Remove stray whitespace.

README.md

@@ -11,7 +11,7 @@ Canu is a hierarchical assembly pipeline which runs in four steps:
 
 ## Install:
 
-* The easiest way to get started is to download a binary [release](http://github.com/marbl/canu/releases).  
+* The easiest way to get started is to download a binary [release](http://github.com/marbl/canu/releases).
 
 * Installing with a 'package manager' is not encouraged, but if you have no other choice:
   * Conda: `conda install -c conda-forge -c bioconda -c defaults canu`

src/bogart/AS_BAT_BestOverlapGraph.C

@@ -615,7 +615,7 @@ BestOverlapGraph::removeSpannedSpurs(const char *prefix, uint32 spurDepth) {
     //     contains, etc.                        --------->
     //                                                  |
     //  2) Score the edge if the exit from the          v         (score this edge if
-    //     read it points to is not a spur path.      -------->    this end isn't a spur-path) 
+    //     read it points to is not a spur path.      -------->    this end isn't a spur-path)
     //
     //     Note that spur reads are also spur-path reads.
     //
@@ -1628,7 +1628,7 @@ BestOverlapGraph::emitGoodOverlaps(const char *prefix, const char *label) {
   ovStoreWriter  *writer = new ovStoreWriter(ovlName, RI->seqStore());
 
   //  The overlap needs a pointer to the seqStore.  Normally this is set
-  //  when the ovlStore is opened, 
+  //  when the ovlStore is opened,
 
   ovOverlap       ovl;
 

src/bogart/AS_BAT_BestOverlapGraph.H

@@ -172,7 +172,7 @@ private:
   //   - Suspected bubble near the end of a read that disrupts all but
   //     short overlaps.  Could also be caused by repeats and low coverage.
   //   - Treated like a normal read, except they cannot seed unitigs.
-  //   - 
+  //   -
   //
   //////////
   //  Backbone   - Read was placed as part of the backbone of a contig.

src/bogart/AS_BAT_MarkRepeatReads.C

@@ -978,7 +978,7 @@ findConfusedEdges(TigVector            &tigs,
 
         isC |= ((ad5 <= confusedAbsolute) &&
                 (pd5 <  confusedPercent));
-        
+
         if (isC == true) {
           writeLog("tig %7u read %8u pos %7u-%-7u 5' end  IS confused by edge to tig %8u read %8u - internal edge score %8.2f external edge score %8.2f - absdiff %8.2f percdiff %8.4f\n",
                    tgAid, rdAid, rdAlo, rdAhi,
@@ -1254,7 +1254,7 @@ markRepeatReads(AssemblyGraph         *AG,
     for (uint32 ii=0; ii<tigMarksU.numberOfIntervals(); ii++)
       writeLog("tigMarksU[%2u] = %d %d\n", ii, tigMarksU.lo(ii), tigMarksU.hi(ii));
 #endif
-    
+
     //  Create the list of intervals we'll use to make new tigs.
 
     vector<breakPointCoords>   BP;

src/bogart/AS_BAT_MergeOrphans.C

@@ -714,7 +714,7 @@ assignReadsToTargets(Unitig                     *orphan,
                      vector<overlapPlacement>   *placed,
                      vector<candidatePop *>     targets) {
 
-  //  For each read in the orphan, 
+  //  For each read in the orphan,
   //  For each placement of the read,
   //  For each target location
   //    If the target tig is the same as the placement tig

src/bogart/AS_BAT_OptimizePositions.C

@@ -298,7 +298,7 @@ Unitig::optimize_initPlace(uint32        ii,
   //  the correct read length here.
 
   op[iid].min = 0;
-  if (hs.size() != 0) 
+  if (hs.size() != 0)
      computeMedian(hs, op[iid].min);
   op[iid].max = op[iid].min + RI->readLength(ufpath[ii].ident);
 
@@ -385,7 +385,7 @@ Unitig::optimize_recompute(uint32        iid,
 
   //  Find the average and save.
 
-  computeMedian(hsmin, np[iid].min); 
+  computeMedian(hsmin, np[iid].min);
   computeMedian(hsmax, np[iid].max);
 
   if ((beVerbose) && (logFileFlagSet(LOG_OPTIMIZE_POSITIONS))) {

src/bogart/AS_BAT_ReadInfo.C

@@ -57,7 +57,7 @@ ReadInfo::ReadInfo(const char *seqStorePath,
   //  Scan the store.
   //    Flag any read 'ignored' in the store as 'not present' in the assembly.
   //    Flag any read too short              as 'not present' in the assembly.
-  //    
+  //
 
   for (uint32 fi=1; fi <= _numReads; fi++) {
     uint32   len  = _seqStore->sqStore_getReadLength(fi);

src/bogart/bogart.C

@@ -271,7 +271,7 @@ main (int argc, char * argv []) {
         lopsidedNoBest = true;
         fprintf(stderr, "LOPSIDED NOBEST %d\n", lopsidedDiff);
       }
-    
+
       else {
         assert(0);
       }

src/bogus/bogus-genome.css

@@ -620,7 +620,7 @@ div.transcript-hist {
 
 .plus-transcript-exon,
 .minus-transcript-exon,
-.plus-transcript-UTR, 
+.plus-transcript-UTR,
 .minus-transcript-UTR,
 .plus-transcript-five_prime_UTR,
 .minus-transcript-five_prime_UTR,
@@ -726,7 +726,7 @@ div.generic_parent-hist {
     z-index: 6;
     min-width: 1px;
     cursor: pointer;
-    background-color: #2AEB2A; 
+    background-color: #2AEB2A;
 }
 div.frag_align-hist {
     position: absolute;

src/gfa/alignGFA.C

@@ -54,7 +54,7 @@ public:
     len = tig->length();
     seq = new char [len + 1];
 
