Update copyrights.

src/AS_UTL/AS_UTL_stackTrace.C

@@ -101,10 +101,10 @@ AS_UTL_catchCrash(int sig_num, siginfo_t *UNUSED(info), void *UNUSED(ctx)) {
   WRITE_STRING("'; backtrace (libbacktrace):\n");
   backtrace_full(backtraceState, 0, AS_UTL_catchCrash_full, NULL, NULL);
 
-  //WRITE_STRING("\nBacktrace (libbacktrace print):\n\n");                                                                                 
-  //backtrace_print(backtraceState, 0, stderr);                                                                                            
+  //WRITE_STRING("\nBacktrace (libbacktrace print):\n\n");
+  //backtrace_print(backtraceState, 0, stderr);
 
-  //  Pass the signal through, only so a core file can get generated.                                                                      
+  //  Pass the signal through, only so a core file can get generated.
 
   struct sigaction sa;
 
@@ -186,7 +186,7 @@ AS_UTL_catchCrash(int sig_num, siginfo_t *UNUSED(info), void *UNUSED(ctx)) {
 
 void
 AS_UTL_catchCrash(int sig_num, siginfo_t *UNUSED(info), void *UNUSED(ctx)) {
- 
+
   //  Report the signal we failed on, be careful to not allocate memory.
 
   WRITE_STRING("\nFailed with '");

src/bogart/AS_BAT_CreateUnitigs.C

@@ -463,7 +463,7 @@ createUnitigs(AssemblyGraph   *AG,
         unitigSource[id].uID  = id;
       }
     }
-    
+
     //  Reset for the next iteration.
 
     ss = ee;

src/bogart/AS_BAT_MergeOrphans.H

@@ -13,9 +13,13 @@
  *  Canu branched from Celera Assembler at its revision 4587.
  *  Canu branched from the kmer project at its revision 1994.
  *
+ *  This file is derived from:
+ *
+ *    src/bogart/AS_BAT_PopBubbles.H
+ *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2016-MAR-11
+ *    Brian P. Walenz beginning on 2016-DEC-07
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

src/falcon_sense/falcon_sense.C

@@ -19,6 +19,10 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Brian P. Walenz beginning on 2016-NOV-28
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
  *  File 'README.licenses' in the root directory of this distribution contains
  *  full conditions and disclaimers for each license.
  */
@@ -107,7 +111,7 @@ main (int argc, char **argv) {
     if (W[0][0] == '+') {
        uint32 splitSeqID = 0;
        FConsensus::consensus_data *consensus_data_ptr = FConsensus::generate_consensus( seqs, min_cov, K, min_idy, min_ovl_len, max_read_len );
-       
+
 #ifdef TRACK_POSITIONS
        //const std::string& sequenceToCorrect = seqs.at(0);
        char * originalStringPointer = consensus_data_ptr->sequence;
@@ -122,9 +126,9 @@ main (int argc, char **argv) {
 #ifdef TRACK_POSITIONS
 			 int distance_from_beginning = split - originalStringPointer;
              std::vector<int> relevantOriginalPositions(consensus_data_ptr->originalPos.begin() + distance_from_beginning, consensus_data_ptr->originalPos.begin() + distance_from_beginning + strlen(split));
-			 int firstRelevantPosition = relevantOriginalPositions.front();		
+			 int firstRelevantPosition = relevantOriginalPositions.front();
 			 int lastRelevantPosition = relevantOriginalPositions.back();
-			 
+
 			 std::string relevantOriginalTemplate = seqs.at(0).substr(firstRelevantPosition, lastRelevantPosition - firstRelevantPosition + 1);
 
 		     // store relevantOriginalTemplate along with corrected read - not implemented

src/gfa/alignGFA.C

@@ -1,4 +1,4 @@
- 
+
 /******************************************************************************
  *
  *  This file is part of canu, a software program that assembles whole-genome
@@ -15,7 +15,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2017-MAR-23
+ *    Brian P. Walenz beginning on 2017-APR-04
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
@@ -235,7 +235,7 @@ checkLink(gfaLink  *link,
 
     edlibFreeAlignResult(result);
 
-    success = true; 
+    success = true;
   } else {
     if (beVerbose)
       fprintf(stderr, " - FAILED\n");

src/gfa/gfa.C

@@ -15,7 +15,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2017-APR-03
+ *    Brian P. Walenz beginning on 2017-APR-04
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
@@ -149,7 +149,7 @@ gfaLink::~gfaLink() {
   delete [] _features;
 }
 
