94d6890bdac9d6c53a6070eef9bcb82611c7d25f
chmalee
  Fri Feb 14 11:32:08 2020 -0800
Adding mouseOver to missense constraint track and finishing up track description, refs #20394

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index f8a601f..6b7647b 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33942,35 +33942,36 @@
     #     uint   chromEnd;   "End position in chromosome"
     #     string name;       "Name of item"
     #     uint   score;      "Score from 0-1000"
     #     char[1] strand;    "+ or -"
     #     uint thickStart;   "Start of where display should be thick (start codon)"
     #     uint thickEnd;     "End of where display should be thick (stop codon)"
     #     uint reserved;     "RGB color of item"
     #     int blockCount;    "Number of blocks"
     #     int[blockCount] blockSizes; "Comma separated list of block sizes"
     #     int[blockCount] chromStarts; "Start positions relative to chromStart"
     #     string geneName;     "Name of corresponding gene"
     #     int observed;      "Number of observed missense variants"
     #     float expected;      "Number of expected missense variants"
     #     float obs_exp;      "Observed/expected score"
     #     float chisq;       "Chi-Squared Difference"
+    #     string _mouseOver; "MouseOver label"
     #     )
 
     # now we can make the bigBed:
     ./aaToGenomic.py trimmedUtrs.txt 148353-3/Table_S4.csv | sort -k1,1 -k2,2n > missenseConstrained.bed
-    bedToBigBed -tab -type=bed12+5 -as=missenseBed.as missenseConstrained.bed /hive/data/genomes/hg19/chrom.sizes missenseConstrained.bb
+    bedToBigBed -tab -type=bed12+6 -as=missenseBed.as missenseConstrained.bed /hive/data/genomes/hg19/chrom.sizes missenseConstrained.bb
     # pass1 - making usageList (24 chroms): 5 millis
     # pass2 - checking and writing primary data (6507 records, 17 fields): 134 millis
     # only a few genes:
     cut -f13 missenseConstrained.bed | sort | uniq | wc -l
     # 2700
     ln -s /gbdb/hg19/gnomAD/missenseConstrained.bb missenseConstrained.bb
 
 ##############################################################################
 # adding RefSeq Select to NCBIRefSeq, Max, Feb 17 2020
 cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2019-11-21
 zcat download/*_genomic.gff.gz | egrep 'tag=(RefSeq|MANE) Select'  | cut -f9- | tr ';' '\n' | grep Name= | grep -v NP_ | cut -d= -f2 | sort -u > refseqSelectTranscripts.txt
 cat process/hg19.curated.gp | fgrep -f refseqSelectTranscripts.txt - > refseqSelect.curated.gp
 hgLoadGenePred -genePredExt hg19 ncbiRefSeqSelect refseqSelect.curated.gp
 wc -l refseqSelect.curated.gp
 21436 refseqSelect.curated.gp