67834b02649fc82ec728bd72a50309d87128007d
hiram
  Fri Apr 30 21:41:59 2021 -0700
correct featureBits result file name refs #26682

diff --git src/hg/utils/automation/doBlastzChainNet.pl src/hg/utils/automation/doBlastzChainNet.pl
index 0de205d..4e58c1d 100755
--- src/hg/utils/automation/doBlastzChainNet.pl
+++ src/hg/utils/automation/doBlastzChainNet.pl
@@ -1124,31 +1124,31 @@
 _EOF_
       );
     } else {
       $bossScript->add(<<_EOF_
 cd $runDir
 hgLoadChain -test -noBin -tIndex $tDb chain$QDb $tDb.$qDb.all.chain.gz
 wget --no-check-certificate -O bigChain.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigChain.as'
 wget --no-check-certificate -O bigLink.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigLink.as'
 sed 's/.000000//' chain.tab | awk 'BEGIN {OFS="\\t"} {print \$2, \$4, \$5, \$11, 1000, \$8, \$3, \$6, \$7, \$9, \$10, \$1}' > chain${QDb}.tab
 bedToBigBed -type=bed6+6 -as=bigChain.as -tab chain${QDb}.tab $defVars{SEQ1_LEN} chain${QDb}.bb
 awk 'BEGIN {OFS="\\t"} {print \$1, \$2, \$3, \$5, \$4}' link.tab | sort -k1,1 -k2,2n > chain${QDb}Link.tab
 bedToBigBed -type=bed4+1 -as=bigLink.as -tab chain${QDb}Link.tab $defVars{SEQ1_LEN} chain${QDb}Link.bb
 set totalBases = `ave -col=2 $defVars{SEQ1_LEN} | grep "^total" | awk '{printf "%d", \$2}'`
 set basesCovered = `bedSingleCover.pl chain${QDb}Link.tab | ave -col=4 stdin | grep "^total" | awk '{printf "%d", \$2}'`
 set percentCovered = `echo \$basesCovered \$totalBases | awk '{printf "%.3f", 100.0*\$1/\$2}'`
-printf "%d bases of %d (%s%%) in intersection\\n" "\$basesCovered" "\$totalBases" "\$percentCovered" > ../fb.$tDb.chain.${QDb}Link.txt
+printf "%d bases of %d (%s%%) in intersection\\n" "\$basesCovered" "\$totalBases" "\$percentCovered" > ../fb.$tDb.chain${QDb}Link.txt
 rm -f link.tab
 rm -f chain.tab
 _EOF_
       );
     }
   }
   if (! $isSelf) {
   my $tRepeats = $opt_tRepeats ? "-tRepeats=$opt_tRepeats" : $defaultTRepeats;
   my $qRepeats = $opt_qRepeats ? "-qRepeats=$opt_qRepeats" : $defaultQRepeats;
   if ($opt_swap) {
     $tRepeats = $opt_qRepeats ? "-tRepeats=$opt_qRepeats" : $defaultQRepeats;
     $qRepeats = $opt_tRepeats ? "-qRepeats=$opt_tRepeats" : $defaultTRepeats;
   }
     if (! $opt_trackHub && $dbExists) {
       if ($qDbExists) {
@@ -1749,31 +1749,31 @@
       }
     } else {
       $bossScript->add(<<_EOF_
 set lineCount = `zcat $tDb.$qDb.syn.chain.gz | wc -l`
 if (\$lineCount > 0) then
   hgLoadChain -test -noBin -tIndex $tDb chainSyn$QDb $tDb.$qDb.syn.chain.gz
   wget --no-check-certificate -O bigChain.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigChain.as'
   wget --no-check-certificate -O bigLink.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigLink.as'
   sed 's/.000000//' chain.tab | awk 'BEGIN {OFS="\\t"} {print \$2, \$4, \$5, \$11, 1000, \$8, \$3, \$6, \$7, \$9, \$10, \$1}' > chainSyn${QDb}.tab
   bedToBigBed -type=bed6+6 -as=bigChain.as -tab chainSyn${QDb}.tab $defVars{SEQ1_LEN} chainSyn${QDb}.bb
   awk 'BEGIN {OFS="\\t"} {print \$1, \$2, \$3, \$5, \$4}' link.tab | sort -k1,1 -k2,2n > chainSyn${QDb}Link.tab
   bedToBigBed -type=bed4+1 -as=bigLink.as -tab chainSyn${QDb}Link.tab $defVars{SEQ1_LEN} chainSyn${QDb}Link.bb
   set totalBases = `ave -col=2 $defVars{SEQ1_LEN} | grep "^total" | awk '{printf "%d", \$2}'`
   set basesCovered = `bedSingleCover.pl chainSyn${QDb}Link.tab | ave -col=4 stdin | grep "^total" | awk '{printf "%d", \$2}'`
   set percentCovered = `echo \$basesCovered \$totalBases | awk '{printf "%.3f", 100.0*\$1/\$2}'`
-  printf "%d bases of %d (%s%%) in intersection\\n" "\$basesCovered" "\$totalBases" "\$percentCovered" > ../fb.$tDb.chainSyn.${QDb}Link.txt
+  printf "%d bases of %d (%s%%) in intersection\\n" "\$basesCovered" "\$totalBases" "\$percentCovered" > ../fb.$tDb.chainSyn${QDb}Link.txt
 netFilter -minGap=10 $tDb.$qDb.syn.net.gz \\
   | hgLoadNet -test -noBin -warn -verbose=0 $tDb netSyn$QDb stdin
 mv align.tab netSyn$QDb.tab
 endif
 rm -f link.tab
 rm -f chain.tab
 _EOF_
       );
     }
 
     $bossScript->add(<<_EOF_
 if (\$lineCount > 0) then
   netToAxt $tDb.$qDb.syn.net.gz $tDb.$qDb.all.chain.gz \\
     $defVars{'SEQ1_DIR'} $defVars{'SEQ2_DIR'} stdout \\
     | axtSort stdin stdout \\