92d312887c6c5fcbec1e53c69bfe739a8da0d1c1
hiram
  Wed Jan 22 15:17:42 2014 -0800
clarify the backslash argument usage refs #11681
diff --git src/hg/featureBits/featureBits.c src/hg/featureBits/featureBits.c
index 496e6a9..4493075 100644
--- src/hg/featureBits/featureBits.c
+++ src/hg/featureBits/featureBits.c
@@ -90,30 +90,32 @@
   "                     alignment gaps and introns.\n"
   "   -bin=output.bin   Put bin counts in output file\n"
   "   -binSize=N        Bin size for generating counts in bin file (default 500000)\n"
   "   -binOverlap=N     Bin overlap for generating counts in bin file (default 250000)\n"
   "   -bedRegionIn=input.bed    Read in a bed file for bin counts in specific regions \n"
   "                     and write to bedRegionsOut\n"
   "   -bedRegionOut=output.bed  Write a bed file of bin counts in specific regions \n"
   "                     from bedRegionIn\n"
   "   -enrichment       Calculates coverage and enrichment assuming first table\n"
   "                     is reference gene track and second track something else\n"
   "                     Enrichment is the amount of table1 that covers table2 vs. the\n"
   "                     amount of table1 that covers the genome. It's how much denser\n"
   "                     table1 is in table2 than it is genome-wide.\n"
   "   '-where=some sql pattern'  Restrict to features matching some sql pattern\n"
   "You can include a '!' before a table name to negate it.\n"
+  "   To prevent your shell from interpreting the '!' you will need\n"
+  "   to use the backslash \\!, for example the gap table: \\!gap\n"
   "Some table names can be followed by modifiers such as:\n"
   "    :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"