Update copyright info.

marbl · Nov 4, 2019 · 4384120 · 4384120
1 parent 843c753
commit 4384120
Show file tree

Hide file tree

Showing 31 changed files with 129 additions and 56 deletions.
diff --git a/src/meryl/meryl-import.C b/src/meryl/meryl-import.C
@@ -15,7 +15,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2018-JUL-21
+ *    Brian P. Walenz beginning on 2018-NOV-02
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/meryl/meryl-lookup.C b/src/meryl/meryl-lookup.C
@@ -15,7 +15,11 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2018-JUL-21
+ *    Brian P. Walenz beginning on 2018-OCT-26
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
+ *    Arang Rhie beginning on 2019-FEB-25
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
@@ -99,7 +103,7 @@ reportExistence(dnaSeqFile           *sf,
           (kl->value(kiter.rmer()) > 0))
         nKmerFound++;
     }
-      
+
     fprintf(stdout, "%s\t%lu\t%lu\t%lu\n", name, nKmer, kl->nKmers(), nKmerFound);
   }
 

diff --git a/src/overlapAlign/clearRangeFile.C b/src/overlapAlign/clearRangeFile.C
@@ -15,7 +15,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2019-JUN-06
+ *    Brian P. Walenz beginning on 2019-JUN-07
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/overlapAlign/clearRangeFile.H b/src/overlapAlign/clearRangeFile.H
@@ -15,7 +15,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2019-JUN-06
+ *    Brian P. Walenz beginning on 2019-JUN-07
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *

diff --git a/src/overlapAlign/computeAlignments.C b/src/overlapAlign/computeAlignments.C
@@ -15,7 +15,11 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2019-APR-22
+ *    Brian P. Walenz beginning on 2019-APR-29
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
+ *    Sergey Koren beginning on 2019-JUL-18
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
@@ -153,7 +157,7 @@ maComputation::trimOverlap_Normal(ovOverlap *ovl) {
   assert(bshift5 >= 0);
   assert(bshift3 >= 0);
 
-  //  But the reads can contain different gappiness, so we need to scale the shift differently for each read.  
+  //  But the reads can contain different gappiness, so we need to scale the shift differently for each read.
 
   double abscale   = (double)(aovlend - aovlbgn) / (bovlend - bovlbgn);   //  One base in B is this many bases in A.
   double bascale   = (double)(bovlend - bovlbgn) / (aovlend - aovlbgn);   //  One base in B is this many bases in A.
@@ -274,7 +278,7 @@ maComputation::trimOverlap_Flipped(ovOverlap *ovl) {
   assert(bshift5 >= 0);
   assert(bshift3 >= 0);
 
-  //  But the reads can contain different gappiness, so we need to scale the shift differently for each read.  
+  //  But the reads can contain different gappiness, so we need to scale the shift differently for each read.
 
   double abscale   = (double)(aovl3 - aovl5) / (bovl5 - bovl3);   //  One base in B is this many bases in A.
   double bascale   = (double)(bovl5 - bovl3) / (aovl3 - aovl5);   //  One base in B is this many bases in A.
@@ -622,6 +626,6 @@ maComputation::computeAlignments(uint32  minOverlapLength,
   //  Step 3:  Align all reads in tig to tig sequence.  Save alignments
   //  in conveninent multialign structure.  This should be part of tgTig.
 
-  //  Step 4:  
+  //  Step 4:
 
 }
diff --git a/src/overlapAlign/overlapAlign.C b/src/overlapAlign/overlapAlign.C
@@ -19,6 +19,10 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Sergey Koren beginning on 2019-JUL-18
+ *      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/overlapAlign/trimRead.C b/src/overlapAlign/trimRead.C
@@ -15,7 +15,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2019-APR-22
+ *    Brian P. Walenz beginning on 2019-APR-29
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
@@ -76,7 +76,7 @@ maComputation::trimRead(uint32   minOverlapLength,
   //  overhang       -- require overlaps to overlap by this much before merging regions.
   //
   //  bextra         -- for the initial alignment, extend the B region by this amount on each end
-  //  slop           -- 
+  //  slop           --
 
