b5cc11d8bbaab382885bffc053b12794c23da66c
giardine
  Mon Nov 8 08:58:54 2010 -0800
Changed errAborts to lineFileAborts so includes line number in error messages.  Improved pgSnp recognizer so type is not required in track line(#1595).
diff --git src/hg/lib/pgSnp.c src/hg/lib/pgSnp.c
index 44e0ba0..cfb4220 100644
--- src/hg/lib/pgSnp.c
+++ src/hg/lib/pgSnp.c
@@ -663,29 +663,29 @@
 item->chromStart = lineFileNeedNum(lf, row, 1);
 item->chromEnd = lineFileNeedNum(lf, row, 2);
 if (item->chromEnd < 1)
     lineFileAbort(lf, "chromEnd less than 1 (%d)", item->chromEnd);
 if (item->chromEnd < item->chromStart)
     lineFileAbort(lf, "chromStart after chromEnd (%d > %d)",
         item->chromStart, item->chromEnd);
 /* use pattern match to check values and counts both */
 /* alleles are separated by / and can be ACTG- */
 item->name = cloneString(row[3]);
 /* allele count, positive integer matching # of alleles */
 item->alleleCount = lineFileNeedNum(lf, row, 4);
 char alleles[128]; /* pattern to match alleles */
 safef(alleles, sizeof(alleles), "^[ACTG-]+(\\/[ACTG-]+){%d}$", item->alleleCount - 1);
 if (! matchRegex(row[3], alleles))
-    errAbort("invalid alleles %s", row[3]);
+    lineFileAbort(lf, "invalid alleles %s", row[3]);
 /* read count, comma separated list of numbers with above # of items */
 item->alleleFreq = cloneString(row[5]);
 char pattern[128];
 safef(pattern, sizeof(pattern), "^[0-9]+(,[0-9]+){%d}$", item->alleleCount - 1);
 if (! matchRegex(row[5], pattern))
-    errAbort("invalid allele frequency, %s with count of %d", row[5], item->alleleCount);
+    lineFileAbort(lf, "invalid allele frequency, %s with count of %d", row[5], item->alleleCount);
 /* scores, comma separated list of numbers with above # of items */
 item->alleleScores = cloneString(row[6]);
 safef(pattern, sizeof(pattern), "^[0-9.]+(,[0-9.]+){%d}$", item->alleleCount - 1);
 if (! matchRegex(row[6], pattern))
-    errAbort("invalid allele scores, %s with count of %d", row[6], item->alleleCount);
+    lineFileAbort(lf, "invalid allele scores, %s with count of %d", row[6], item->alleleCount);
 return item;
 }