Update copyright message.

Jolvii85 · Nov 21, 2016 · bbbdcd0 · bbbdcd0
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diff --git a/src/AS_UTL/AS_UTL_alloc.C b/src/AS_UTL/AS_UTL_alloc.C
@@ -31,7 +31,6 @@
  *  full conditions and disclaimers for each license.
  */
 
-
 #include "AS_UTL_alloc.H"
 
 

diff --git a/src/AS_UTL/bitPackedArray.C b/src/AS_UTL/bitPackedArray.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-OCT-17
+ *      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.
  */

diff --git a/src/AS_UTL/bitPackedArray.H b/src/AS_UTL/bitPackedArray.H
@@ -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-OCT-17
+ *      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.
  */

diff --git a/src/AS_UTL/bitPackedFile.H b/src/AS_UTL/bitPackedFile.H
@@ -35,6 +35,10 @@
  *      are Copyright 2014 Battelle National Biodefense Institute, and
  *      are subject to the BSD 3-Clause License
  *
+ *    Brian P. Walenz beginning on 2016-OCT-17
+ *      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.
  */

diff --git a/src/AS_UTL/hexDump.C b/src/AS_UTL/hexDump.C
@@ -1,3 +1,4 @@
+
 /******************************************************************************
  *
  *  This file is part of canu, a software program that assembles whole-genome

diff --git a/src/AS_UTL/hexDump.H b/src/AS_UTL/hexDump.H
@@ -1,3 +1,4 @@
+
 /******************************************************************************
  *
  *  This file is part of canu, a software program that assembles whole-genome

diff --git a/src/AS_UTL/intervalListTest.C b/src/AS_UTL/intervalListTest.C
@@ -41,7 +41,7 @@ typedef uint64_t uint64;
 
 #include "intervalList.H"
 
-//  g++ -o intervalListTest -I.. -I. intervalListTest.C 
+//  g++ -o intervalListTest -I.. -I. intervalListTest.C
 
 int
 main(int argc, char **argv) {

diff --git a/src/AS_UTL/kMerHuge.H b/src/AS_UTL/kMerHuge.H
@@ -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-OCT-17
+ *      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.
  */

diff --git a/src/AS_UTL/sweatShop.C b/src/AS_UTL/sweatShop.C
@@ -27,6 +27,10 @@
  *      are Copyright 2014-2015 Battelle National Biodefense Institute, and
  *      are subject to the BSD 3-Clause License
  *
+ *    Brian P. Walenz beginning on 2016-OCT-17
+ *      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.
  */

diff --git a/src/bogart/AS_BAT_AssemblyGraph.C b/src/bogart/AS_BAT_AssemblyGraph.C
@@ -576,7 +576,7 @@ AssemblyGraph::rebuildGraph(TigVector     &tigs) {
                (t5 == UINT32_MAX) ||   //  5' overlap isn't set
                (t3 == UINT32_MAX)) {   //  3' overlap isn't set
         nSame++;
-        placeAsDovetail(tigs, fi, bp); 
+        placeAsDovetail(tigs, fi, bp);
       }
 
       //  Otherwise, yikes, our overlapping reads are in different tigs!  We need to make new
@@ -749,7 +749,7 @@ AssemblyGraph::filterEdges(TigVector     &tigs) {
     for (uint32 ff=0; ff<_pForward[fi].size(); ff++) {
       BestPlacement   &bp = _pForward[fi][ff];
 
-      if (bp.isUnitig == true)   { nUnitig++;  continue; } 
+      if (bp.isUnitig == true)   { nUnitig++;  continue; }
       if (bp.isContig == true)   { nContig++;  continue; }
       if (bp.isRepeat == true)   { nRepeatEdges++;       }
       if (bp.isRepeat == false)  { nBubbleEdges++;       }

diff --git a/src/bogart/AS_BAT_AssemblyGraph.H b/src/bogart/AS_BAT_AssemblyGraph.H
@@ -99,7 +99,7 @@ public:
                 bool          tigEndsOnly = false) {
     buildGraph(prefix, deviationRepeat, tigs, tigEndsOnly);
   }
-  
+
   ~AssemblyGraph() {
     delete [] _pForward;
     delete [] _pReverse;

