Swarm 2.1.6: Fix bug in seed output and problems with old compilers

torognes · Dec 14, 2015 · 26c5d25 · 26c5d25
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diff --git a/README.md b/README.md
@@ -42,6 +42,7 @@ Table of Content
 * [Third-party pipelines](#pipelines)
 * [Alternatives](#alternatives)
 * [New features](#features)
+  * [version 2.1.6](#version216)
   * [version 2.1.5](#version215)
   * [version 2.1.4](#version214)
   * [version 2.1.3](#version213)
@@ -383,13 +384,13 @@ released since 2004.
 
 To cite **swarm**, please refer to:
 
-Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2014) Swarm:
-robust and fast clustering method for amplicon-based studies. PeerJ
-2:e593 http://dx.doi.org/10.7717/peerj.593
+Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2014)
+Swarm: robust and fast clustering method for amplicon-based studies.
+PeerJ 2:e593 doi: [10.7717/peerj.593](http://dx.doi.org/10.7717/peerj.593)
 
-Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (in preparation)
-Swarm v2: highly-scalable and high-resolution amplicon
-clustering. https://dx.doi.org/10.7287/peerj.preprints.1222v2
+Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2015)
+Swarm v2: highly-scalable and high-resolution amplicon clustering.
+PeerJ 3:e1420 doi: [10.7717/peerj.1420](http://dx.doi.org/10.7717/peerj.1420)
 
 
 <a name="contact"/>
@@ -433,6 +434,13 @@ methods, here are some links:
 <a name="features"/>
 ## New features##
 
+<a name="version216"/>
+### version 2.1.6 ###
+
+**swarm** 2.1.6 fixes problems with older compilers that do not have
+the x86intrin.h header file. It also fixes a bug in the output of seeds
+with the `-w` option when d>1.
+
 <a name="version215"/>
 ### version 2.1.5 ###
 

diff --git a/man/swarm.1 b/man/swarm.1
@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH swarm 1 "September 8, 2015" "version 2.1.5" "USER COMMANDS"
+.TH swarm 1 "December 14, 2015" "version 2.1.6" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 swarm \(em find clusters of nearly-identical nucleotide amplicons
@@ -277,13 +277,13 @@ option) using 4 computation threads. OTUs are written to the file
 Concept by Frédéric Mahé, implementation by Torbjørn Rognes.
 .\" ============================================================================
 .SH CITATION
-Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2014) Swarm:
-robust and fast clustering method for amplicon-based
-studies. \fIPeerJ\fR 2:e593 <http://dx.doi.org/10.7717/peerj.593>
+Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2014)
+Swarm: robust and fast clustering method for amplicon-based studies.
+\fIPeerJ\fR 2:e593 <http://dx.doi.org/10.7717/peerj.593>
 .PP
-Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2015) Swarm v2:
-highly-scalable and high-resolution amplicon clustering. \fIPeerJ
-PrePrints\fR 3:e1503 <http://dx.doi.org/10.7287/peerj.preprints.1222v2>
+Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2015)
+Swarm v2: highly-scalable and high-resolution amplicon clustering.
+\fIPeerJ\fR 3:e1420 <http://dx.doi.org/10.7717/peerj.1420>
 .\" ============================================================================
 .SH REPORTING BUGS
 Submit suggestions and bug-reports at
@@ -329,6 +329,11 @@ New features and important modifications of \fBswarm\fR (short lived
 or minor bug releases are not mentioned):
 .RS
 .TP
+.BR v2.1.6\~ "released December 14, 2015"
+Version 2.1.6 fixes problems with older compilers that do not have
+the x86intrin.h header file. It also fixes a bug in the output of seeds
+with the `-w` option when d>1.
+.TP
 .BR v2.1.5\~ "released September 8, 2015"
 Version 2.1.5 fixes minor bugs.
 .TP

diff --git a/man/swarm_manual.pdf b/man/swarm_manual.pdf
diff --git a/src/algo.cc b/src/algo.cc
@@ -516,6 +516,7 @@ void algo_run()
       unsigned long mass = 0;
       unsigned previd = amps[0].swarmid;
       unsigned prevamp = amps[0].ampliconid;
+      unsigned seed = prevamp;
       mass += db_getabundance(prevamp);
 
       for (unsigned long i=1; i<amplicons; i++)
@@ -525,10 +526,11 @@ void algo_run()
           if (id != previd)
             {
               fprintf(fp_seeds, ">");
-              fprint_id_with_new_abundance(fp_seeds, prevamp, mass);
+              fprint_id_with_new_abundance(fp_seeds, seed, mass);
               fprintf(fp_seeds, "\n");
               db_fprintseq(fp_seeds, prevamp, 0);
               mass = 0;
+              seed = amps[i].ampliconid;
             }
 
           previd = id;
@@ -538,7 +540,7 @@ void algo_run()
         }
 
       fprintf(fp_seeds, ">");
-      fprint_id_with_new_abundance(fp_seeds, prevamp, mass);
+      fprint_id_with_new_abundance(fp_seeds, seed, mass);
       fprintf(fp_seeds, "\n");
       db_fprintseq(fp_seeds, prevamp, 0);
 

diff --git a/src/swarm.h b/src/swarm.h
@@ -25,26 +25,34 @@
 #include <string.h>
 #include <pthread.h>
 #include <getopt.h>
-#include <x86intrin.h>
 #include <stdlib.h>
 #include <regex.h>
 #include <limits.h>
 #include <city.h>
 #include <sys/types.h>
 #include <sys/resource.h>
+
 #ifdef __APPLE__
 #include <sys/sysctl.h>
 #else
 #include <sys/sysinfo.h>
 #endif
 
+#ifdef __SSE2__
+#include <emmintrin.h>
+#endif
+
+#ifdef __SSSE3__
+#include <tmmintrin.h>
+#endif
+
 /* constants */
 
 #ifndef LINE_MAX
 #define LINE_MAX 2048
 #endif
 
-#define SWARM_VERSION "2.1.5"
+#define SWARM_VERSION "2.1.6"
 #define WIDTH 32
 #define WIDTH_SHIFT 5
 #define BLOCKWIDTH 32