06d7be056190c14b85e71bc12523f18ea6815b5e
markd
  Mon Dec 7 00:50:29 2020 -0800
BLAT mmap index support merge with master

diff --git src/hg/makeDb/doc/hg38/mane.txt src/hg/makeDb/doc/hg38/mane.txt
index d62bd98..c548369 100644
--- src/hg/makeDb/doc/hg38/mane.txt
+++ src/hg/makeDb/doc/hg38/mane.txt
@@ -1,23 +1,15 @@
-#DONE braney 2020-06-01
+#DONE braney 2020-10-27
 
-mkdir /cluster/data/hg38/bed/mane.0.9
-cd /cluster/data/hg38/bed/mane.0.9
+mkdir /cluster/data/hg38/bed/mane.0.92
+cd /cluster/data/hg38/bed/mane.0.92
 
-bigBedToBed https://ftp.ncbi.nlm.nih.gov/refseq/MANE/trackhub/data/release_0.9/MANE.GRCh38.v0.9.select.bb mane.bed
-tawk '{if (NR % 2) print}' mane.bed > ens.mane.bed
-tawk '{if ((NR % 2) == 0) print}' mane.bed > nm.mane.bed
+bigBedToBed https://ftp.ncbi.nlm.nih.gov/refseq/MANE/trackhub/data/release_0.92/MANE.GRCh38.v0.92.select_ensembl.bb our.bed
 
-tawk '{print $4,$18,$21,$19}' nm.mane.bed > nm.extra
-
-# make sure the gene symbols are matching up
-paste ens.mane.bed nm.extra | awk '{if ($19 != $25) print}'
-
-paste ens.mane.bed nm.extra | cut -f 1-24  > our.bed
-bedToBigBed -extraIndex=name our.bed /cluster/data/hg38/chrom.sizes our.bb -type=bed12+12 -as=$HOME/kent/src/hg/lib/mane.as -tab
+bedToBigBed -extraIndex=name our.bed /cluster/data/hg38/chrom.sizes our.bb -type=bed12+13 -as=$HOME/kent/src/hg/lib/mane.as -tab
 mkdir /gbdb/hg38/mane
-ln -s `pwd`/our.bb /gbdb/hg38/mane/mane.0.9.bb
+ln -s `pwd`/our.bb /gbdb/hg38/mane/mane.0.92.bb
 
 tawk '{print $13, $18, $19, $21, $22, $23, $24}' our.bed > our.ixInput
-ixIxx our.ixInput mane.0.9.ix mane.0.9.ixx
-ln -s `pwd`/mane.0.9.ix /gbdb/hg38/mane
-ln -s `pwd`/mane.0.9.ixx /gbdb/hg38/mane
+ixIxx our.ixInput mane.0.92.ix mane.0.92.ixx
+ln -s `pwd`/mane.0.92.ix /gbdb/hg38/mane
+ln -s `pwd`/mane.0.92.ixx /gbdb/hg38/mane