Swarm 1.2.7: Fix seed output, ignore some CR in FASTA files, etc

man/swarm.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH swarm 1 "February 24, 2016" "version 2.1.6" "USER COMMANDS"
+.TH swarm 1 "February 24, 2016" "version 2.1.7" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 swarm \(em find clusters of nearly-identical nucleotide amplicons
@@ -279,11 +279,11 @@ 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>
+\fIPeerJ\fR 2:e593 <https://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\fR 3:e1420 <http://dx.doi.org/10.7717/peerj.1420>
+\fIPeerJ\fR 3:e1420 <https://doi.org/10.7717/peerj.1420>
 .\" ============================================================================
 .SH REPORTING BUGS
 Submit suggestions and bug-reports at
@@ -296,7 +296,7 @@ Torbjørn Rognes <[email protected]>.
 The software is available from <https://github.com/torognes/swarm>
 .\" ============================================================================
 .SH COPYRIGHT
-Copyright (C) 2012, 2013, 2014, 2015, 2016 Frédéric Mahé & Torbjørn Rognes
+Copyright (C) 2012-2016 Frédéric Mahé & Torbjørn Rognes
 .PP
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU Affero General Public License as
@@ -329,10 +329,17 @@ New features and important modifications of \fBswarm\fR (short lived
 or minor bug releases are not mentioned):
 .RS
 .TP
+.BR v2.1.7\~ "released February 24, 2016"
+Version 2.1.7 fixes a bug in the output of seeds with the \-w option
+when \fId\fR > 1 that was not properly fixed in version 2.1.6. It also
+handles ascii character no 13 (CR) in FASTA files better. Swarm will
+now exit with status 0 if the \-h or the \-v option is specified. The
+help text and some error messages have been improved.
+.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 \fId\fR > 1.
+with the \-w option when \fId\fR > 1.
 .TP
 .BR v2.1.5\~ "released September 8, 2015"
 Version 2.1.5 fixes minor bugs.

src/Makefile

@@ -1,6 +1,6 @@
 # SWARM
 #
-# Copyright (C) 2012-2015 Torbjorn Rognes and Frederic Mahe
+# Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 # 
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU Affero General Public License as

src/algo.cc

@@ -1,24 +1,24 @@
 /*
-  SWARM
+    SWARM
 
-  Copyright (C) 2012-2015 Torbjorn Rognes and Frederic Mahe
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
-  This program is free software: you can redistribute it and/or modify
-  it under the terms of the GNU Affero General Public License as
-  published by the Free Software Foundation, either version 3 of the
-  License, or (at your option) any later version.
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as
+    published by the Free Software Foundation, either version 3 of the
+    License, or (at your option) any later version.
 
-  This program is distributed in the hope that it will be useful,
-  but WITHOUT ANY WARRANTY; without even the implied warranty of
-  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  GNU Affero General Public License for more details.
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
 
-  You should have received a copy of the GNU Affero General Public License
-  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+    You should have received a copy of the GNU Affero General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-  Contact: Torbjorn Rognes <[email protected]>,
-  Department of Informatics, University of Oslo,
-  PO Box 1080 Blindern, NO-0316 Oslo, Norway
+    Contact: Torbjorn Rognes <[email protected]>,
+    Department of Informatics, University of Oslo,
+    PO Box 1080 Blindern, NO-0316 Oslo, Norway
 */
 
 #include "swarm.h"
@@ -515,9 +515,8 @@ void algo_run()
 
       unsigned long mass = 0;
       unsigned previd = amps[0].swarmid;
-      unsigned prevamp = amps[0].ampliconid;
-      unsigned seed = prevamp;
-      mass += db_getabundance(prevamp);
+      unsigned seed = amps[0].ampliconid;
+      mass += db_getabundance(seed);
 
       for (unsigned long i=1; i<amplicons; i++)
         {
@@ -528,21 +527,21 @@ void algo_run()
               fprintf(fp_seeds, ">");
               fprint_id_with_new_abundance(fp_seeds, seed, mass);
               fprintf(fp_seeds, "\n");
-              db_fprintseq(fp_seeds, prevamp, 0);
+              db_fprintseq(fp_seeds, seed, 0);
+
               mass = 0;
               seed = amps[i].ampliconid;
             }
 
+          mass += db_getabundance(amps[i].ampliconid);
           previd = id;
-          prevamp = amps[i].ampliconid;
-          mass += db_getabundance(prevamp);
           progress_update(i);
         }
 
       fprintf(fp_seeds, ">");
       fprint_id_with_new_abundance(fp_seeds, seed, mass);
       fprintf(fp_seeds, "\n");
-      db_fprintseq(fp_seeds, prevamp, 0);
+      db_fprintseq(fp_seeds, seed, 0);
 
       progress_done();
     }

src/algod1.cc

@@ -1,30 +1,30 @@
 /*
-  SWARM
+    SWARM
 
-  Copyright (C) 2012-2015 Torbjorn Rognes and Frederic Mahe
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
-  This program is free software: you can redistribute it and/or modify
-  it under the terms of the GNU Affero General Public License as
-  published by the Free Software Foundation, either version 3 of the
-  License, or (at your option) any later version.
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as
+    published by the Free Software Foundation, either version 3 of the
+    License, or (at your option) any later version.
 
