8149f2d63d04238813b626ab194b45eeaa91e32f
hiram
  Tue Sep 29 15:20:22 2026 -0700
fixup swap directory recognition refs #34360

diff --git src/hg/utils/automation/asmHubMiniMap2ChainNetComposite.pl src/hg/utils/automation/asmHubMiniMap2ChainNetComposite.pl
index 92fbce829e5..9ab906bc525 100755
--- src/hg/utils/automation/asmHubMiniMap2ChainNetComposite.pl
+++ src/hg/utils/automation/asmHubMiniMap2ChainNetComposite.pl
@@ -1,297 +1,302 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use FindBin qw($Bin);
 use lib "$Bin";
 use AsmHub;
 use HgAutomate;
 use File::Basename;
 
 my $argc = scalar(@ARGV);
 
 if ($argc != 3) {
   printf STDERR "usage: asmHubMiniMap2ChainNetComposite.pl asmId ncbiAsmId asmId.names.tab > asmId.miniMap2ChainNet.html\n";
   printf STDERR "where asmId is the assembly identifier,\n";
   printf STDERR "and   asmId.names.tab is naming file for this assembly,\n";
   printf STDERR "for UCSC database assemblies, use the third argument asmId.names.tab\n";
   printf STDERR "   as the Scientific_name for the organism.\n";
   exit 255;
 }
 
 # specific to UCSC environment
 my $dbHost = "hgwdev";
 
 my $asmId = shift;
 my $ncbiAsmId = shift;
 my $namesFile = shift;
 
 my $targetBuildDir = "";
 if ($asmId =~ m/^GC/) {
   my $gcX = substr($asmId,0,3);
   my $d0 = substr($asmId,4,3);
   my $d1 = substr($asmId,7,3);
   my $d2 = substr($asmId,10,3);
   my $hubBuildDir = "refseqBuild";
   $hubBuildDir = "genbankBuild" if ($gcX eq "GCA");
   $targetBuildDir = "/hive/data/genomes/asmHubs/$hubBuildDir/$gcX/$d0/$d1/$d2/$asmId";
 } else {
   $targetBuildDir = "/hive/data/genomes/$asmId";
 }
 
 # doMiniMap2.pl names buildDir/trackData/miniMap2.$QDb where $QDb is
 # ucfirst() of the actual query db/accession.  Reconstruct the actual
 # db name/accession, except for a GenArk accession (already starts with
 # the uppercase 'GC', ucfirst is a no-op there).
 sub queryDbFromQDb($) {
   my ($qDb) = @_;
   return $qDb if ($qDb =~ m/^GC/);
   return lcfirst($qDb);
 }
 
 my %queryDates;	# key is asmId, value is assembly date
 my %queryCommonName;	# key is asmId, value is assembly common name
 my %querySubmitter;	# key is asmId, value is assembly submitter
 my %fbStats;	# key is asmId, value is featureBits measure for chains
 my %loStats;	# key is asmId, value is featureBits measure for lift over
 
 open (TD, "ls -d ${targetBuildDir}/trackData/miniMap2.*|") or die "can not ls -d ${targetBuildDir}/trackData/miniMap2.*";
 while (my $mm2Dir = <TD>) {
   chomp $mm2Dir;
+  # a -swap run's default swapDir is itself named 'miniMap2.<otherDb>.swap',
+  # which also matches this glob alongside its own dateless symlink
+  # 'miniMap2.<otherDb>' -- skip that real *.swap work directory so this
+  # query genome is only processed once, via its dateless symlink.
+  next if ($mm2Dir =~ m/\.swap$/);
   my $Qdb = basename($mm2Dir);
   # the hubDateName will translate the accessionId into an asmId
   # side effect it also returns the date
   my $accession = &queryDbFromQDb($Qdb);
   my ($qDate, $qAsmName) = &HgAutomate::hubDateName($accession);
   my $qAsmId = "${accession}";
   if ($accession =~ m/^GC/) {
      $qAsmId = "${accession}${qAsmName}";
   }
   $queryDates{$qAsmId} = $qDate;
   my ($qCommonName, undef, $qSubmitter) = &HgAutomate::getAssemblyInfo($dbHost, $qAsmId);
   $queryCommonName{$qAsmId} = $qCommonName;
   $querySubmitter{$qAsmId} = $qSubmitter;
   my $fbTxt = `ls ${targetBuildDir}/trackData/miniMap2.${Qdb}/fb.*chain${Qdb}Link.txt 2> /dev/null`;
   chomp $fbTxt;
   if ( -s "${fbTxt}" ) {
     my $fBits = `cut -d' ' -f5 $fbTxt | tr -d '()%'`;
     chomp $fBits;
     $fbStats{$qAsmId} = $fBits;
   } else {
     $fbStats{$qAsmId} = "n/a";
   }
   $fbTxt = `ls ${targetBuildDir}/trackData/miniMap2.${Qdb}/fb.*chainLiftOver${Qdb}.txt 2> /dev/null`;
   chomp $fbTxt;
   if ( -s "${fbTxt}" ) {
     my $fBits = `cut -d' ' -f5 $fbTxt | tr -d '()%'`;
     chomp $fBits;
     $loStats{$qAsmId} = $fBits;
   } else {
     $loStats{$qAsmId} = "n/a";
   }
 }
 close (TD);
 
