428e9023e880b56314b2a1b9725415f269f1e54a
angie
  Fri Aug 26 11:42:45 2022 -0700
Use minimap2 -x asm20 --score-N=0 as pangolin does, to ensure consistent alignment to reference before masking & hashing.

diff --git src/hg/utils/otto/sarscov2phylo/pangoHash.sh src/hg/utils/otto/sarscov2phylo/pangoHash.sh
index 8756977..9cc8253 100755
--- src/hg/utils/otto/sarscov2phylo/pangoHash.sh
+++ src/hg/utils/otto/sarscov2phylo/pangoHash.sh
@@ -1,33 +1,33 @@
 #!/bin/bash
 source ~/.bashrc
 conda activate pangolin
 set -beEu -o pipefail
 
 inputFasta=$1
 outputHash=$2
 if [ $# -ge 3 ]; then
     threads=$3
 else
     threads=1
 fi
 
 pangoReference=~angie/github/pangolin/pangolin/data/reference.fasta
 trimStart=265
 trimEnd=29674
 
 tmpSam=$(mktemp)
 tmpLog=$(mktemp)
 tmpAliMaskedFasta=$(mktemp)
 
-minimap2 -a -x asm5 --sam-hit-only --secondary=no  -t $threads \
+minimap2 -a -x asm20 --sam-hit-only --secondary=no --score-N=0 -t $threads \
     $pangoReference $inputFasta -o $tmpSam &> $tmpLog
 gofasta sam toMultiAlign \
     -s $tmpSam \
     -t $threads \
     --reference $pangoReference \
     --trimstart $trimStart \
     --trimend $trimEnd \
     --trim \
     --pad > $tmpAliMaskedFasta 2>>$tmpLog
 faMd5 -threads=$threads $tmpAliMaskedFasta $outputHash
 rm $tmpSam $tmpLog $tmpAliMaskedFasta