b6d7e4446453c3ab019b30024741247171a2f040
markd
  Mon Jun 29 20:04:40 2020 +0000
make sure data is 64-bit aligned, store offsets in headers to simplify

diff --git src/gfServer/gfServer.c src/gfServer/gfServer.c
index 160dde0..032ed0e 100644
--- src/gfServer/gfServer.c
+++ src/gfServer/gfServer.c
@@ -132,32 +132,31 @@
   "                   tile. Default is %d.\n"
   "   -noSimpRepMask  Suppresses simple repeat masking.\n"
   "   -maxDnaHits=N   Maximum number of hits for a DNA query that are sent from the server.\n"
   "                   Default is %d.\n"
   "   -maxTransHits=N Maximum number of hits for a translated query that are sent from the server.\n"
   "                   Default is %d.\n"
   "   -maxNtSize=N    Maximum size of untranslated DNA query sequence.\n"
   "                   Default is %d.\n"
   "   -maxAaSize=N    Maximum size of protein or translated DNA queries.\n"
   "                   Default is %d.\n"
   "   -perSeqMax=file File contains one seq filename (possibly with ':seq' suffix) per line.\n"
   "                   -maxDnaHits will be applied to each filename[:seq] separately: each may\n"
   "                   have at most maxDnaHits/2 hits.\n"
   "                   Useful for assemblies with many alternate/patch sequences.\n"
   "   -canStop        If set, a quit message will actually take down the server.\n"
-  "   -indexFile      File for index.  If -writeIndex is specified, the file is created,\n"
-  "                   otherwise it is loaded from this file.  Saving index can speed up\n"
+  "   -indexFile      Index file create by `gfServer index'. Saving index can speed up\n"
   "                   gfServer startup by two orders of magnitude.  The parameters must\n"
   "                   exactly match the parameters when the file is written or bad things\n"
   "                   will happen.\n"
   ,	gfVersion, repMatch, maxDnaHits, maxTransHits, maxNtSize, maxAaSize
   );
 
 }
 /*
   Note about file(s) specified in the start command:
       The path(s) specified here are sent back exactly as-is
       to clients such as gfClient, hgBlat, webBlat.
       It is intended that relative paths are used.
       Absolute paths starting with '/' tend not to work
       unless the client is on the same machine as the server.
       For use with hgBlat and webBlat, cd to the directory where the file is