[med-svn] [Git][med-team/last-align][upstream] New upstream version 1257

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / last-align


Commits:
08c0f517 by Andreas Tille at 2022-01-10T09:43:12+01:00
New upstream version 1257
- - - - -


4 changed files:

- README.rst
- doc/last-dotplot.rst
- makefile
- src/makefile


Changes:

=====================================
README.rst
=====================================
@@ -23,8 +23,9 @@ Usage
 -----
 
 Please see the cookbook_.  **Warning:** this documentation may not
-apply to older versions of LAST!  You can see your version with
-``lastal --version``.
+apply to older versions of LAST!  You can see your version with::
+
+  lastal --version
 
 Install
 -------
@@ -38,8 +39,16 @@ into the downloaded directory and type::
 This assumes you have a C++ compiler.  On Linux, you might need to
 install a package called "g++".  On Mac, you might need to install
 command-line developer tools.  On Windows, you might need to install
-Cygwin.  (It's possible to specify a compiler like this:
-``make CXX=MyOtherCompiler``.)
+Cygwin.  You might also need to install something like "zlib-devel".
+
+For ARM CPUs, the default "make" seems to work in some cases but not
+others (sigh).  This seems to be good for ARM::
+
+  make CXXFLAGS="-mcpu=native -O3 -pthread"
+
+It's possible to specify a compiler like this: ``make CXX=MyOtherCompiler``.
+If you re-run ``make`` in different ways, it may be good to do ``make clean``
+first, to remove any previously-made files.
 
 The programs are in the ``bin`` directory.  For convenient usage, set
 up your computer to find them automatically.  Some possible ways:


=====================================
doc/last-dotplot.rst
=====================================
@@ -159,10 +159,10 @@ Options ``-a`` and ``-b`` can read annotations in these formats:
 * AGP_, gap.txt: Unsequenced gaps are shown, but only if the gap
   covers at least one whole pixel.
 
-You can use these options multiple times, e.g. ``-a stuff.bed -a
-more.bed -a rmsk.txt``.  Annotations look good only if reasonably
-sparse, e.g. you can't sensibly view 20000 gene annotations in one
-small dotplot.
+You can use these options multiple times, e.g.
+``-a stuff.bed -a more.bed -a rmsk.txt``.  Annotations look good only
+if reasonably sparse, e.g. you can't sensibly view 20000 gene
+annotations in one small dotplot.
 
 Choosing sequences
 ------------------


=====================================
makefile
=====================================
@@ -1,4 +1,4 @@
-CXXFLAGS = -msse4 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS
+CXXFLAGS = -msse4 -O3 -std=c++11 -pthread
 all:
 	@cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
 


=====================================
src/makefile
=====================================
@@ -1,11 +1,11 @@
-CXXFLAGS = -msse4 -O3 -Wall -g -std=c++11 -pthread -DHAS_CXX_THREADS
+CXXFLAGS = -msse4 -O3 -Wall -g -std=c++11 -pthread
 # -fomit-frame-pointer ?
 
 # The number of symbol types that we can keep in sequences (e.g. 20
 # amino acids, plus ambiguous ones, in upper & lower case, plus one
 # delimiter):
 ALPHABET_CAPACITY = 66
-CPPF = -DALPHABET_CAPACITY=$(ALPHABET_CAPACITY) $(CPPFLAGS)
+CPPF = -DALPHABET_CAPACITY=$(ALPHABET_CAPACITY) -DHAS_CXX_THREADS $(CPPFLAGS)
 
 CFLAGS = -Wall -O2
 
@@ -143,7 +143,7 @@ ScoreMatrixData.hh: ../data/*.mat
 	../build/mat-inc.sh ../data/*.mat > $@
 
 VERSION1 = git describe --dirty
-VERSION2 = echo ' (HEAD -> main, tag: 1256) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 1257) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
 
 VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
 



View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/08c0f517b26d8aba14bb4844b279baabf9d07c24

-- 
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/08c0f517b26d8aba14bb4844b279baabf9d07c24
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