src/hg/encode/validateFiles/validateFiles.c 1.29

Index: src/hg/encode/validateFiles/validateFiles.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/validateFiles/validateFiles.c,v
retrieving revision 1.28
retrieving revision 1.29
diff -b -B -U 4 -r1.28 -r1.29
--- src/hg/encode/validateFiles/validateFiles.c	30 Sep 2009 21:40:00 -0000	1.28
+++ src/hg/encode/validateFiles/validateFiles.c	10 Nov 2009 21:52:08 -0000	1.29
@@ -86,8 +86,9 @@
   "   -printOkLines                Print lines which pass validation to stdout\n"
   "   -quick[=N]                   Just test the first N lines of each file (default 1000)\n"
   "   -printFailLines              Print lines which fail validation to stdout\n"
   "   -isSort                      input is sorted by chrom\n"
+//"   -acceptDot                   Accept '.' as 'N' in DNA sequence\n"
   "   -nMatch                      N's do not count as a mismatch\n"
   "   -version                     Print version\n"
   , MAX_ERRORS);
 }
@@ -108,8 +109,9 @@
    {"mmPerPair", OPTION_BOOLEAN},
    {"mmCheckOneInN", OPTION_INT},
    {"quick", OPTION_INT},
    {"nMatch", OPTION_BOOLEAN},
+// {"acceptDot", OPTION_BOOLEAN},
    {"isSort", OPTION_BOOLEAN},
    {"version", OPTION_BOOLEAN},
    {NULL, 0},
 };
@@ -708,11 +710,8 @@
 int line = 0;
 int errs = 0;
 unsigned chromSize;
 int size;
-// Dot in place of N for tagaligns from Larry's group. Maybe remove this later.
-int savedot = dnaChars[(int)'.'];
-dnaChars[(int)'.'] = 1;
 verbose(2,"[%s %3d] paired=%d file(%s)\n", __func__, __LINE__, paired, file);
 while (lineFileNext(lf, &row, &size))
     {
     unsigned start, end;
@@ -745,9 +744,8 @@
 	if (++errs >= maxErrors)
 	    errAbort("Aborting .. found %d errors\n", errs);
 	}
     }
-dnaChars[(int)'.'] = savedot;
 return errs;
 }
 
 // tagAlign
@@ -1086,9 +1084,12 @@
 isSort         = optionExists("isSort");
 mmCheckOneInN  = optionInt("mmCheckOneInN", 1);
 quick          = optionExists("quick") ? optionInt("quick",QUICK_DEFAULT) : 0;
 colorSpace     = optionExists("colorSpace") || sameString(type, "csfasta");
+
 initArrays();
+dnaChars[(int)'.'] = 1;//optionExists("acceptDot");   // I don't think this is worth adding another option.  But it could be done.
+
 // Get chromInfo from DB or file
 if ( (chromDb = optionVal("chromDb", NULL)) != NULL)
     {
     if (!(ci = createChromInfoList(NULL, chromDb)))