-  This program is distributed in the hope that it will be useful,
-  but WITHOUT ANY WARRANTY; without even the implied warranty of
-  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  GNU Affero General Public License for more details.
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
 
-  You should have received a copy of the GNU Affero General Public License
-  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+    You should have received a copy of the GNU Affero General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-  Contact: Torbjorn Rognes <[email protected]>,
-  Department of Informatics, University of Oslo,
-  PO Box 1080 Blindern, NO-0316 Oslo, Norway
+    Contact: Torbjorn Rognes <[email protected]>,
+    Department of Informatics, University of Oslo,
+    PO Box 1080 Blindern, NO-0316 Oslo, Norway
 */
 
 /*
   This version of the swarm algorithm uses Frederic's idea for d=1 to
-  enumerate all of the maximum 7L+4 possible variants of a sequence with only
-  one difference, where L is the length of the sequence.
+  enumerate all of the maximum 7L+4 possible variants of a sequence
+  with only one difference, where L is the length of the sequence.
 */
 
 #include "swarm.h"

src/arch.cc

@@ -1,5 +1,7 @@
 /*
-    Copyright (C) 2014-2015 Torbjorn Rognes
+    SWARM
+
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as

src/bitmap.h

@@ -1,5 +1,7 @@
 /*
-    Copyright (C) 2012-2015 Torbjorn Rognes and Frederic Mahe
+    SWARM
+
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as

src/bloom.h

@@ -1,5 +1,7 @@
 /*
-    Copyright (C) 2012-2015 Torbjorn Rognes and Frederic Mahe
+    SWARM
+
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as

src/db.cc

@@ -1,24 +1,24 @@
 /*
-  SWARM
+    SWARM
 
-  Copyright (C) 2012-2015 Torbjorn Rognes and Frederic Mahe
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
-  This program is free software: you can redistribute it and/or modify
-  it under the terms of the GNU Affero General Public License as
-  published by the Free Software Foundation, either version 3 of the
-  License, or (at your option) any later version.
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as
+    published by the Free Software Foundation, either version 3 of the
+    License, or (at your option) any later version.
 
-  This program is distributed in the hope that it will be useful,
-  but WITHOUT ANY WARRANTY; without even the implied warranty of
-  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  GNU Affero General Public License for more details.
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
 
-  You should have received a copy of the GNU Affero General Public License
-  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+    You should have received a copy of the GNU Affero General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-  Contact: Torbjorn Rognes <[email protected]>,
-  Department of Informatics, University of Oslo,
-  PO Box 1080 Blindern, NO-0316 Oslo, Norway
+    Contact: Torbjorn Rognes <[email protected]>,
+    Department of Informatics, University of Oslo,
+    PO Box 1080 Blindern, NO-0316 Oslo, Norway
 */
 
 #include "swarm.h"
@@ -215,7 +215,7 @@ void db_read(const char * filename)
         fatal("Illegal header line in fasta file.");
 
       long headerlen = 0;
-      if (char * stop = strpbrk(line+1, " \n"))
+      if (char * stop = strpbrk(line+1, " \r\n"))
         headerlen = stop - (line+1);
       else
         headerlen = strlen(line+1);
@@ -278,10 +278,13 @@ void db_read(const char * filename)
                 *(datap+datalen) = m;
                 datalen++;
               }
-            else if (c != '\n')
+            else if ((c != 10) && (c != 13))
               {
                 char msg[100];
-                snprintf(msg, 100, "Illegal character '%c' in sequence on line %u", c, lineno);
+                if ((c >= 32) && (c <= 126))
+                  snprintf(msg, 100, "Illegal character '%c' in sequence on line %u", c, lineno);
+                else
+                  snprintf(msg, 100, "Illegal character (ascii no %d) in sequence on line %u", c, lineno);
                 fatal(msg);
               }
           line[0] = 0;
@@ -434,12 +437,10 @@ void db_read(const char * filename)
     {
       char * msg;
       if (asprintf(&msg,
-                   "Abundance annotations not found for %d sequences, "
-                   "starting on line %u.\n"
-                   "Fasta headers must end with abundance annotations "
-                   "(_INT or ;size=INT)\n"
-                   "Abundance annotations can be produced by "
-                   "dereplicating the sequences\n",
+                   "Abundance annotations not found for %d sequences, starting on line %u.\n"
+                   "Fasta headers must end with abundance annotations (_INT or ;size=INT).\n"
+                   "The -z option must be used if the abundance annotation is in the latter format.\n"
+                   "Abundance annotations can be produced by dereplicating the sequences.\n",
                    missingabundance,
                    missingabundance_lineno) == -1)
         fatal("Out of memory");

src/derep.cc

@@ -1,5 +1,7 @@
 /*
-    Copyright (C) 2014-2015 Torbjorn Rognes
+    SWARM
+
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as

src/matrix.cc

@@ -1,7 +1,7 @@
 /*
     SWARM
 
-    Copyright (C) 2012-2015 Torbjorn Rognes and Frederic Mahe
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as

src/nw.cc

@@ -1,7 +1,7 @@
 /*
     SWARM
 
-    Copyright (C) 2012-2015 Torbjorn Rognes and Frederic Mahe
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as

src/qgram.cc

@@ -1,7 +1,7 @@
 /*
     SWARM
 
-    Copyright (C) 2012-2014 Torbjorn Rognes and Frederic Mahe
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as

src/scan.cc

@@ -1,7 +1,7 @@
 /*
     SWARM
 
-    Copyright (C) 2012-2015 Torbjorn Rognes and Frederic Mahe
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as

src/search16.cc

@@ -1,7 +1,7 @@
 /*
     SWARM
 
-    Copyright (C) 2012-2014 Torbjorn Rognes and Frederic Mahe
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as

src/search8.cc

@@ -1,7 +1,7 @@
 /*
     SWARM
 
-    Copyright (C) 2012-2014 Torbjorn Rognes and Frederic Mahe
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as

src/ssse3.cc

@@ -1,7 +1,7 @@
 /*
     SWARM
 
-    Copyright (C) 2012-2014 Torbjorn Rognes and Frederic Mahe
+    Copyright (C) 2012-2016 Torbjorn Rognes and Frederic Mahe
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as