   double   maxAlignErate  = maxErate + 0.2;
   double   maxAcceptErate = maxErate;

diff --git a/src/overlapBasedTrimming/mergeRanges.C b/src/overlapBasedTrimming/mergeRanges.C
@@ -15,11 +15,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz beginning on 2017-OCT-03
- *      are a 'United States Government Work', and
- *      are released in the public domain
- *
- *    Sergey Koren beginning on 2017-OCT-18
+ *    Brian P. Walenz beginning on 2019-MAR-01
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
@@ -115,7 +111,7 @@ main (int argc, char **argv) {
 
       if (verbose == true)
         fprintf(stderr, "%u\t%7u-%-7u\t%7u-%-7u\n",
-                rid, 
+                rid,
                 read->sqRead_clearBgn(), read->sqRead_clearEnd(),
                 clrRange->bgn(rid), clrRange->end(rid));
 

diff --git a/src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C b/src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C
@@ -23,6 +23,14 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Sergey Nurk beginning on 2019-AUG-23
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
+ *    Sergey Koren beginning on 2019-OCT-01
+ *      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/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C b/src/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C
@@ -19,6 +19,10 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Sergey Nurk beginning on 2019-SEP-05
+ *      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/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C b/src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C
@@ -23,6 +23,14 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Sergey Nurk beginning on 2019-AUG-23
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
+ *    Sergey Koren beginning on 2019-OCT-14
+ *      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.
  */
@@ -516,7 +524,7 @@ PrepareRead(/*const*/ sqStore *seqStore, uint32 curID, sqReadData *readData,
 //returns error rate of the alignment or -1. if (!match_to_end || invalid_olap)
 static
 double
-ProcessAlignment(int32 a_part_len, const char *a_part, int64 a_hang, int32 b_part_len, const char *b_part, 
+ProcessAlignment(int32 a_part_len, const char *a_part, int64 a_hang, int32 b_part_len, const char *b_part,
                  int32 error_bound, bool check_trivial_dna,
                  pedWorkArea_t *ped, bool *match_to_end, bool *invalid_olap) {
   int32   a_end        = 0;
@@ -666,10 +674,10 @@ Redo_Olaps(coParameters *G, /*const*/ sqStore *seqStore) {
 
     assert(curID == G->olaps[thisOvl].b_iid);
 
-    //  Load and correct the B read 
-    PrepareRead(seqStore, curID, readData, 
-                fseqLen, fseq, rseq, 
-                fadjLen, fadj, radj, 
+    //  Load and correct the B read
+    PrepareRead(seqStore, curID, readData,
+                fseqLen, fseq, rseq,
+                fadjLen, fadj, radj,
                 C, Cpos, Clen);
 
     //  Recompute alignments for ALL overlaps involving the B read
@@ -753,7 +761,7 @@ Redo_Olaps(coParameters *G, /*const*/ sqStore *seqStore) {
         //  I can't find any patterns in these errors.  I thought that it was caused by the corrections, but I
         //  found a case where no corrections were made and the alignment still failed.  Perhaps it is differences
         //  in the alignment code (the forward vs reverse prefix distance in overlapper vs only the forward here)?
-      
+
         fprintf(stderr, "Redo_Olaps()--\n");
         fprintf(stderr, "Redo_Olaps()--\n");
         fprintf(stderr, "Redo_Olaps()--  Bad alignment  errors %d  a_end %d  b_end %d  match_to_end %d  olapLen %d\n",
@@ -767,9 +775,9 @@ Redo_Olaps(coParameters *G, /*const*/ sqStore *seqStore) {
                 G->reads[ G->olaps[thisOvl].b_iid ].basesLen);
         fprintf(stderr, "Redo_Olaps()--  A %s\n", a_part);
         fprintf(stderr, "Redo_Olaps()--  B %s\n", b_part);
-      
+
         Display_Alignment(a_part, a_part_len, b_part, b_part_len, ped->delta, ped->deltaLen);
-      
+
         fprintf(stderr, "\n");
       #endif
 

