From 8f96517f3ccbce77f1c0bf3c2c80582e2c822613 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Tue, 7 Nov 2023 21:20:45 +0200 Subject: [PATCH] small changes Former-commit-id: 1fee30445f03ff627dab1c335e75c3f278621f6e --- Release-notes.md | 10 +++++----- pkg/obiformats/embl_read.go | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/Release-notes.md b/Release-notes.md index f1242b6..e6495dd 100644 --- a/Release-notes.md +++ b/Release-notes.md @@ -4,18 +4,18 @@ ### 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 - 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. - 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. + 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. - + 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. - 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: @@ -245,7 +245,7 @@ to use the git ticket system to mention them. But they seems to produce now reli ### New features - 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 `obidistribute` execution to preexisting files. - Adding of a `--directory|-d` option to the `obidistribute` tool. It allows to declare a secondary diff --git a/pkg/obiformats/embl_read.go b/pkg/obiformats/embl_read.go index a29136b..c184418 100644 --- a/pkg/obiformats/embl_read.go +++ b/pkg/obiformats/embl_read.go @@ -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 buff = make([]byte, _FileChunkSize) copy(buff, remains) - l = len(remains) + //l = len(remains) } }