diff --git a/src/bogart/AS_BAT_BestOverlapGraph.C b/src/bogart/AS_BAT_BestOverlapGraph.C
@@ -277,7 +277,7 @@ BestOverlapGraph::removeLopsidedEdges(const char *UNUSED(prefix)) {
 #pragma omp critical (suspInsert)
     {
       _suspicious.insert(fi);
-      
+
       if ((percDiff5 > 5.0) && (percDiff3 > 5.0))
         _n2EdgeIncompatible++;
       else

diff --git a/src/bogart/AS_BAT_ChunkGraph.C b/src/bogart/AS_BAT_ChunkGraph.C
@@ -263,6 +263,6 @@ ChunkGraph::countFullWidth(ReadEnd firstEnd) {
     fprintf(_chunkLog, "\n");
   }
 
-  
+
   return(_pathLen[firstIdx]);
 }
diff --git a/src/bogart/AS_BAT_CreateUnitigs.C b/src/bogart/AS_BAT_CreateUnitigs.C
@@ -249,7 +249,7 @@ checkRead(AssemblyGraph *AG,
     //  and if it is the first or last read.
     //
     //           first == true                  first == false
-    //  best5    fwd   == true  --------->      fwd   == false  <---------    
+    //  best5    fwd   == true  --------->      fwd   == false  <---------
     //  best3    fwd   == false <----------     fwd   == true   --------->
 
     BAToverlap     best = (isFirst == rdA->position.isForward()) ? pf.best5 : pf.best3;
@@ -327,7 +327,7 @@ createUnitigs(AssemblyGraph  *AG,
 
     if (tig == NULL)
       continue;
- 
+
     if (tig->_isUnassembled == true)    //  Edge is FROM an unassembled thing, ignore it.
       continue;
 
@@ -372,7 +372,7 @@ createUnitigs(AssemblyGraph  *AG,
 
   uint32  ss = 0;
   uint32  ee = 0;
-  
+
   while (ss < breaks.size()) {
     Unitig  *tig = contigs[breaks[ss]._tigID];
 

diff --git a/src/bogart/AS_BAT_MarkRepeatReads.C b/src/bogart/AS_BAT_MarkRepeatReads.C
@@ -275,7 +275,7 @@ splitTig(TigVector                &tigs,
 
 //  Over all reads in tgA, return a vector of olapDat (tigBgn, tigEnd, eviRid)
 //  for all reads that overlap into this tig.
-//  
+//
 //  The current AssemblyGraph is backwards to what we need.  It has, for each read, the
 //  overlaps from that read that are compatible - but we need to the overlaps to each
 //  read that are compatible, and the two are not symmetric.  A can be compatible in tig 1,

diff --git a/src/bogart/AS_BAT_OverlapCache.C b/src/bogart/AS_BAT_OverlapCache.C
@@ -414,7 +414,7 @@ OverlapCache::filterDuplicates(uint32 &no) {
       continue;
 
     //  Found duplicate B IDs.  Drop one of them.
-    
+
     nFiltered++;
 
     //  If they're the same length, make the one with the higher evalue be length zero so it'll be
@@ -827,7 +827,7 @@ OverlapCache::symmetrizeOverlaps(void) {
     for (uint32 oo=0; oo<_overlapLen[rr]; oo++) {
       if (_overlaps[rr][oo].symmetric == true)
         continue;
-   
+
       uint32  rb = _overlaps[rr][oo].b_iid;
       uint32  nn = _overlapLen[rb]++;
 