-  
+
 void
 gfaLink::load(char *inLine) {
   splitToWords W(inLine);
@@ -214,7 +214,7 @@ gfaLink::alignmentLength(int32 &queryLen, int32 &refceLen, int32 &alignLen) {
         alignLen += val;
         break;
       case 'D':  //  Deletion from the reference - gap in reference
-        refceLen += val; 
+        refceLen += val;
         alignLen += val;
        break;
       case 'N':  //  Skipped in the reference (e.g., intron)

src/gfa/gfa.H

@@ -15,7 +15,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2017-APR-03
+ *    Brian P. Walenz beginning on 2017-APR-04
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
@@ -59,7 +59,7 @@ public:
   gfaLink();
   gfaLink(char *inLine);
   ~gfaLink();
-  
+
   void    load(char *inLine);
   void    save(FILE *outFile);
 

src/meryl/compare-counts.C

@@ -27,6 +27,10 @@
  *      are Copyright 2014 Battelle National Biodefense Institute, and
  *      are subject to the BSD 3-Clause License
  *
+ *    Brian P. Walenz beginning on 2016-NOV-22
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
  *  File 'README.licenses' in the root directory of this distribution contains
  *  full conditions and disclaimers for each license.
  */

src/meryl/maskMers.C

@@ -27,6 +27,10 @@
  *      are Copyright 2014 Battelle National Biodefense Institute, and
  *      are subject to the BSD 3-Clause License
  *
+ *    Brian P. Walenz beginning on 2016-NOV-22
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
  *  File 'README.licenses' in the root directory of this distribution contains
  *  full conditions and disclaimers for each license.
  */

src/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C

@@ -23,6 +23,10 @@
  *      are Copyright 2015 Battelle National Biodefense Institute, and
  *      are subject to the BSD 3-Clause License
  *
+ *    Brian P. Walenz beginning on 2017-FEB-02
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
  *  File 'README.licenses' in the root directory of this distribution contains
  *  full conditions and disclaimers for each license.
  */

src/overlapInCore/liboverlap/prefixEditDistance-forward.C

@@ -23,6 +23,10 @@
  *      are Copyright 2015 Battelle National Biodefense Institute, and
  *      are subject to the BSD 3-Clause License
  *
+ *    Brian P. Walenz beginning on 2017-FEB-02
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
  *  File 'README.licenses' in the root directory of this distribution contains
  *  full conditions and disclaimers for each license.
  */

src/overlapInCore/liboverlap/prefixEditDistance-reverse.C

@@ -23,6 +23,10 @@
  *      are Copyright 2015 Battelle National Biodefense Institute, and
  *      are subject to the BSD 3-Clause License
  *
+ *    Brian P. Walenz beginning on 2017-FEB-02
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
  *  File 'README.licenses' in the root directory of this distribution contains
  *  full conditions and disclaimers for each license.
  */

src/overlapInCore/overlapPair.C

@@ -597,7 +597,7 @@ recomputeOverlaps(void *ptr) {
           }
           localStats.nExt3b++;
         }
-      
+
         //  Now reset the overlap.
 
         ovl->dat.ovl.ahg5 = ahg5;

src/pipelines/canu-object-store.pl

@@ -16,7 +16,7 @@
  #
  #  Modifications by:
  #
- #    Brian P. Walenz beginning on 2015-MAR-14
+ #    Brian P. Walenz beginning on 2017-MAR-14
  #      are a 'United States Government Work', and
  #      are released in the public domain
  #

src/pipelines/canu/Configure.pm

@@ -400,7 +400,7 @@ sub getAllowedResources ($$$$@) {
     my $job = substr("    $concurrent",  -3) . " job" . (($concurrent == 1) ? " " : "s");
     my $thr = substr("    $taskThreads", -3) . " CPU" . (($taskThreads == 1) ? " " : "s");
     my $mem = substr("    $taskMemory",  -4) . " GB";
-    
+
     $all .= "-- Run $job concurrently using $mem and $thr for stage '$nam'.\n"   if ( defined($concurrent));
     $all .= "-- Run under grid control using $mem and $thr for stage '$nam'.\n"   if (!defined($concurrent));
 

src/pipelines/canu/ErrorEstimate.pm

@@ -19,6 +19,10 @@
  #      are a 'United States Government Work', and
  #      are released in the public domain
  #
+ #    Brian P. Walenz beginning on 2016-DEC-12
+ #      are a 'United States Government Work', and
+ #      are released in the public domain
+ #
  #  File 'README.licenses' in the root directory of this distribution contains
  #  full conditions and disclaimers for each license.
  ##

src/pipelines/canu/Grid_Cloud.pm

@@ -15,7 +15,7 @@
  #
  #  Modifications by:
  #
- #    Brian P. Walenz beginning on 2017-JAN-17
+ #    Brian P. Walenz beginning on 2017-FEB-15
  #      are a 'United States Government Work', and
  #      are released in the public domain
  #

src/pipelines/canu/Grid_DNANexus.pm

@@ -15,7 +15,7 @@
  #
  #  Modifications by:
  #
- #    Brian P. Walenz beginning on 2015-FEB-11
+ #    Brian P. Walenz beginning on 2017-FEB-11
  #      are a 'United States Government Work', and
  #      are released in the public domain
  #
@@ -78,7 +78,7 @@ sub configureDNANexus () {
 
     my %hosts;
 
-    #  Probe for how to request multiple CPUs on each node, set 
+    #  Probe for how to request multiple CPUs on each node, set
 