 my $ncbiAssemblyId = $ncbiAsmId;
 
 if ( -s "${namesFile}" ) {
   $ncbiAssemblyId = `grep -v "^#" $namesFile | cut -f10`;
   chomp $ncbiAssemblyId;
 }
 
 my $sciName = ${namesFile};
 
 if ( -s "${namesFile}" ) {
   my $sciName = `grep -v "^#" $namesFile | cut -f5`;
   chomp $sciName;
 }
 
 my ($tGenome, $tDate, $tSource) = &HgAutomate::getAssemblyInfo($dbHost, $asmId);
 
 
 print <<_EOF_
 <h2>Description</h2>
 <p>
 This track shows regions of this <em>target</em> genome ($tGenome - $tDate - $tSource) that has alignment
 to other very similar <em>query</em> genomes (&quot;chain&quot; subtracks), and the
 subset of each chain used to lift over coordinates to that query
 (&quot;lift over&quot; subtracks).
 The alignable parts are shown with thick blocks that look like exons.
 Non-alignable parts between these are shown like introns.
 </p>
 
 <p>
 These alignments were made with <em>minimap2</em> rather than
 <em>lastz</em>.  They are intended for pairs of very similar
 same-species/same-individual assemblies -- for example the haplotypes of
 a trio-binned or hifiasm/verkko diploid assembly, or closely related
 strain assemblies -- where minimap2's splice-free asm5/asm10/asm20
 presets do a better job with the larger indels and structural
 differences seen between such assemblies than lastz's general-purpose
 scoring does.
 </p>
 
 <p>
 Other <em>query</em> genome assemblies aligning to this <em>target</em> genome assembly:
 <ul>
 _EOF_
     ;
 
 my @orderedByFBits;
 foreach my $qDb ( sort {$fbStats{$b} <=> $fbStats{$a}} keys %fbStats) {
   push @orderedByFBits, $qDb;
 }
 
 foreach my $oAsmId (@orderedByFBits) {
   my $fbPercent = "";
   $fbPercent = "% $fbStats{$oAsmId} " if (defined($fbStats{$oAsmId}));
   if ($oAsmId =~ m/^GC/) {
     printf "<li>%s<a href='https://genome.ucsc.edu/h/%s' target=_blank>%s</a> %s %s %s</li>\n", $fbPercent, $oAsmId, $oAsmId, $queryCommonName{$oAsmId}, $queryDates{$oAsmId}, $querySubmitter{$oAsmId};
   } else {
     printf "<li>%s<a href='https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s' target=_blank>%s</a> %s %s %s</li>\n", $fbPercent, $oAsmId, $oAsmId, $queryCommonName{$oAsmId}, $queryDates{$oAsmId}, $querySubmitter{$oAsmId};
   }
 }
 
 printf "</ul>
 </p>\n";
 
 printf "<h3>Alignments identity</h3>\n";
 printf "<table border='1'>\n";
 printf "<caption>showing percent identity, how much of the target is matched by the query</caption>\n";
 printf "<thead style='position:sticky; top:0; background-color: white;'><tr>\n";
 printf "<th>chains</th><th>lift<br>over</th><th>common<br>name</th><th>assembly</th>\n";
 printf "</tr></thead><tbody>\n";
 foreach my $oAsmId (@orderedByFBits) {
  printf "<tr>";
  if (defined($fbStats{$oAsmId})) {
    printf "<td style='text-align:right;'>%s</td>", $fbStats{$oAsmId};
  } else {
    printf "<td style='text-align:right;'>&nbsp;</td>";
  }
  if (defined($loStats{$oAsmId})) {
    printf "<td style='text-align:right;'>%s</td>", $loStats{$oAsmId};
  } else {
    printf "<td style='text-align:right;'>&nbsp;</td>";
  }
  printf "<td>%s</td><td>%s</td></tr>\n", $queryCommonName{$oAsmId}, $oAsmId;
 }
 printf "</tbody></table>\n";
 