diff --git a/src/bogart/AS_BAT_PlaceReadUsingOverlaps.C b/src/bogart/AS_BAT_PlaceReadUsingOverlaps.C
@@ -15,19 +15,11 @@
  *
  *  This file is derived from:
  *
- *    src/AS_BAT/AS_BAT_PlaceFragUsingOverlaps.C
+ *    src/bogart/AS_BAT_PlaceFragUsingOverlaps.C
  *
  *  Modifications by:
  *
- *    Brian P. Walenz from 2010-NOV-23 to 2013-SEP-08
- *      are Copyright 2010-2013 J. Craig Venter Institute, and
- *      are subject to the GNU General Public License version 2
- *
- *    Brian P. Walenz from 2014-OCT-09 to 2015-AUG-05
- *      are Copyright 2014-2015 Battelle National Biodefense Institute, and
- *      are subject to the BSD 3-Clause License
- *
- *    Brian P. Walenz beginning on 2016-JAN-11
+ *    Brian P. Walenz beginning on 2016-AUG-12
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
@@ -326,7 +318,7 @@ placeRead_computeVerified(overlapPlacement &op, uint32 tigLen) {
     op.verified.end = op.position.bgn + op.covered.end;
 
     if (op.verified.end > op.position.end)   //  verified.bgn is always valid if covered.bgn > 0
-      op.verified.end = op.position.end;     //  
+      op.verified.end = op.position.end;     //
 
     if (op.verified.bgn < 0)
       op.verified.bgn = 0;

diff --git a/src/bogart/AS_BAT_PlaceReadUsingOverlaps.H b/src/bogart/AS_BAT_PlaceReadUsingOverlaps.H
@@ -15,19 +15,11 @@
  *
  *  This file is derived from:
  *
- *    src/AS_BAT/AS_BAT_PlaceFragUsingOverlaps.H
+ *    src/bogart/AS_BAT_PlaceFragUsingOverlaps.H
  *
  *  Modifications by:
  *
- *    Brian P. Walenz from 2010-DEC-06 to 2013-AUG-01
- *      are Copyright 2010-2013 J. Craig Venter Institute, and
- *      are subject to the GNU General Public License version 2
- *
- *    Brian P. Walenz from 2014-DEC-19 to 2015-JUN-03
- *      are Copyright 2014-2015 Battelle National Biodefense Institute, and
- *      are subject to the BSD 3-Clause License
- *
- *    Brian P. Walenz beginning on 2016-JAN-11
+ *    Brian P. Walenz beginning on 2016-AUG-12
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_PopBubbles.C b/src/bogart/AS_BAT_PopBubbles.C
@@ -472,7 +472,7 @@ popBubbles(TigVector &tigs,
 
       targetIntervals[tid]->add(bgn, bubbleLen);  //  Don't care if it goes off the high end of the tig.
     }
-    
+
     //  Add extended intervals for the last read.
 
     for (uint32 pp=0; pp<placed[lReadID].size(); pp++) {
@@ -504,7 +504,7 @@ popBubbles(TigVector &tigs,
       //  Merge.
 
       IL->merge();
-      
+
       //  Figure out if each interval has both the first and last read of some bubble, and if those
       //  are properly sized.
 
@@ -574,7 +574,7 @@ popBubbles(TigVector &tigs,
         bool  alignInnie = (alignFwd  && fPosFwd && !rPosFwd);
 
 
-        //if ((bubbleInnie  == true) && 
+        //if ((bubbleInnie  == true) &&
         //if ((bubbleOuttie == true) && ((alignFwd == true) || (fPosFwd == true) || (rPosFwd == false)));
         //if ((bubbleFwd    == true) && ((alignFwd == true) || (fPosFwd == true) || (rPosFwd == false)));
         //if ((bubbleRev    == true) && ((alignFwd == true) || (fPosFwd == true) || (rPosFwd == false)));
@@ -596,7 +596,7 @@ popBubbles(TigVector &tigs,
     }  //  Over all targets
 
     //  Done with the targetIntervals.  Clean up.
-    
+
     for (map<uint32, intervalList<uint32> *>::iterator it=targetIntervals.begin(); it != targetIntervals.end(); ++it)
       delete it->second;
 

