b9e6acf3e5397b6be14a3071198e5aff2105f88f
jcasper
  Mon Apr 3 13:07:47 2017 -0700
featureBits usage message now says it will contact database for gap sizes unless -countGaps is specified

diff --git src/hg/featureBits/featureBits.c src/hg/featureBits/featureBits.c
index 4b78318..de33a58 100644
--- src/hg/featureBits/featureBits.c
+++ src/hg/featureBits/featureBits.c
@@ -111,30 +111,35 @@
   "    :exon:N          Break into exons and add N to each end of each exon\n"
   "    :cds             Break into coding exons\n"
   "    :intron:N        Break into introns, remove N from each end\n"
   "    :utr5, :utr3     Break into 5' or 3' UTRs\n" 
   "    :upstream:N      Consider the region of N bases before region\n"
   "    :end:N           Consider the region of N bases after region\n"
   "    :score:N         Consider records with score >= N \n"
   "    :upstreamAll:N   Like upstream, but doesn't filter out genes that \n"
   "                     have txStart==cdsStart or txEnd==cdsEnd\n"
   "    :endAll:N        Like end, but doesn't filter out genes that \n"
   "                     have txStart==cdsStart or txEnd==cdsEnd\n"
   "The tables can be bed, psl, or chain files, or a directory full of\n"
   "such files as well as actual database tables.  To count the bits\n"
   "used in dir/chrN_something*.bed you'd do:\n"
   "   featureBits database dir/_something.bed\n"
+  "NB: by default, featureBits omits gap regions from its calculation of the total\n"
+  "number of bases.  This requires a connecting to a database server using credentials\n"
+  "from a .hg.conf file (or similar).  If such a connection is not available, you will\n"
+  "need to specify -countGaps (which skips the database connection) in addition to\n"
+  "providing all tables as files or directories.\n"
   );
 }
 
 static struct chromInfo *fbCreateChromInfoList(char *name, char *database)
 /* Load up all chromosome infos. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 struct sqlResult *sr = NULL;
 char **row;
 int loaded=0;
 struct chromInfo *ret = NULL;
 unsigned totalSize = 0;
 
 if (sameWord(name, "all"))
     sr = sqlGetResult(conn, NOSQLINJ "select * from chromInfo");