swarm 3.1.0: improved code and documentation, bugfix, and macOS on ARM64

Author: torognes

README.md

@@ -403,6 +403,15 @@ methods, here are some links:
 
 ## Version history ##
 
+
+### version 3.1 ###
+
+**swarm** 3.1 includes a fix for a bug in the 16-bit SIMD alignment
+code that was exposed with a combination of d>1, long sequences, and
+very high gap penalties. The code has also been been cleaned up,
+tested and improved substantially, and it is now fully C++11
+compliant. Support for macOS on Apple Silicon (ARM64) has been added.
+
 ### version 3.0 ###
 
 **swarm** 3.0 is much faster when _d_ = 1, and consumes less memory.

man/Makefile

@@ -25,11 +25,7 @@ all : swarm_manual.pdf
 
 swarm_manual.pdf : swarm.1
 	sed -e 's/\\-/-/g' $< | \
-        if [ $$(uname) == "Darwin" ] ; then \
-		iconv -f UTF-8 -t ISO-8859-1 ; \
-	else \
-		cat ; \
-	fi | \
+	iconv -f UTF-8 -t ISO-8859-1 | \
 	groff -t -m mandoc -T ps -P -pa4 | ps2pdf - $@
 
 clean : swarm_manual.pdf

man/swarm.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH swarm 1 "October 24, 2019" "version 3.0.0" "USER COMMANDS"
+.TH swarm 1 "March 1, 2021" "version 3.1.0" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 swarm \(em find clusters of nearly-identical nucleotide amplicons
@@ -110,9 +110,9 @@ results obtained during the clustering process allows \fBswarm\fR to
 avoid most of the amplicon comparisons needed in a naïve approach. To
 speed up the remaining amplicon comparisons, \fBswarm\fR implements an
 extremely fast Needleman-Wunsch algorithm making use of the Streaming
-SIMD Extensions (SSE2) of modern x86-64 CPUs, or NEON instructions of
-ARM-64 CPUs. If SSE2 instructions are not available, \fBswarm\fR exits
-with an error message.
+SIMD Extensions (SSE2) of x86-64 CPUs, NEON instructions of ARM64
+CPUs, or Altivec/VMX instructions of POWER8 CPUs. If SSE2 instructions
+are not available, \fBswarm\fR exits with an error message.
 .PP
 \fBswarm\fR can read nucleotide amplicons in fasta format from a
 normal file or from the standard input (using a pipe or a
@@ -462,7 +462,7 @@ Submit suggestions and bug-reports at
 .UR https://github.com/torognes/swarm/issues
 .UE ,
 send a pull request at
-.UR https://github.com/torognes/swarm
+.UR https://github.com/torognes/swarm/pulls
 .UE ,
 or compose a friendly or curmudgeonly e-mail to
 .MT frederic.mahe@cirad.fr
@@ -493,7 +493,7 @@ Affero General Public License for more details.
 .PP
 You should have received a copy of the GNU Affero General Public
 License along with this program.  If not, see
-.UR http://www.gnu.org/licenses/
+.UR https://www.gnu.org/licenses/
 .UE .
 .PP
 .\" ============================================================================
@@ -516,6 +516,13 @@ New features and important modifications of \fBswarm\fR (short lived
 or minor bug releases are not mentioned):
 .RS
 .TP
+.BR v3.1.0\~ "released March 1, 2021"
+Version 3.1.0 includes a fix for a bug in the 16-bit SIMD alignment
+code that was exposed with a combination of d>1, long sequences, and
+very high gap penalties. The code has also been been cleaned up,
+tested and improved substantially, and it is now fully C++11
+compliant. Support for macOS on Apple Silicon (ARM64) has been added.
+.TP
 .BR v3.0.0\~ "released October 24, 2019"
 Version 3.0.0 introduces a faster algorithm for \fId\fR = 1, and a
 reduced memory footprint. Swarm has been ported to Windows x86-64,

man/swarm_manual.pdf

@@ -108,7 +108,7 @@ static_assert(INT_MAX > INT16_MAX, "Your compiler uses very short integers.");
 
 /* constants */
 
-const std::string swarm_version = {"Swarm 3.0.0"};
+const std::string swarm_version = {"Swarm 3.1.0"};
 constexpr char sepchar {' '};
 constexpr unsigned int bloom_bits_default {16};
 constexpr unsigned int qgramlength {5};