diff --git a/src/bogart/AS_BAT_ReadInfo.C b/src/bogart/AS_BAT_ReadInfo.C
@@ -13,21 +13,9 @@
  *  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/AS_BAT/AS_BAT_FragmentInfo.C
- *
  *  Modifications by:
  *
- *    Brian P. Walenz from 2010-NOV-23 to 2013-AUG-01
- *      are Copyright 2010-2013 J. Craig Venter Institute, and
- *      are subject to the GNU General Public License version 2
- *
- *    Brian P. Walenz from 2014-DEC-19 to 2015-JUN-16
- *      are Copyright 2014-2015 Battelle National Biodefense Institute, and
- *      are subject to the BSD 3-Clause License
- *
- *    Brian P. Walenz beginning on 2016-JAN-11
+ *    Brian P. Walenz beginning on 2016-AUG-12
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_ReadInfo.H b/src/bogart/AS_BAT_ReadInfo.H
@@ -13,13 +13,9 @@
  *  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_Datatypes.H
- *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2016-APR-28
+ *    Brian P. Walenz beginning on 2016-AUG-12
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_TigGraph.C b/src/bogart/AS_BAT_TigGraph.C
@@ -329,7 +329,7 @@ emitEdges(TigVector &tigs,
                edges[ee].bgn, edges[ee].end, tigs[edges[ee].tigID]->getLength(),
                rdA->ident, fi);
 #endif
-                 
+
       edges[ee].deleted = true;
     }
 

diff --git a/src/bogart/AS_BAT_TigVector.C b/src/bogart/AS_BAT_TigVector.C
@@ -15,7 +15,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2016-APR-06
+ *    Brian P. Walenz beginning on 2016-AUG-09
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_TigVector.H b/src/bogart/AS_BAT_TigVector.H
@@ -15,7 +15,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2016-APR-06
+ *    Brian P. Walenz beginning on 2016-AUG-09
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_Unitig_AddRead.C b/src/bogart/AS_BAT_Unitig_AddRead.C
@@ -15,19 +15,11 @@
  *
  *  This file is derived from:
  *
- *    src/AS_BAT/AS_BAT_Unitig_AddFrag.C
+ *    src/bogart/AS_BAT_Unitig_AddFrag.C
  *
  *  Modifications by:
  *
- *    Brian P. Walenz from 2010-NOV-23 to 2013-AUG-01
- *      are Copyright 2010,2012-2013 J. Craig Venter Institute, and
- *      are subject to the GNU General Public License version 2
- *
- *    Brian P. Walenz on 2014-DEC-19
- *      are Copyright 2014 Battelle National Biodefense Institute, and
- *      are subject to the BSD 3-Clause License
- *
- *    Brian P. Walenz beginning on 2016-JAN-11
+ *    Brian P. Walenz beginning on 2016-AUG-12
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C b/src/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C
@@ -15,19 +15,11 @@
  *
  *  This file is derived from:
  *
- *    src/AS_BAT/AS_BAT_Unitig_PlaceFragUsingEdges.C
+ *    src/bogart/AS_BAT_Unitig_PlaceFragUsingEdges.C
  *
  *  Modifications by:
  *
- *    Brian P. Walenz from 2010-NOV-23 to 2013-AUG-01
- *      are Copyright 2010-2013 J. Craig Venter Institute, and
- *      are subject to the GNU General Public License version 2
- *
- *    Brian P. Walenz from 2014-DEC-19 to 2015-MAR-06
- *      are Copyright 2014-2015 Battelle National Biodefense Institute, and
- *      are subject to the BSD 3-Clause License
- *
- *    Brian P. Walenz beginning on 2016-JAN-11
+ *    Brian P. Walenz beginning on 2016-AUG-12
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/bogart/bogart.C b/src/bogart/bogart.C
@@ -507,7 +507,7 @@ main (int argc, char * argv []) {
   createUnitigs(EG, contigs, unitigs);
 
   delete EG;
-  
+
   splitDiscontinuous(unitigs, minOverlap);
 
   setParentAndHang(unitigs);
Original file line number	Diff line number	Diff line change
Expand Up		@@ -31,7 +31,6 @@
		* full conditions and disclaimers for each license.
		*/


		#include "AS_UTL_alloc.H"


Expand Down
-Original file line number
+Diff line change
@@ Expand Up / @@ -263,6 +263,6 @@ ChunkGraph::countFullWidth(ReadEnd firstEnd) { @@
         fprintf(_chunkLog, "\n");
       }
       return(_pathLen[firstIdx]);
     }