From 7894890e2abfba428fa491cf4394861bcacc9bc6 Mon Sep 17 00:00:00 2001
From: arvestad <arve@math.su.se>
Date: Sat, 2 Mar 2024 18:14:36 +0100
Subject: [PATCH] Preparing for next release

---
 CHANGES.md     | 13 +++++++++++++
 README.md      |  8 ++++++++
 THANKS.md      |  3 ++-
 alv/version.py |  2 +-
 4 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index 7536e14..36100d6 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,23 +1,33 @@
 # Changes since last version
 
+
+## v1.8.0
+
+* Added support for selecting sub-alignments. See option `-sa`
+
+
 ## v1.7.2
 
 * Ed Davies fixed a bug: sorting using option -so was broken
 
+
 ## v1.7.1
 
 * What??
 
+
 ## v1.7.0
 
 * Added the option --alignment-index to support files with multiple MSAs.
 * Added two functions, view and glimpse, to enable use of alv in notebook environments.
 
+
 ## v1.6.1
 
 * Fixed accession abbreviation so that short accessions are left as they are.
 * Requiring python 3.5 or later, because Colorama has droppen support for 3.4.
 
+
 ## v1.6.0
 
 * New options: --only-variable and --only-variable-excluding-indels, contributed by nikostr. Constrains coloring
@@ -25,18 +35,21 @@
 * Fixed the --dotted option, which only worked with the first block for DNA sequences. Also improved the coloring
   which was too ugly in dotted mode (due to laziness).
 
+
 ## v1.5.0
 
 * New option: `-d` or `--dotted`: the first sequence in the output alignment is used as a template and for positions
   in subsequent sequences that are identical, a period ('.') is output instead of a symbol.
 * Adjustment: replacing blue with cyan in the DNA coloring scheme.
 
+
 ## v1.4.0
 
 * New option: `-r k` or `--random-accessions k` for only showing a sample of _k_ sequences.
 * New option: `-g` or `--glimpse`: display an informative cut-out of the input MSA, if it does
   not fit without scrolling or line-breaking.
 
+
 ## v1.3.4
 
 * For some reason, setup.py was/is not putting proper Markdown to PyPi. Solved it halfway. Weird issue.
diff --git a/README.md b/README.md
index 26e0f5e..2cce2e4 100644
--- a/README.md
+++ b/README.md
@@ -95,6 +95,14 @@ alv -k msa.fa | less -R
 The `-k` option ensures that `alv` keeps coloring the alignment (by default, piping
 and redirection removes colors), and the `-R` option instructs `less` to interpret color codes.
 
+
+Choose to view a sub-alignment:
+```
+alv -sa 30 60 msa.fa
+```
+This selects and views columns 30 to 59 of msa.fa, keeping track of the "original" columns indexes in the output.
+
+
 ## For developers
 
 Run `python setup.py develop test` for development install and to execute tests.
diff --git a/THANKS.md b/THANKS.md
index fbd4ddc..876c571 100644
--- a/THANKS.md
+++ b/THANKS.md
@@ -10,4 +10,5 @@
   completely without "codons".
 * Michael Milton suggested the --alignment-index option.
 * Marina Herrera Sarrias suggested the notebook functionality.
-* Ed Davies fixed a bug: sorting using option -so was broken
\ No newline at end of file
+* Ed Davies fixed a bug: sorting using option -so was broken.
+* Artem Kushner pointed out the missing support for sub-alignments.
\ No newline at end of file
diff --git a/alv/version.py b/alv/version.py
index 8adfee4..b280975 100644
--- a/alv/version.py
+++ b/alv/version.py
@@ -1 +1 @@
-__version__ = '1.7.2'
+__version__ = '1.8.0'