cae80adef9ad9f897401c1fbe857eba5bb6679f0
hiram
  Fri Apr 15 19:06:23 2022 -0700
always user itemsPerSlot=4 on bedToBigBed for bigMaf.as for performance improvement refs #29263

diff --git src/hg/utils/automation/doBlastzChainNet.pl src/hg/utils/automation/doBlastzChainNet.pl
index 0417402..c8b8e1b 100755
--- src/hg/utils/automation/doBlastzChainNet.pl
+++ src/hg/utils/automation/doBlastzChainNet.pl
@@ -1047,31 +1047,31 @@
     if ($opt_trackHub) {
       $bossScript->add(<<_EOF_
 mkdir -p ../bigMaf
 ln -s ../mafNet/$tDb.$qDb.net.maf.gz ../bigMaf
 _EOF_
       );
     }
   }
   if ($opt_trackHub) {
     $bossScript->add(<<_EOF_
 cd $buildDir/bigMaf
 wget --no-check-certificate -O bigMaf.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigMaf.as'
 wget --no-check-certificate -O mafSummary.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/mafSummary.as'
 mafToBigMaf $tDb $tDb.$qDb.net.maf.gz stdout \\
   | sort -k1,1 -k2,2n > $tDb.$qDb.net.txt
-bedToBigBed -type=bed3+1 -as=bigMaf.as -tab \\
+bedToBigBed -itemsPerSlot=4 -type=bed3+1 -as=bigMaf.as -tab \\
   $tDb.$qDb.net.txt  $defVars{SEQ1_LEN} $tDb.$qDb.net.bb
 hgLoadMafSummary -minSeqSize=1 -test $tDb $tDb.$qDb.net.summary \\
   $tDb.$qDb.net.maf.gz
 cut -f2- $tDb.$qDb.net.summary.tab | sort -k1,1 -k2,2n \\
   > $tDb.$qDb.net.summary.bed
 bedToBigBed -type=bed3+4 -as=mafSummary.as -tab \\
         $tDb.$qDb.net.summary.bed $defVars{SEQ1_LEN} \\
         $tDb.$qDb.net.summary.bb
 rm -f $tDb.$qDb.net.txt $tDb.$qDb.net.summary.tab \\
         $tDb.$qDb.net.summary.bed
 _EOF_
       );
   }
 
   $bossScript->execute();
@@ -1829,31 +1829,31 @@
       stdout \\
   | gzip -c > $tDb.$qDb.synNet.maf.gz
   md5sum $tDb.$qDb.syn.net.gz $tDb.$qDb.synNet.maf.gz > synNet.md5sum.txt
 endif
 _EOF_
       );
     if ($opt_trackHub) {
       $bossScript->add(<<_EOF_
 if (\$lineCount > 0) then
   mkdir -p ../bigMaf
   cd ../bigMaf
   wget --no-check-certificate -O bigMaf.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigMaf.as'
   wget --no-check-certificate -O mafSummary.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/mafSummary.as'
   mafToBigMaf $tDb ../axtChain/$tDb.$qDb.synNet.maf.gz stdout \\
     | sort -k1,1 -k2,2n > $tDb.$qDb.synNet.txt
-  bedToBigBed -type=bed3+1 -as=bigMaf.as -tab  $tDb.$qDb.synNet.txt \\
+  bedToBigBed -itemsPerSlot=4 -type=bed3+1 -as=bigMaf.as -tab  $tDb.$qDb.synNet.txt \\
     $defVars{SEQ1_LEN} $tDb.$qDb.synNet.bb
   hgLoadMafSummary -minSeqSize=1 -test $tDb $tDb.$qDb.synNet.summary \\
         ../axtChain/$tDb.$qDb.synNet.maf.gz
   cut -f2- $tDb.$qDb.synNet.summary.tab | sort -k1,1 -k2,2n \\
         > $tDb.$qDb.synNet.summary.bed
   bedToBigBed -type=bed3+4 -as=mafSummary.as -tab \\
         $tDb.$qDb.synNet.summary.bed \\
         $defVars{SEQ1_LEN} $tDb.$qDb.synNet.summary.bb
   rm -f $tDb.$qDb.synNet.txt $tDb.$qDb.synNet.summary.tab \\
         $tDb.$qDb.synNet.summary.bed
 endif
 _EOF_
       );
     }