ae8dc8ab5e2c121398f31531c701ea064fb19aeb
braney
  Thu Apr 4 07:05:40 2019 -0700
add the ability to search the MANE track

diff --git src/hg/makeDb/doc/hg38/mane.txt src/hg/makeDb/doc/hg38/mane.txt
index 938653a..936c873 100644
--- src/hg/makeDb/doc/hg38/mane.txt
+++ src/hg/makeDb/doc/hg38/mane.txt
@@ -1,18 +1,23 @@
 #DONE braney 2019-03-13
 
 mkdir /cluster/data/hg38/bed/mane.0.5
 cd /cluster/data/hg38/bed/mane.0.5
 
 bigBedToBed https://ftp.ncbi.nlm.nih.gov/refseq/MANE/trackhub/data/release_0.5/MANE.GRCh38.v0.5.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
 
 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 our.bed /cluster/data/hg38/chrom.sizes our.bb -type=bed12+12 -as=$HOME/kent/src/hg/lib/mane.as -tab
+bedToBigBed -extraIndex=name our.bed /cluster/data/hg38/chrom.sizes our.bb -type=bed12+12 -as=$HOME/kent/src/hg/lib/mane.as -tab
 mkdir /gbdb/hg38/mane
 ln -s `pwd`/our.bb /gbdb/hg38/mane/mane.0.5.bb
+
+tawk '{print $13, $18, $19, $21, $22, $23, $24}' our.bed > our.ixInput
+ixIxx our.ixInput mane.0.5.ix mane.0.5.ixx
+ln -s `pwd`/mane.0.5.ix /gbdb/hg38/mane
+ln -s `pwd`/mane.0.5.ixx /gbdb/hg38/mane