From 6c5fc8f65bc2c6b983bef6499f49d69af16c9155 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 23 Feb 2023 23:45:41 +0100
Subject: [PATCH] Save change in various files

Former-commit-id: 428f8ee77c584b79cc2ef45eef2902c3e0754c77
---
 .gitignore       | 23 +++++++++++++++--------
 Makefile         |  6 ++++++
 Release-notes.md | 35 ++++++++++++++++++++++++++++++++++-
 go.mod           |  1 +
 go.sum           |  2 ++
 5 files changed, 58 insertions(+), 9 deletions(-)

diff --git a/.gitignore b/.gitignore
index c735893..492a871 100644
--- a/.gitignore
+++ b/.gitignore
@@ -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
diff --git a/Makefile b/Makefile
index 7b65899..152b767 100644
--- a/Makefile
+++ b/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
\ No newline at end of file
diff --git a/Release-notes.md b/Release-notes.md
index 6291fa6..b4ada2f 100644
--- a/Release-notes.md
+++ b/Release-notes.md
@@ -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.
diff --git a/go.mod b/go.mod
index 666587c..f76cfbc 100644
--- a/go.mod
+++ b/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
diff --git a/go.sum b/go.sum
index b1ed170..f80d992 100644
--- a/go.sum
+++ b/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=