0cef6a4b1d730f0ecb4a5c8a0c0de6ce7a2fb13a
hiram
  Fri Sep 12 18:53:51 2025 -0700
temporary work-around to fix the align.tsv issue for RM 4.2.1

diff --git src/hg/utils/automation/doRepeatMasker.pl src/hg/utils/automation/doRepeatMasker.pl
index 0126f268c50..1180773c30e 100755
--- src/hg/utils/automation/doRepeatMasker.pl
+++ src/hg/utils/automation/doRepeatMasker.pl
@@ -622,31 +622,34 @@
 
   $split = "-nosplit";
   $split = "-split" if ($opt_splitTables);
   my $installDir = "$HgAutomate::clusterData/$db";
   $bossScript->add(<<_EOF_
 export db=$db
 
 # ensure sort functions properly despite kluster node environment
 export LC_COLLATE=C
 
 hgLoadOut -table=rmsk$updateTable $split \$db \$db.sorted.fa.out
 hgLoadOut -verbose=2 -tabFile=\$db.rmsk$updateTable.tab -table=rmsk$updateTable -nosplit \$db \$db.sorted.fa.out 2> \$db.bad.records.txt
 # construct bbi files for assembly hub
 $RepeatMaskerPath/util/rmToTrackHub.pl -out \$db.sorted.fa.out -align \$db.fa.align
 # in place same file sort using the -o output option
-sort -k1,1 -k2,2n -o \$db.fa.align.tsv \$db.fa.align.tsv &
+awk -F\$'\\t' '\$15 > -1' \$db.fa.align.tsv sort -k1,1 -k2,2n > t.tsv
+rm -f \$db.fa.align.tsv
+mv t.tsv \$db.fa.align.tsv
+# sort -k1,1 -k2,2n -o \$db.fa.align.tsv \$db.fa.align.tsv &
 sort -k1,1 -k2,2n -o \$db.sorted.fa.join.tsv \$db.sorted.fa.join.tsv
 wait
 bedToBigBed -tab -as=\$HOME/kent/src/hg/lib/bigRmskAlignBed.as -type=bed3+14 \\
   \$db.fa.align.tsv ../../chrom.sizes \$db.rmsk.align.bb &
 bedToBigBed -tab -as=\$HOME/kent/src/hg/lib/bigRmskBed.as -type=bed9+5 \\
   \$db.sorted.fa.join.tsv ../../chrom.sizes \$db.rmsk.bb
 wait
 rm -fr classBed classBbi rmskClass
 mkdir classBed classBbi rmskClass
 sort -k12,12 \$db.rmsk$updateTable.tab \\
   | splitFileByColumn -ending=tab  -col=12 -tab stdin rmskClass
 for T in SINE LINE LTR DNA Simple Low_complexity Satellite
 do
     fileCount=`(ls rmskClass/\${T}*.tab 2> /dev/null || true) | wc -l`
     if [ "\$fileCount" -gt 0 ]; then