Enhancement
- A new completely rewritten GO version of the fastq and fasta parser is now used instead of the original C version. - A new completely rewritten GO version of the fastq and fasta parser is now used instead of the original C version.
- A new file format guesser is now implemented. This is a first step towards allowing new formats to be managed by obitools. - A new file format guesser is now implemented. This is a first step towards allowing new formats to be managed by OBITools.
- New way of handling header definitions of fasta and fastq formats with JSON headers. - New way of handling header definitions of fasta and fastq formats with JSON headers.
The sequence definition is now printed in new files as an attribute of the json header named "definition". The sequence definition is now printed in new files as an attribute of the JSON header named "definition".
- The -D (--delta) option has been added to `obipcr`. It allows extracting flanking sequences of the barcode. - The -D (--delta) option has been added to `obipcr`. It allows extracting flanking sequences of the barcode.
+ If -D is not set, the output sequence is the barcode itself without the priming sites. + If -D is not set, the output sequence is the barcode itself without the priming sites.
+ If -D is set to 0, the output sequence is the barcode with the priming sites. + 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. + 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. and ### base pairs of flanking sequences.
- A new output format in JSON is proposed using the **--json-output**. The sequence file is printed as a JSON vector, - A new output format in JSON is proposed using the **--json-output**. The sequence file is printed as a JSON vector,
where each element is a map corresponding to a sequence. The map has at most four elements: where each element is a map corresponding to a sequence. The map has at most four elements:
@ -245,7 +245,7 @@ to use the git ticket system to mention them. But they seems to produce now reli
### New features ### New features
- Adding of a `--compress|-Z` option to every obitools allowing to produce `gz` compressed output. OBITools - Adding of a `--compress|-Z` option to every obitools allowing to produce `gz` compressed output. OBITools
were already able to deal with gziped input files transparently. They can now produce their résults in the same format. were already able to deal with gziped input files transparently. They can now produce their results in the same format.
- Adding of a `--append|-A` option to the `obidistribute` tool. It allows to append the result of an - Adding of a `--append|-A` option to the `obidistribute` tool. It allows to append the result of an
`obidistribute` execution to preexisting files. `obidistribute` execution to preexisting files.
- Adding of a `--directory|-d` option to the `obidistribute` tool. It allows to declare a secondary - Adding of a `--directory|-d` option to the `obidistribute` tool. It allows to declare a secondary

2
pkg/obiformats/embl_read.go
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@ -232,7 +232,7 @@ func _ReadFlatFileChunk(reader io.Reader, readers chan _FileChunk) {
// Set the buffer to the size of a chunk of data and copy any remaining data to the new buffer // Set the buffer to the size of a chunk of data and copy any remaining data to the new buffer
buff = make([]byte, _FileChunkSize) buff = make([]byte, _FileChunkSize)
copy(buff, remains) copy(buff, remains)
l = len(remains) //l = len(remains)
} }
} }