src/hg/makeDb/doc/hg19.txt 1.60

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.59
retrieving revision 1.60
diff -b -B -U 4 -r1.59 -r1.60
--- src/hg/makeDb/doc/hg19.txt	9 Nov 2009 19:06:29 -0000	1.59
+++ src/hg/makeDb/doc/hg19.txt	9 Nov 2009 19:17:24 -0000	1.60
@@ -7870,8 +7870,13 @@
 # File emailed from Tin Louie <tinlouie at u.washington.edu>
 # in Evan Eichler's lab.
 # (2009-11-07, hartera, DONE) Re-loaded table after correcting some chromosome
 # names.  
+# NOTE: Received e-mail from Tin Louie suggesting that the otherSize 
+# column could be dropped. It is just the size of the otherChrom and it 
+# does not seem to be used for the track display or details page. It has the
+# correct description in the table schema so it is ok to keep it for now. 
+# In the future, this column could be dropped if it not useful.
     mkdir /hive/data/genomes/hg19/bed/genomicSuperDups
     cd /hive/data/genomes/hg19/bed/genomicSuperDups
    
     wget ftp://mesh.gs.washington.edu/pub/UCSC/hg19genomicSuperDups.gz
@@ -7909,9 +7914,17 @@
     # These are the contig names for random chroms that need to be corrected:
     grep -v random chroms | grep rando | sort | uniq > chromsToCorrect
     grep -v random otherChroms | grep rando | sort | uniq > otherChromsToCorrect
     diff chromsToCorrect otherChromsToCorrect
-    # No difference so use chromsToCorrect file. 
+    # No difference so use chromsToCorrect file. There are 7 chrom names that 
+    # need to be corrected and they are:
+#chr11_gl000202_rando
+#chr17_gl000203_rando
+#chr17_gl000204_rando
+#chr17_gl000205_rando
+#chr17_gl000206_rando
+#chr19_gl000209_rando
+#chr21_gl000210_rando 
     cp hg19genomicSuperDups hg19genomicSuperDups.orig
     foreach c (`cat chromsToCorrect`)
        perl -pi.bak -e "s/${c}/${c}m/g" hg19genomicSuperDups
     end