7931c9562bb9808463e9b3ede322b0d415986de3
angie
  Wed Mar 11 10:37:13 2026 -0700
Made galGal6ToGCF_016699485.2.chainBridge.over.chain.gz for MLQ #37185

diff --git src/hg/makeDb/doc/galGal6/lastzRuns.txt src/hg/makeDb/doc/galGal6/lastzRuns.txt
index ff056f563a8..50b9d068633 100644
--- src/hg/makeDb/doc/galGal6/lastzRuns.txt
+++ src/hg/makeDb/doc/galGal6/lastzRuns.txt
@@ -4126,30 +4126,58 @@
     # 1037750321 bases of 1053332251 (98.521%) in intersection
     sed -e 's/^/    # /;' fb.GCF_016699485.2.chainSynGalGal6Link.txt
     # 1023011548 bases of 1053332251 (97.121%) in intersection
 \    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
     \
    -target2bit="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt" \
    GCF_016699485.2 galGal6) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	32m40.423s
 
     sed -e 's/^/    # /;' fb.GCF_016699485.2.chainRBest.GalGal6.txt
     # 1017361581 bases of 1053332251 (96.585%) in intersection
 
+##############################################################################
+# Bridge small double-sided gaps in Chicken GalGal6 vs. chicken GCF_016699485.2 liftOver chain (DONE - 2026-03-10 - Angie)
+    # See MLQs #37156, #37185
+    cd /hive/data/genomes/galGal6/bed/lastzGCF_016699485.2.2021-10-14/axtChain
+    # Turn double-sided gaps in the all.chain into mismatches where appropriate:
+    chainBridge \
+        galGal6.GCF_016699485.2.all.chain.gz \
+        /hive/data/genomes/galGal6/galGal6.2bit \
+        /hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.2bit \
+        stdout \
+    | pigz -p 8 > galGal6.GCF_016699485.2.chainBridge.all.chain.gz
+
+# chainNet the .chainBridge.all.chain file:
+    chainNet \
+        galGal6.GCF_016699485.2.chainBridge.all.chain.gz \
+        /hive/data/genomes/galGal6/chrom.sizes \
+        /hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.chrom.sizes \
+        galGal6.GCF_016699485.2.chainBridge.net /dev/null
+
+# Extract the new & improved .over.chain from the .chainBridge all.chain and net:
+    netChainSubset \
+        galGal6.GCF_016699485.2.chainBridge.net \
+        galGal6.GCF_016699485.2.chainBridge.all.chain.gz \
+        stdout \
+    | chainStitchId stdin stdout \
+    | pigz -p 8 \
+         > galGal6ToGCF_016699485.2.chainBridge.over.chain.gz
+
 ##############################################################################
 # LASTZ Chicken GalGal6 vs. Ferret MusFur1
 #    (DONE - 2025-06-16 - Gerardo)
 
     mkdir /hive/data/genomes/galGal6/bed/lastzMusFur1.2025-06-16
     cd /hive/data/genomes/galGal6/bed/lastzMusFur1.2025-06-16
 
     printf '# Ferret MusFur1 vs. Chicken GalGal6
 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
 
 # TARGET: Chicken  galGal6
 SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
 SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
 SEQ1_CHUNK=20000000
 SEQ1_LAP=10000