     #  .
     #  .

src/pipelines/canu/Meryl.pm

@@ -624,7 +624,7 @@ sub merylProcess ($$) {
         fetchFile("$path/$ofile.mcdat");
         fetchFile("$path/$ofile.mcidx");
 
-        if ((! -e "$path/$ofile.mcdat") || 
+        if ((! -e "$path/$ofile.mcdat") ||
             (! -e "$path/$ofile.mcdat")) {
             caFailure("meryl can't dump frequent mers, databases don't exist.  Remove $path/meryl.success to try again.", undef);
         }

src/pipelines/canu/OverlapBasedTrimming.pm

@@ -27,6 +27,10 @@
  #      are a 'United States Government Work', and
  #      are released in the public domain
  #
+ #    Sergey Koren beginning on 2017-MAR-03
+ #      are a 'United States Government Work', and
+ #      are released in the public domain
+ #
  #  File 'README.licenses' in the root directory of this distribution contains
  #  full conditions and disclaimers for each license.
  ##

src/pipelines/canu/OverlapMMap.pm

@@ -287,7 +287,7 @@ sub mmapConfigure ($$$) {
     print F "  exit\n";
     print F "fi\n";
     print F "\n";
- 
+
     print F fetchFileShellCode("$path", "queries.tar", "");
     print F "\n";
     print F "if [ -e ./queries.tar -a ! -d ./queries ] ; then\n";

src/pipelines/canu/Report.pm

@@ -15,7 +15,7 @@
  #
  #  Modifications by:
  #
- #    Brian P. Walenz beginning on 2015-NOV-08
+ #    Brian P. Walenz beginning on 2017-MAR-20
  #      are a 'United States Government Work', and
  #      are released in the public domain
  #
@@ -118,7 +118,7 @@ sub saveReport ($) {
     my $tag;
 
     open(F, "> $asm.report") or caExit("can't open '$asm.report' for writing: $!", undef);
-    
+
     saveReportItem("CORRECTION/READS",       $report{"corGkpStore"});
     saveReportItem("CORRECTION/MERS",        $report{"corMeryl"});
     saveReportItem("CORRECTION/FILTERING",   $report{"correctionFiltering"});
@@ -168,5 +168,5 @@ sub getFromReport ($) {
     return($report{$_[0]});
 }
 
-  
+
 1;

src/pipelines/simple-repeat-test.pl

@@ -1,5 +1,29 @@
 #!/usr/bin/env perl
 
+###############################################################################
+ #
+ #  This file is part of canu, a software program that assembles whole-genome
+ #  sequencing reads into contigs.
+ #
+ #  This software is based on:
+ #    'Celera Assembler' (http://wgs-assembler.sourceforge.net)
+ #    the 'kmer package' (http://kmer.sourceforge.net)
+ #  both originally distributed by Applera Corporation under the GNU General
+ #  Public License, version 2.
+ #
+ #  Canu branched from Celera Assembler at its revision 4587.
+ #  Canu branched from the kmer project at its revision 1994.
+ #
+ #  Modifications by:
+ #
+ #    Brian P. Walenz beginning on 2017-JAN-09
+ #      are a 'United States Government Work', and
+ #      are released in the public domain
+ #
+ #  File 'README.licenses' in the root directory of this distribution contains
+ #  full conditions and disclaimers for each license.
+ ##
+
 use strict;
 
 #  Generate a circular 'genome' with nUnique pieces and nUnique+1 repeats, the pair at the start/end
@@ -42,7 +66,7 @@ ($)
         print STDERR "REPEAT $len ", $len + $Rlen, "\n";
         print O "$R\n";
         $len += $Rlen;
-    
+
         my $U    = randomSequence($uniqueSize);
         my $Ulen = length($U);
 

src/utgcns/libcns/unitigConsensus.C

@@ -391,9 +391,9 @@ unitigConsensus::generatePBDAG(char aligner,
 
     while ((aligned == false) && (bandTolerance < errorRate * (aLen + bLen))) {
        bandTolerance *= 2;
-       if (aligner == 'E') 
+       if (aligner == 'E')
           edlibFreeAlignResult(align);
- 
+
        fprintf(stderr, "generatePBDAG()-- retry with bandTolerance = %d\n",
               bandTolerance);
 
@@ -459,7 +459,7 @@ unitigConsensus::generatePBDAG(char aligner,
        aln.end = aln.start + (ndaln._tgt_end - ndaln._tgt_bgn) - 1;
        aln.qstr = std::string(ndaln._qry_aln_str);
        aln.tstr = std::string(ndaln._tgt_aln_str);
-    } 
+    }
     aln.start++;
     cnspos[i].setMinMax(aln.start, aln.end);
     assert(aln.qstr.length() == aln.tstr.length());
@@ -509,7 +509,7 @@ unitigConsensus::generatePBDAG(char aligner,
   memcpy(tig->getChild(0), cnspos, sizeof(tgPosition) * numfrags);
 
   // trim consensus if needed
-  if (maxPos < cns.size()) 
+  if (maxPos < cns.size())
      cns = cns.substr(0, maxPos);
   assert(minPos == 0);
   assert(maxPos == cns.size());