19abdc13a11b5599c4cf96b29431d47cabb8e563
angie
  Mon Aug 29 21:48:05 2011 -0700
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR.  In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.

diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c
index 7b3efe0..fac0a14 100644
--- src/hg/hgTracks/simpleTracks.c
+++ src/hg/hgTracks/simpleTracks.c
@@ -12655,39 +12655,38 @@
 registerTrackHandler("fishClones", fishClonesMethods);
 registerTrackHandler("mapGenethon", genethonMethods);
 registerTrackHandler("stsMarker", stsMarkerMethods);
 registerTrackHandler("stsMap", stsMapMethods);
 registerTrackHandler("stsMapMouseNew", stsMapMouseMethods);
 registerTrackHandler("stsMapRat", stsMapRatMethods);
 registerTrackHandler("snpMap", snpMapMethods);
 registerTrackHandler("snp", snpMethods);
 registerTrackHandler("snp125", snp125Methods);
 registerTrackHandler("snp126", snp125Methods);
 registerTrackHandler("snp127", snp125Methods);
 registerTrackHandler("snp128", snp125Methods);
 registerTrackHandler("snp129", snp125Methods);
 registerTrackHandler("snp130", snp125Methods);
 registerTrackHandler("snp131", snp125Methods);
-registerTrackHandler("snp131Composite", snp125Methods);
-registerTrackHandler("snp131Clinical", snp125Methods);
-registerTrackHandler("snp131NonClinical", snp125Methods);
 registerTrackHandler("snp132", snp125Methods);
 registerTrackHandler("snp132Common", snp125Methods);
 registerTrackHandler("snp132Flagged", snp125Methods);
 registerTrackHandler("snp132Mult", snp125Methods);
-registerTrackHandler("snp132Patient", snp125Methods);
-registerTrackHandler("snp132NonUnique", snp125Methods);
+registerTrackHandler("snp134", snp125Methods);
+registerTrackHandler("snp134Common", snp125Methods);
+registerTrackHandler("snp134Flagged", snp125Methods);
+registerTrackHandler("snp134Mult", snp125Methods);
 registerTrackHandler("ld", ldMethods);
 registerTrackHandler("cnpSharp", cnpSharpMethods);
 registerTrackHandler("cnpSharp2", cnpSharp2Methods);
 registerTrackHandler("cnpIafrate", cnpIafrateMethods);
 registerTrackHandler("cnpIafrate2", cnpIafrate2Methods);
 registerTrackHandler("cnpSebat", cnpSebatMethods);
 registerTrackHandler("cnpSebat2", cnpSebat2Methods);
 registerTrackHandler("cnpFosmid", cnpFosmidMethods);
 registerTrackHandler("cnpRedon", cnpRedonMethods);
 registerTrackHandler("cnpLocke", cnpLockeMethods);
 registerTrackHandler("cnpTuzun", cnpTuzunMethods);
 registerTrackHandler("delConrad", delConradMethods);
 registerTrackHandler("delConrad2", delConrad2Methods);
 registerTrackHandler("delMccarroll", delMccarrollMethods);
 registerTrackHandler("delHinds", delHindsMethods);