-    if (tig->consensusExists()) 
+    if (tig->consensusExists())
        memcpy(seq, tig->bases(), len);
     else
        memset(seq, 0, len);

src/haplotyping/splitHaplotype.C

@@ -558,7 +558,7 @@ loadReadBatch(void *G) {
         g->_seqs.pop();
         continue;
       }
-      if (g->_seqCounts == 0) 
+      if (g->_seqCounts == 0)
          fprintf(stdout, "-- Begin    processing file %s\n", g->_seqs.front()->filename());
 
       if (seq.length() >= g->_minOutputLength) {            //  Loaded something.  If it's long
@@ -573,7 +573,7 @@ loadReadBatch(void *G) {
         g->_filteredBases += seq.length();
       }
 
-      g->_seqCounts++; 
+      g->_seqCounts++;
       continue;      //  Loaded (or skipped) a sequence.  Thank you, may I have another?
     }
 

src/main.mk

@@ -3,7 +3,7 @@
 #  point to the upper level build directory.
 
 ifeq "$(strip ${DESTDIR})" ""
-  DESTDIR      := 
+  DESTDIR      :=
 endif
 
 ifeq "$(strip ${PREFIX})" ""

src/meryl/meryl-lookup.C

@@ -130,7 +130,7 @@ reportExistence(dnaSeqFile                      *sfile,
           (klookup[0]->value(kiter.rmer()) > 0))
         nKmerFound++;
     }
-      
+
     fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound);
   }
 }

src/overlapAlign/computeAlignments.C

@@ -153,7 +153,7 @@ 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 +274,7 @@ 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 +622,6 @@ 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:
 
 }

src/overlapAlign/trimRead.C

@@ -89,7 +89,7 @@ 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;

src/overlapBasedTrimming/mergeRanges.C

@@ -113,7 +113,7 @@ main (int argc, char **argv) {
     for (uint32 rid=bgnID[ii]; rid<=endID[ii]; rid++) {
       if (verbose == true)
         fprintf(stderr, "%u\t%7u-%-7u\t%7u-%-7u\n",
-                rid, 
+                rid,
                 seqStore->sqStore_getClearBgn(rid), seqStore->sqStore_getClearEnd(rid),
                 clrRange->bgn(rid), clrRange->end(rid));
 

src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C

@@ -514,7 +514,7 @@ PrepareRead(/*const*/ sqStore *seqStore, uint32 curID,
 //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;
@@ -754,7 +754,7 @@ 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",
@@ -768,9 +768,9 @@ 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
       }

src/pipelines/canu-time.pl

@@ -292,7 +292,7 @@ ($)
 #  Slurm returns YYYY-MM-DDTHH:MM:SS
 #                %Y-%m-%dT%H:%M:%S
 sub parseDate ($) {
-    my $d = $_[0];                     
+    my $d = $_[0];
     my $t;
 
     if ($d =~ m/^\d+-\d+-\d/) {

src/pipelines/canu.pl

@@ -525,7 +525,7 @@
     my $st;
 
     #  If no mode set, default -pacbio-hifi to trimmed status.
-    
+
     if (($mode eq "") && ($numHiFi > 0)) {
         $readsAreTrimmed = 1;
     }

src/pipelines/canu/Execution.pm

@@ -535,7 +535,7 @@ sub setWorkDirectory ($$) {
 
     elsif (getGlobal("gridEngine") eq "PBSPRO") {
         chdir($ENV{"PBS_O_WORKDIR"})   if (exists($ENV{"PBS_O_WORKDIR"}));
-        delete $ENV{"PBS_O_WORKDIR"}; 
+        delete $ENV{"PBS_O_WORKDIR"};
     }
 
     #  Now move into the assembly directory.
@@ -797,7 +797,7 @@ sub submitScript ($$) {
     print STDERR "-- Failed to submit Canu executive.  Delay 10 seconds and try again.\n";
 
     sleep(10);
-    
+
     if (runCommand(getcwd(), $qcmd) == 0) {
         exit(0);
     }

src/pipelines/canu/Grid_Cloud.pm

@@ -45,7 +45,7 @@ require Exporter;
              fetchFile            fetchFileShellCode
              fetchFileFromLink    fetchFileFromLinkShellCode
              stashFile            stashFileShellCode
-                                  stashFilesShellCode         
+                                  stashFilesShellCode
              fetchSeqStore        fetchSeqStoreShellCode
              fetchOvlStore        fetchOvlStoreShellCode
              fetchTigStore        fetchTigStoreShellCode
@@ -319,7 +319,7 @@ sub stashFile ($) {
     if ($path eq ".") {
         $link = sanitizeName("$pr:$ns/$name");
         $path = sanitizeName("$ns");
-    } else { 
+    } else {
         $link = sanitizeName("$pr:$ns/$path/$name");
         $path = sanitizeName("$ns/$path");
     }
@@ -341,7 +341,7 @@ sub stashFile ($) {
 
