c7da6212382f6efa86b8c2f4ca9f267d8273bfdc
max
  Mon Mar 9 03:08:07 2015 -0700
fixing the help message and the tester in hgBeacon.

diff --git src/hg/hgBeacon/help.txt src/hg/hgBeacon/help.txt
index 45272eb..f62b782 100644
--- src/hg/hgBeacon/help.txt
+++ src/hg/hgBeacon/help.txt
@@ -1,45 +1,52 @@
 <pre>
 A Genomics Alliance Beacon at UCSC, see http://ga4gh.org/#/beacon
 
 In collaboration with the Leiden Open Variation Database and Biobase/HGMD.
 
 parameters:
 - chromosome: 1 - 22, X, Y or M
 - position: 0-based position on chromosome
-- dataset: either lovd or hgmd. If not provided, queries both LOVD and HGMD.
-- reference: optional. if specified, has to be GRCh37
-- allele: A,C,T,G. Ignored for HGMD (HGMD gives out only
+- dataset: either "lovd" or "hgmd". If not provided, queries both LOVD and HGMD.
+"- reference: optional. if specified, has to be "GRCh37"
+- alternateBases: A,C,T or G. Ignored for HGMD (HGMD gives out only
   positions, not the alleles, these are only on their website)
 - format: if "text",  does not return JSON, but just one of the words "true",
       "false" or "overlap".  Easier to parse for simple shell scripts.
 
-To get more details about a variant:
+For alleles with a "true" reply, you can get more details about a variant from
+the source databases:
 - dataset lovd: Use the LOVD API to get all info, see chapter 9 of the 
   LOVD manual, http://www.lovd.nl/3.0/docs/LOVD_manual_3.0.pdf
   Or search manually on http://www.lovd.nl/3.0/home
 - dataset hgmd: Create an account on http://www.hgmd.cf.ac.uk/ and search
   manually for the variant.
 
 Note that only single-basepair substitutions are available from both databases.
 Insertions and deletions might be available with later versions of the Beacon
 API.
 
 Examples:
-http://%(host)s/cgi-bin/hgBeacon/query?dataset=lovd&chromosome=1&position=808921&allele=T
+http://%(host)s/cgi-bin/hgBeacon/query?dataset=lovd&chromosome=1&position=808921&alternateBases=T&format=text
 - returns "true"
 
-http://%(host)s/cgi-bin/hgBeacon/query?dataset=hgmd&chromosome=1&position=985954&allele=T
+http://%(host)s/cgi-bin/hgBeacon/query?dataset=lovd&chromosome=1&position=808921&alternateBases=T
+- same as before, but as a JSON string
+
+http://%(host)s/cgi-bin/hgBeacon/query?dataset=hgmd&chromosome=1&position=985954&alternateBases=T&format=text
 - returns "true", for any allele, as HGMD does not share the alleles
 
-http://%(host)s/cgi-bin/beacon3/query?dataset=hgmd&chromosome=1&position=2160493&allele=T
+http://%(host)s/cgi-bin/hgBeacon?dataset=hgmd&chromosome=1&position=2160493&alternateBases=T&format=text
 - returns "false", no information at this position
 
+http://%(host)s/cgi-bin/hgBeacon?dataset=hgmd&chromosome=1&position=2160493&alternateBases=T
+- same as before, but as a JSON string
+
 IP-based throttling:
 For each incoming request from an IP address, 75 msecs are added after every
 request, and every 15 secs 75 seconds are removed. No delay is imposed when
 fewer than 10 seconds have accumulated. This means that about 150 queries
 can be sent before a delay of about 10 seconds is imposed for an IP
 address. If a delay of 20 seconds has accumulated (=the client is using
 multi-threaded requests) the client IP is blocked from further requests
 until the delay falls under 20 seconds.
 </pre>