0ede364a2dcb452681933d5a3579b4f05d90a245
markd
  Sun Jul 5 15:16:27 2020 -0700
fixed bug where totalSeqSize was not stored in index, now hgBlat works

diff --git src/gfServer/tests/dynTester src/gfServer/tests/dynTester
index 119b7e0..0af4fa7 100755
--- src/gfServer/tests/dynTester
+++ src/gfServer/tests/dynTester
@@ -1,44 +1,48 @@
 #!/usr/bin/env python3
 
 # Test driver for dynamic server.  This is required because of the need to interact on stdin/stdout
 # using a somewhat binary protocol.
 
 import sys
 import argparse
 import subprocess
 
 debug = False
+valGrind = False
 
 def parseArgs():
     usage = """Run a test of qfServer dynserver"""
     parser = argparse.ArgumentParser(description=usage)
     parser.add_argument('--debug', action="store_true", default=False,
                         help="enable debug tracing")
+    parser.add_argument('--valgrind', action="store_true", default=False,
+                        help="run valgrind on gfServer without to valgrind.out")
     parser.add_argument('rootDir', type=str,
                         help="data root directory")
     parser.add_argument('queryType', type=str, choices=("query", "protQuery", "transQuery"),
                         help="query request: query, protQuery, or transQuery")
     parser.add_argument('genome', type=str,
                         help="genome name")
     parser.add_argument('queryFa', type=str,
                         help="query fasta")
     parser.add_argument('resultsOut', type=str,
                         help="out is saved here for checking ")
     args = parser.parse_args()
-    global debug
+    global debug, valgrind
     debug = args.debug
+    valgrind = args.valgrind
     return args
 
 gfSignature = "0ddf270562684f29"
 
 def readFastaSeqsFh(faFh):
     """read from one sequence from fasta"""
     seqs = []
     seq = ""
     for line in faFh:
         line = line.strip()
         if line.startswith('>'):
             if len(seq) > 0:
                 seqs.append(seq)
                 seq = ""
         elif len(line) > 0:
@@ -73,31 +77,34 @@
     fh.write(buf)
 
 def netSendString(fh, data):
     "Send a string down a socket - length byte first. (matches net.c)"
     fh.write(fh, bytes(len(data)))
     fh.write(data)
 
 def netRecieveString(fd):
     "Read string return it (matches net.c)"
     buf = readBytes(fd, 1)
     return readBytes(fd, buf[0])
 
 def serverStart(rootDir):
     "start server process"
     # unbuffered is required, as protocol is not line-terminate
-    cmd = ["gfServer"]
+    cmd = []
+    if valgrind:
+        cmd += ["valgrind", "--log-file=valgrind.out"]
+    cmd += ["gfServer"]
     if debug:
         cmd += ["-log=/dev/stderr", "-debugLog"]
     cmd += ["dynserver", rootDir]
     if debug:
         print("debug: start:", " ".join(cmd), file=sys.stderr)
     return subprocess.Popen(cmd, bufsize=0,
                             stdin=subprocess.PIPE, stdout=subprocess.PIPE)
 
 def serverWait(gfServer):
     "wait for server process to exit"
     gfServer.wait()
     if gfServer.returncode != 0:
         raise Exception("gfServer process exited with {}".format(gfServer.returncode))
 
 def readResults(gfServer, resultsFh):