         #  Try a couple of times to upload the file.  If the UA fails, delay a bit and retry.
         while (($retries > 0) &&
-               (runCommandSilently(".", "$ua --do-not-compress --wait-on-close --project \"$pr\" --folder \"$path/\" --name \"$name\" \"$pathname\"", 0))) { 
+               (runCommandSilently(".", "$ua --do-not-compress --wait-on-close --project \"$pr\" --folder \"$path/\" --name \"$name\" \"$pathname\"", 0))) {
             $retries--;
             print STDERR "-- WARNING:\n";
             print STDERR "-- WARNING:  Failed to store '$pathname'.  Wait $delay seconds and try again ($retries times left).\n";
@@ -378,7 +378,7 @@ sub fetchFile ($) {
 
     if ($path eq ".") {
         $link = sanitizeName("$pr:$ns/$name");
-    } else { 
+    } else {
         $link = sanitizeName("$pr:$ns/$path/$name");
     }
 
@@ -446,7 +446,7 @@ sub stashFileShellCode ($$$) {
     #if ($path eq ".") {
     #    $link = sanitizeName("$pr:$ns/$name");
     #    $path = sanitizeName("$ns");
-    #} else { 
+    #} else {
     #    $link = sanitizeName("$pr:$ns/$path/$name");
     #    $path = sanitizeName("$ns/$path");
     #}
@@ -564,7 +564,7 @@ sub fetchFileShellCode ($$$) {
 
     if ($path eq ".") {
         $link = sanitizeName("$pr:$ns/$name");
-    } else { 
+    } else {
         $link = sanitizeName("$pr:$ns/$path/$name");
     }
 

src/pipelines/canu/Grid_Slurm.pm

@@ -65,11 +65,11 @@ sub configureSlurm () {
     my $maxArraySize  = 65535;
     my $maxArrayTasks = 65535;
 
-    #  Slurm has one or two configuration variables we need to check.                                                                                         
-    #    MaxArraySize    is (one more than) the maximum index value of any array task.                                                                        
-    #    max_array_tasks is the maximum number of array tasks per array job.                                                                                  
-    #                                                                                                                                                         
-    #  Usually they're the same value.  We just need to pick the smaller of the two.                                                                          
+    #  Slurm has one or two configuration variables we need to check.
+    #    MaxArraySize    is (one more than) the maximum index value of any array task.
+    #    max_array_tasks is the maximum number of array tasks per array job.
+    #
+    #  Usually they're the same value.  We just need to pick the smaller of the two.
 
     open(F, "scontrol show config |") or caExit("can't run 'scontrol' to get SLURM config", undef);
     while (<F>) {
@@ -84,7 +84,7 @@ sub configureSlurm () {
     }
     close(F);
 
-    if ($maxArraySize > $maxArrayTasks) {   #  Now just pick the smaller.                                                                                     
+    if ($maxArraySize > $maxArrayTasks) {   #  Now just pick the smaller.
         $maxArraySize = $maxArrayTasks;
     }
 

src/pipelines/canu/HaplotypeReads.pm

@@ -943,7 +943,7 @@ sub haplotypeSubtractCheck ($@) {
     foreach my $hap (@haplotypes) {
         if (getGlobal("saveMerCounts") == 0) {
             print STDERR "-- Removing meryl database '$path/reads-$hap.meryl'.\n";
-            remove_tree("$path/reads-$hap.meryl")   
+            remove_tree("$path/reads-$hap.meryl")
         } else {
             print STDERR "-- Meryl database '$path/reads-$hap.meryl' saved because 'saveMerCounts=true'.\n";
         }

src/pipelines/canu/Meryl.pm

@@ -923,7 +923,7 @@ sub merylProcessCheck ($$) {
     if (getGlobal("saveMerCounts") == 0) {
         print STDERR "--\n";
         print STDERR "-- Removing meryl database '$path/$name'.\n";
-        remove_tree("$path/$name")   
+        remove_tree("$path/$name")
     } else {
         print STDERR "--\n";
         print STDERR "-- Meryl database '$path/$name' saved because 'saveMerCounts=true'.\n";

src/pipelines/dx-canu/dxapp.json

@@ -70,7 +70,7 @@
         "hours": 120
       }
     },
-    "restartableEntryPoints": "all", 
+    "restartableEntryPoints": "all",
     "interpreter": "bash",
     "file": "src/canu-job-launcher.sh",
     "executionPolicy": {"restartOn": {"*": 2}},