 print <<_EOF_
 <h3>Chain Track</h3>
 <p>
 The chain tracks shows alignments of the other genome assemblies to the
 $tGenome/$sciName/$ncbiAssemblyId/$tDate genome using a gap scoring system that allows longer gaps
 than traditional affine gap scoring systems. It can also tolerate gaps in both
 <em>query</em> and <em>target</em> genomes simultaneously. These
 &quot;double-sided&quot; gaps can be caused by local inversions and
 overlapping deletions in both species.
 </p>
 <p>
 The chain track displays boxes joined together by either single or
 double lines. The boxes represent aligning regions.
 Single lines indicate gaps that are largely due to a deletion in the
 <em>query</em> assembly or an insertion in the <em>target</em>
 assembly.  Double lines represent more complex gaps that involve substantial
 sequence in both species. This may result from inversions, overlapping
 deletions, an abundance of local mutation, or an unsequenced gap in one
 species.</p>
 <p>
 In the &quot;pack&quot; and &quot;full&quot; display
 modes, the individual feature names indicate the chromosome, strand, and
 location (in thousands) of the match for each matching alignment.</p>
 <p>
 There are two different types of chain tracks:
 <ul>
 <li><b>Chains</b> - The first level of chain track showing all potential chains.
   The lift over chain track is derived from this chain data.</li>
 <li><b>Lift over</b> - filtered first level chain selecting out the
   best/longest syntenic regions used to translate coordinates from the
   target genome to the query genome.</li>
 </ul>
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>By default, the chains to chromosome-based assemblies are colored
 based on which chromosome they map to in the aligning organism. To turn
 off the coloring, check the &quot;off&quot; button next to: Color
 track based on chromosome.</p>
 <p>
 To display only the chains of one chromosome in the aligning
 organism, enter the name of that chromosome (e.g. chr4) in box next to:
 Filter by chromosome.</p>
 
 <h2>Methods</h2>
 <h3>Chain track</h3>
 <p>
 Each <em>query</em> genome was aligned to the <em>target</em> genome with
 <em>minimap2</em>, one job per target sequence against the whole query
 genome. The resulting PAF alignments were converted into PSL format using
 the <em>pafToPsl</em> program. The PSL alignments were fed into
 <em>axtChain</em>, which organizes all alignments between a single
 <em>query</em> chromosome and a single <em>target</em> chromosome into a
 group and creates a kd-tree out of the gapless subsections (blocks) of
 the alignments. A dynamic program was then run over the kd-trees to find
 the maximally scoring chains of these blocks.
 </p>
 
 <h3>Lift over chain track</h3>
 <p>
 Each chain was placed with <em>chainNet</em>, trimming it as necessary to
 fit into sections not already covered by a higher-scoring part of the
 chain, then classified with <em>netSyntenic</em> and <em>netClass</em>.
 The program <em>netChainSubset</em> was then used to extract the
 best/longest syntenic part of that net back out of the chain, giving the
 chain used to lift over coordinates between the two assemblies.
 </p>
 
 <h2>Credits</h2>
 <p>
 <em>minimap2</em> was developed by Heng Li.
 </p>
 <p>
 The <em>mash</em> program, used to estimate the divergence between the
 target and each query assembly and automatically select the minimap2
 alignment preset, was developed by Brian Ondov, Todd Treangen, and
 colleagues at the National Biodefense Analysis and Countermeasures
 Center and the University of Maryland.
 </p>
 <p>
 The <em>axtChain</em> program was developed at the University of California at
 Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</p>
 <p>
 The <em>chainNet</em>, <em>netSyntenic</em>, and <em>netClass</em> programs
 were developed at the University of California
 Santa Cruz by Jim Kent.</p>
 
 <h2>References</h2>
 <p>
 Li H.
 <a href="https://doi.org/10.1093/bioinformatics/bty191"
 target=_blank>Minimap2: pairwise alignment for nucleotide sequences</a>.
 <em>Bioinformatics</em>. 2018 Sep 15;34(18):3094-3100.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29750242" target="_blank">29750242</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137996/" target="_blank">PMC6137996</a>
 </p>
 
 <p>
 Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM.
 <a href="https://doi.org/10.1186/s13059-016-0997-x"
 target=_blank>Mash: fast genome and metagenome distance estimation using MinHash</a>.
 <em>Genome Biol</em>. 2016 Jun 20;17(1):132.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27323842" target="_blank">27323842</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915045/" target="_blank">PMC4915045</a>
 </p>
 
 <p>
 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
 <A HREF="https://www.pnas.org/content/100/20/11484"
 TARGET=_blank>Evolution's cauldron:
 duplication, deletion, and rearrangement in the mouse and human genomes</A>.
 <em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>
 </p>
 
 _EOF_
     ;