de697f3424320f0679649fcba305e3b8641d3cad
hiram
  Fri Jun 19 12:19:07 2020 -0700
attempt to work without an NCBI lift file and issue warning refs #23367

diff --git src/hg/utils/automation/doRepeatMasker.pl src/hg/utils/automation/doRepeatMasker.pl
index 5699889..b823e36 100755
--- src/hg/utils/automation/doRepeatMasker.pl
+++ src/hg/utils/automation/doRepeatMasker.pl
@@ -439,30 +439,44 @@
     if ($opt_debug);
 
   if ($ncbiRmsk) {
     my $zippedSource = 0;	# asssume not a gz zipped file
     $zippedSource = 1 if ($ncbiRmsk =~ m/.gz$/);
     my $liftOpts = "";
     if (-s "${liftSpec}" ) {
       $liftOpts = "| liftUp -type=.out stdout $liftSpec warn stdin";
     }
     $bossScript->add(<<_EOF_
 export db="${db}"
 export ncbiRmOutFile="${ncbiRmsk}"
 cat /dev/null > "\${db}.sorted.fa.out"
 _EOF_
     );
+    if (! -s "${liftSpec}" ) {
+    printf STDERR "# WARNING: no liftSpec given with ncbiRmsk file, probably will need one ?\n";
+    $bossScript->add(<<_EOF_
+#########
+# WARNING: no liftSpec given with ncbiRmsk file, probably will need one ?
+#########
+
+printf "   SW  perc perc perc  query      position in query           matching       repeat              position in  repeat
+score  div. del. ins.  sequence    begin     end    (left)    repeat         class/family         begin  end (left)   ID
+
+" >> "\${db}.sorted.fa.out"
+_EOF_
+    );
+    }
     if ($zippedSource) {
     $bossScript->add(<<_EOF_
 zcat "\${ncbiRmOutFile}" | tail -n +4 | sort -k5,5 -k6,6n $liftOpts >> "\${db}.sorted.fa.out"
 _EOF_
     );
     } else {
     $bossScript->add(<<_EOF_
 tail -n +4 "\${ncbiRmOutFile}" sort -k5,5 -k6,6n $liftOpts >> "\${db}.sorted.fa.out"
 _EOF_
     );
     }
   } else {	# not using the NCBI supplied file, use local cluster run result
   my $partDir = "$buildDir/RMPart";
   my $levels = $opt_debug ? 1 : `cat $partDir/levels`;
   chomp $levels;