diff --git a/src/overlapErrorAdjustment/correctOverlaps.H b/src/overlapErrorAdjustment/correctOverlaps.H
@@ -19,6 +19,10 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Sergey Koren beginning on 2019-OCT-14
+ *      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/overlapErrorAdjustment/correctionOutput.H b/src/overlapErrorAdjustment/correctionOutput.H
@@ -15,9 +15,14 @@
  *
  *  Modifications by:
  *
+ *    Sergey Nurk beginning on 2019-AUG-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.
  */
+
 #pragma once
 
 //  Definitions for our exportable data.

diff --git a/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C b/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C
@@ -27,6 +27,10 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Sergey Nurk beginning on 2019-AUG-15
+ *      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/overlapErrorAdjustment/findErrors-Output.C b/src/overlapErrorAdjustment/findErrors-Output.C
@@ -19,6 +19,10 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Sergey Nurk beginning on 2019-AUG-15
+ *      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/overlapErrorAdjustment/findErrors-Process_Olap.C b/src/overlapErrorAdjustment/findErrors-Process_Olap.C
@@ -19,6 +19,10 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Sergey Nurk beginning on 2019-AUG-15
+ *      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/overlapErrorAdjustment/findErrors-Read_Frags.C b/src/overlapErrorAdjustment/findErrors-Read_Frags.C
@@ -23,6 +23,10 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Sergey Koren beginning on 2019-SEP-26
+ *      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/overlapErrorAdjustment/findErrors.H b/src/overlapErrorAdjustment/findErrors.H
@@ -19,6 +19,14 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Sergey Nurk beginning on 2019-AUG-15
+ *      are a 'United States Government Work', and
+ *      are released in the public domain
+ *
+ *    Sergey Koren beginning on 2019-SEP-26
+ *      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/pipelines/canu-time.pl b/src/pipelines/canu-time.pl
@@ -14,13 +14,9 @@
  #  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/pipelines/ca3g.pl
- #
  #  Modifications by:
  #
- #    Brian P. Walenz beginning on 2019-MAR-29
+ #    Brian P. Walenz beginning on 2019-APR-01
  #      are a 'United States Government Work', and
  #      are released in the public domain
  #
@@ -292,7 +288,7 @@ ($)
 #  Slurm returns YYYY-MM-DDTHH:MM:SS
 #                %Y-%m-%dT%H:%M:%S
 sub parseDate ($) {
-    my $d = $_[0];                     
+    my $d = $_[0];
     my $t;
 
     if ($d =~ m/^\d+-\d+-\d/) {

diff --git a/src/sequence/sequence-mutate.C b/src/sequence/sequence-mutate.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 2018-JUL-21
+ *    Brian P. Walenz beginning on 2019-JAN-09
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
@@ -157,7 +157,7 @@ doMutate(vector<char *> &inputs, mutateParameters &mutPar) {
 
       //  All done changing.  Output the modified read.
 
-      AS_UTL_writeFastA(stdout, nBases, oLen, 0, ">%s\n", seq.name()); 
+      AS_UTL_writeFastA(stdout, nBases, oLen, 0, ">%s\n", seq.name());
     }
 
     delete sf;

diff --git a/src/stores/ovStore.C b/src/stores/ovStore.C
@@ -48,6 +48,10 @@
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *
+ *    Sergey Nurk beginning on 2019-SEP-18
+ *      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/stores/sqCache.C b/src/stores/sqCache.C
@@ -15,11 +15,7 @@
  *
  *  Modifications by:
  *
- *    Brian P. Walenz from 2015-JUN-25 to 2015-JUL-01
- *      are Copyright 2015 Battelle National Biodefense Institute, and
- *      are subject to the BSD 3-Clause License
- *
- *    Brian P. Walenz beginning on 2016-OCT-17
+ *    Brian P. Walenz beginning on 2019-FEB-12
  *      are a 'United States Government Work', and
  *      are released in the public domain
  *