mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
Save change in various files
Former-commit-id: 428f8ee77c584b79cc2ef45eef2902c3e0754c77
This commit is contained in:
23
.gitignore
vendored
23
.gitignore
vendored
@ -5,6 +5,7 @@ bin
|
||||
vendor
|
||||
*.fastq
|
||||
*.fasta
|
||||
.DS_Store
|
||||
|
||||
/obiconvert
|
||||
/obicount
|
||||
@ -42,16 +43,22 @@ Stat_error.Rmd
|
||||
/obitools.code-workspace
|
||||
doc/.DS_Store
|
||||
.DS_Store/
|
||||
sample/euka03.ecotag.fasta.gz
|
||||
sample/ratio.csv
|
||||
sample/STD_PLN_1.dat
|
||||
sample/STD_PLN_2.dat
|
||||
sample/subset_Pasvik_R1.fastq.gz
|
||||
sample/subset_Pasvik_R2.fastq.gz
|
||||
sample/test_gobitools.fasta.bz2
|
||||
.RData
|
||||
x
|
||||
xxx
|
||||
y
|
||||
/doc/wolf_diet.tgz
|
||||
doc/.DS_Store
|
||||
/doc/man/depends
|
||||
/sample/wolf_R1.fasta.gz
|
||||
/sample/wolf_R2.fasta.gz
|
||||
/sample/euka03.ecotag.fasta.gz
|
||||
/sample/ratio.csv
|
||||
/sample/STD_PLN_1.dat
|
||||
/sample/STD_PLN_2.dat
|
||||
/sample/subset_Pasvik_R1.fastq.gz
|
||||
/sample/subset_Pasvik_R2.fastq.gz
|
||||
/sample/test_gobitools.fasta.bz2
|
||||
euka03.csv*
|
||||
gbbct793.seq.gz
|
||||
gbinv1003.seq.gz
|
||||
gbpln210.seq
|
||||
|
||||
6
Makefile
6
Makefile
@ -43,6 +43,11 @@ all: obitools
|
||||
packages: $(patsubst %,pkg-%,$(PACKAGES))
|
||||
obitools: $(patsubst %,$(OBITOOLS_PREFIX)%,$(OBITOOLS))
|
||||
|
||||
man:
|
||||
make -C doc man
|
||||
obibook:
|
||||
make -C doc obibook
|
||||
doc: man obibook
|
||||
|
||||
macos-pkg:
|
||||
@bash pkgs/macos/macos-installer-builder-master/macOS-x64/build-macos-x64.sh \
|
||||
@ -57,3 +62,4 @@ $(foreach P,$(PACKAGE_DIRS),$(eval $(call MAKE_PKG_RULE,$(P))))
|
||||
|
||||
$(foreach P,$(OBITOOLS_DIRS),$(eval $(call MAKE_OBITOOLS_RULE,$(P))))
|
||||
|
||||
.PHONY: all packages obitools man obibook doc
|
||||
@ -1,5 +1,38 @@
|
||||
# OBITools release notes
|
||||
|
||||
## On going changes
|
||||
|
||||
### Corrected bugs
|
||||
|
||||
- Makes progress bar updating at most 10 times per second.
|
||||
- Makes the command exiting on error if undefined options are used.
|
||||
|
||||
### New features
|
||||
|
||||
- Takes into account the `OBIMAXCPU` environmental variable to limit the number of CPU cores used
|
||||
by OBITools in bash the below command will limit to 4 cores the usage of OBITools
|
||||
|
||||
```bash
|
||||
export OBICPUMAX=4
|
||||
```
|
||||
|
||||
- Adds a new option --out|-o allowing to specify the name of an outpout file.
|
||||
|
||||
```bash
|
||||
obiconvert -o xyz.fasta xxx.fastq
|
||||
```
|
||||
|
||||
is thus equivalent to
|
||||
|
||||
```bash
|
||||
obiconvert xxx.fastq > xyz.fasta
|
||||
````
|
||||
|
||||
That option is actually mainly useful for dealing with paired reads sequence files.
|
||||
|
||||
- Some OBITools (now `obigrep` and `obiconvert`) are capable of using paired read files.
|
||||
Options have been added for this (**--paired-with** _FILENAME_, and **--paired-mode** _forward|reverse|and|andnot|xor_). This, in combination with the **--out** option shown above, ensures that the two matched files remain consistent when processed.
|
||||
|
||||
## February $18^th$, 2023. Release 4.0.0
|
||||
|
||||
It is the first version of the *OBITools* version 4. I decided to tag then following two weeks
|
||||
@ -17,7 +50,7 @@ to use the git ticket system to mention them. But they seems to produce now reli
|
||||
- The `obipairing` tools had a non deterministic comportment when aligning a paor very low quality reads.
|
||||
This induced that the result of the same low quality read pair was not the same from run to run.
|
||||
|
||||
### New functionality
|
||||
### 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.
|
||||
|
||||
1
go.mod
1
go.mod
@ -24,6 +24,7 @@ require (
|
||||
github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
|
||||
github.com/rivo/uniseg v0.2.0 // indirect
|
||||
github.com/rrethy/ahocorasick v1.0.0 // indirect
|
||||
github.com/spf13/pflag v1.0.5 // indirect
|
||||
github.com/vc60er/deptree v0.0.0-20220713110736-c48b0387dddc // indirect
|
||||
github.com/yuin/goldmark v1.4.13 // indirect
|
||||
golang.org/x/crypto v0.0.0-20220131195533-30dcbda58838 // indirect
|
||||
|
||||
2
go.sum
2
go.sum
@ -44,6 +44,8 @@ github.com/schollz/progressbar/v3 v3.8.6 h1:QruMUdzZ1TbEP++S1m73OqRJk20ON11m6Wqv
|
||||
github.com/schollz/progressbar/v3 v3.8.6/go.mod h1:W5IEwbJecncFGBvuEh4A7HT1nZZ6WNIL2i3qbnI0WKY=
|
||||
github.com/sirupsen/logrus v1.8.1 h1:dJKuHgqk1NNQlqoA6BTlM1Wf9DOH3NBjQyu0h9+AZZE=
|
||||
github.com/sirupsen/logrus v1.8.1/go.mod h1:yWOB1SBYBC5VeMP7gHvWumXLIWorT60ONWic61uBYv0=
|
||||
github.com/spf13/pflag v1.0.5 h1:iy+VFUOCP1a+8yFto/drg2CJ5u0yRoB7fZw3DKv/JXA=
|
||||
github.com/spf13/pflag v1.0.5/go.mod h1:McXfInJRrz4CZXVZOBLb0bTZqETkiAhM9Iw0y3An2Bg=
|
||||
github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
|
||||
github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs=
|
||||
github.com/stretchr/testify v1.3.0 h1:TivCn/peBQ7UY8ooIcPgZFpTNSz0Q2U6UrFlUfqbe0Q=
|
||||
|
||||
Reference in New Issue
Block a user