6e5ee11ca95cd971984038cf65bae00d9c898707
galt
  Wed Jun 4 15:40:02 2014 -0700
Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
diff --git src/blatz/client.c src/blatz/client.c
index 685ad5f..ae667e5 100644
--- src/blatz/client.c
+++ src/blatz/client.c
@@ -1,122 +1,122 @@
 /* blatz client main routine.  The server does almost all the 
  * work.  This just loads DNA, sends it to the server, and
  * prints the response.  It also allows most of the server
  * alignment options to be overridden from the command line. */
 /* Copyright 2005 Jim Kent.  All rights reserved. */
 
 #include "common.h"   /* Compiler directives. Strings. Lists. */
 #include "options.h"  /* Command line option handling. */
-#include "errabort.h" /* Error and warning handling. */
+#include "errAbort.h" /* Error and warning handling. */
 #include "dnautil.h"  /* Byte <-> 2 bit conversion, reverseComplement etc. */
 #include "dnaseq.h"   /* Sequence, name, and size in a struct. */
 #include "obscure.h"  /* Handy eclectic utility collection. */
 #include "fa.h"       /* Read/write fasta sequence files. */
 #include "dnaLoad.h"  /* Read write dna sequences in many formats. */
 #include "net.h"      /* Network i/o, mostly TCP/IP oriented. */
 #include "bzp.h"      /* Blatz parameter structure. */
 #include "blatz.h"    /* Alignment routines. */
 
 int port = bzpDefaultPort;       /* Server TCP/IP port. */
 char *host = "localhost";        /* Name of computer server is running on. */
 
 static void usage()
 /* Explain usage and exit. */
 {
 struct bzp *bzp = bzpDefault();
 printf("blatzClient version %d - Ask server to do\n", bzpVersion());
 printf("cross-species DNA alignments and save results.\n");
 printf("usage:\n");
 printf("   blatzClient queryFile outputFile.\n");
 printf("The queryFile can be in fasta, nib, or 2bit format or a \n");
 printf("text file containing the names of the above files one per line.\n");
 printf("It's important that the sequence be repeat masked with repeats in\n");
 printf("lower case.\n");
 printf("Options: (defaults are shown for numerical parameters)\n");
 bzpClientOptionsHelp(bzp);
 printf("  -port=%d Use specified TCP/IP port\n", bzpDefaultPort);
 printf("  -host=%s Query specified host\n", host);
 noWarnAbort();
 }
 
 static struct optionSpec options[] = {
    BZP_CLIENT_OPTIONS
    {"host", OPTION_STRING},
    {"port", OPTION_INT},
    {NULL, 0},
 };
 
 
 static void sendOption(int sd, char *option)
 /* If option exists send it down socket. */
 {
 if (optionExists(option))
     {
     char buf[256];
     safef(buf, sizeof(buf), "%s %s", option, optionVal(option, NULL));
     netSendString(sd, buf);
     }
 }
 
 static void blatzClient(char *input, char *output)
 /* Send query message and dna to server and print result. */
 {
 struct dnaLoad *dl = dnaLoadOpen(input);
 struct dnaSeq *seq;
 FILE *f = mustOpen(output, "w");
 static struct optionSpec options[] = {
    BZP_CLIENT_OPTIONS
 };
 int i;
 while ((seq = dnaLoadNext(dl)) != NULL)
     {
     /* Connect */
     int sd = netMustConnect(host, port);
     FILE *sf = NULL;
 
     /* Send query command. */
     netSendString(sd, "query");
 
     /* Send options. */
     for (i=0; i<ArraySize(options); ++i)
         sendOption(sd, options[i].name);
 
     /* Send sequence. */
     if (optionExists("rna") || optionExists("unmask"))
         toUpperN(seq->dna, seq->size);
     else
 	{
 	if (seqIsLower(seq))
 	    warn("Sequence %s is all lower case, and thus ignored. Use -unmask "
 	         "flag to unmask lower case sequence.", seq->name);
 	}
     netSendString(sd, "seq");
     netSendString(sd, seq->name);
     netSendHugeString(sd, seq->dna);
     verbose(1, "%s\n", seq->name);
     dnaSeqFree(&seq);
 
     /* Get and save response. */
     sf = netFileFromSocket(sd);
     copyOpenFile(sf, f);
     carefulClose(&sf);
 
     /* Close connection */
     close(sd);
     }
 dnaLoadClose(&dl);
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 bzpTime(NULL);
 dnaUtilOpen();
 optionInit(&argc, argv, options);
 port = optionInt("port", port);
 host = optionVal("host", host);
 if (argc != 3)
     usage();
 blatzClient(argv[1], argv[2]);
 return 0;
 }