src/hg/encode/validateFiles/validateFiles.c 1.37

Index: src/hg/encode/validateFiles/validateFiles.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/validateFiles/validateFiles.c,v
retrieving revision 1.36
retrieving revision 1.37
diff -b -B -U 4 -r1.36 -r1.37
--- src/hg/encode/validateFiles/validateFiles.c	21 Mar 2010 18:03:25 -0000	1.36
+++ src/hg/encode/validateFiles/validateFiles.c	29 Mar 2010 20:25:45 -0000	1.37
@@ -28,8 +28,9 @@
 boolean mmPerPair;
 boolean nMatch;
 boolean isSort;
 boolean privateData;
+boolean allowOther;
 int quick;
 struct hash *chrHash = NULL;
 char dnaChars[256];
 char qualChars[256];
@@ -97,8 +98,9 @@
   "   -printFailLines              Print lines which fail validation to stdout\n"
   "   -isSort                      input is sorted by chrom\n"
 //"   -acceptDot                   Accept '.' as 'N' in DNA sequence\n"
   "   -version                     Print version\n"
+  "   -allowOther                  allow chromosomes that aren't native in BAM's\n"
   , MAX_ERRORS);
 }
 
 static struct optionSpec options[] = {
@@ -120,8 +122,9 @@
    {"privateData", OPTION_BOOLEAN},
 // {"acceptDot", OPTION_BOOLEAN},
    {"isSort", OPTION_BOOLEAN},
    {"version", OPTION_BOOLEAN},
+   {"allowOther", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 boolean checkMismatch(int ch1, int ch2)
@@ -1067,9 +1070,9 @@
 
 int validateBigWig(struct lineFile *lf, char *file)
 {
 if (chrHash == NULL)
-    errAbort("BAM validation requires the -chromInfo or -chromDb option\n");
+    errAbort("bigWig validation requires the -chromInfo or -chromDb option\n");
 
 int errs = 0;
 struct bbiFile *bbiFile;
 bbiFile = bigWigFileOpen(file);
@@ -1089,17 +1092,17 @@
     unsigned *size;
 
     if ( (size = hashFindVal(chrHash, chroms->name)) == NULL)
 	{
-	printf("bigWig contains invalid chromosome name: %s\n", 
+	warn("bigWig contains invalid chromosome name: %s\n", 
 	    chroms->name);
 	errs++;
 	}
     else
 	{
 	if (*size != chroms->size)
 	    {
-	    printf("bigWig contains chromosome with wrong length: %s should be %d bases, not %d bases\n", 
+	    warn("bigWig contains chromosome with wrong length: %s should be %d bases, not %d bases\n", 
 		chroms->name,
 		*size, chroms->size);
 	    errs++;
 	    }
@@ -1136,17 +1139,20 @@
     unsigned *size;
 
     if ( (size = hashFindVal(chrHash, head->target_name[ii])) == NULL)
 	{
-	printf("BAM contains invalid chromosome name: %s\n", 
+	if (!allowOther)
+	    {
+	    warn("BAM contains invalid chromosome name: %s\n", 
 	    head->target_name[ii]);
 	errs++;
 	}
+	}
     else
 	{
 	if (*size != head->target_len[ii])
 	    {
-	    printf("BAM contains chromosome with wrong length: %s should be %d bases, not %d bases\n", 
+	    warn("BAM contains chromosome with wrong length: %s should be %d bases, not %d bases\n", 
 		head->target_name[ii],
 		*size, head->target_len[ii]);
 	    errs++;
 	    }
@@ -1236,8 +1242,9 @@
 isSort         = optionExists("isSort");
 mmCheckOneInN  = optionInt("mmCheckOneInN", 1);
 quick          = optionExists("quick") ? optionInt("quick",QUICK_DEFAULT) : 0;
 colorSpace     = optionExists("colorSpace") || sameString(type, "csfasta");
+allowOther     = optionExists("allowOther");
 
 initArrays();
 dnaChars[(int)'.'] = 1;//optionExists("acceptDot");   // I don't think this is worth adding another option.  But it could be done.