src/hg/encode/validateFiles/validateFiles.c 1.13

Index: src/hg/encode/validateFiles/validateFiles.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/validateFiles/validateFiles.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -b -B -U 4 -r1.12 -r1.13
--- src/hg/encode/validateFiles/validateFiles.c	24 Mar 2009 15:51:04 -0000	1.12
+++ src/hg/encode/validateFiles/validateFiles.c	26 Mar 2009 06:55:39 -0000	1.13
@@ -2,9 +2,8 @@
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
-#include "sqlNum.h"
 #include "chromInfo.h"
 #include "jksql.h"
 
 static char const rcsid[] = "$Id$";
@@ -129,8 +128,64 @@
     }
 return h;
 }
 
+boolean checkUnsigned(char *file, int line, char *row, char *s, unsigned *val, char *name)
+/* Convert series of digits to unsigned integer about
+ * twice as fast as atoi (by not having to skip white
+ * space or stop except at the null byte.) 
+ * Returns true if conversion possible, and value is returned in 'val'
+ * Otherwise prints warning and returns false */
+{
+unsigned res = 0;
+char *p = s;
+char c;
+
+while (((c = *(p++)) >= '0') && (c <= '9'))
+    {
+    res *= 10;
+    res += c - '0';
+    }
+if (c != '\0')
+    {
+    warn("Error [file=%s, line=%d]: %s field invalid unsigned number (%s) [%s]", file, line, name, s, row);
+    return FALSE;
+    }
+*val = res;
+return TRUE;
+}
+
+boolean checkSigned(char *file, int line, char *row, char *s, int *val, char *name)
+/* Convert string to signed integer.  Unlike atol assumes
+ * all of string is number. 
+ * Returns true if conversion possible, and value is returned in 'val'
+ * Otherwise prints warning and returns false */
+{
+int res = 0;
+char *p, *p0 = s;
+
+if (*p0 == '-')
+    p0++;
+p = p0;
+while ((*p >= '0') && (*p <= '9'))
+    {
+    res *= 10;
+    res += *p - '0';
+    p++;
+    }
+/* test for invalid character, empty, or just a minus */
+if ((*p != '\0') || (p == p0))
+    {
+    warn("Error [file=%s, line=%d]: %s field invalid signed number (%s) [%s]", file, line, name, s, row);
+    return FALSE;
+    }
+if (*s == '-')
+    *val = -res;
+else
+    *val = res;
+return TRUE;
+}
+
 boolean checkString(char *file, int line, char *row, char *s, char *name)
 // Return TRUE if string has non-zero length
 // Othewise print warning that name column is empty and return FALSE
 {
@@ -339,10 +394,12 @@
 //        otherwise  then start < end
 // Othewise print warning and return FALSE
 {
 verbose(3,"[%s %3d] inputLine=%d [%s..%s] (chrom=%s,size=%u) [%s]\n", __func__, __LINE__, line, start, end, chrom, chromSize, row);
-unsigned s = sqlUnsigned(start);
-unsigned e = sqlUnsigned(end);
+unsigned s, e; 
+if (   !checkUnsigned(file, line, row, start, &s, "chromStart")
+    || !checkUnsigned(file, line, row, end, &e, "chromEnd"))
+    return FALSE;
 if (chromSize > 0)
     {
     if (e > chromSize)
 	{
@@ -379,11 +436,13 @@
 // Return TRUE if peak is >= 0 and <= (end-start)
 // Othewise print warning and return FALSE
 {
 verbose(3,"[%s %3d] inputLine=%d peak(%s) (%s,%s) [%s]\n", __func__, __LINE__, line, peak, start, end, row);
-unsigned p = sqlUnsigned(peak);
-unsigned s = sqlUnsigned(start);
-unsigned e = sqlUnsigned(end);
+unsigned p, s, e;
+if (   !checkUnsigned(file, line, row, peak, &p, "peak") 
+    || !checkUnsigned(file, line, row, start, &s, "chromStart")
+    || !checkUnsigned(file, line, row, end, &e, "chromEnd"))
+    return FALSE;
 if (p > e - s)
     {
     warn("Error [file=%s, line=%d]: peak(%u) past block length (%u) [%s]", file, line, p, e - s, row);
     return FALSE;
@@ -394,9 +453,11 @@
 boolean checkIntBetween(char *file, int line, char *row, char *val, char *name, int min, int max)
 // Return TRUE if val is integer between min and max
 // Othewise print warning and return FALSE
 {
-int i = sqlSigned(val);
+int i;
+if (!checkSigned(file, line, row, val, &i, name))
+    return FALSE;
 verbose(2,"[%s %3d] inputLine=%d [%s] -> [%d] [%s,%d..%d]\n", __func__, __LINE__, line, val, i, name, min, max);
 if (i >= min && i <= max)
     {
     verbose(2,"[%s %3d] min <= value <= max (%d <= %d <= %d)\n", __func__, __LINE__, min, i, max);
@@ -463,8 +524,11 @@
 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))
     {
     safecpy(buf, sizeof(buf), row);
@@ -491,8 +555,9 @@
 	if (++errs >= maxErrors)
 	    errAbort("Aborting .. found %d errors\n", errs);
 	}
     }
+dnaChars[(int)'.'] = savedot;
 return errs;
 }
 
 // tagAlign