c28c1ef92c57fb16bdb8b1ad6e78879d03d39311
donnak
  Mon Oct 14 13:47:24 2013 -0700
Fixed some typos and formatting probs in the usage message in conjunction with updating blat spec.
diff --git src/hg/pslReps/pslReps.c src/hg/pslReps/pslReps.c
index 9d76eac..be112e8 100644
--- src/hg/pslReps/pslReps.c
+++ src/hg/pslReps/pslReps.c
@@ -32,54 +32,54 @@
 double minCover = 0.0;
 boolean ignoreNs = FALSE; /* Ignore the n's when calculating coverage score, other
 			     wise n's count as mismatches. */
 boolean ignoreSize = FALSE;
 boolean noIntrons = FALSE;
 boolean singleHit = FALSE;
 boolean noHead = FALSE;
 boolean quiet = FALSE;
 int minNearTopSize = 30;
 char *coverQSizeFile = NULL;
 
 void usage()
 /* Print usage instructions and exit. */
 {
 errAbort(
-    "pslReps - analyse repeats and generate genome wide best\n"
-    "alignments from a sorted set of local alignments\n"
+    "pslReps - Analyze repeats and generate genome-wide best alignments from a\n"
+    "sorted set of local alignments\n"
     "usage:\n"
     "    pslReps in.psl out.psl out.psr\n"
-    "where in.psl is an alignment file generated by psLayout and\n"
-    "sorted by pslSort, out.psl is the best alignment output\n"
-    "and out.psr contains repeat info\n"
+    "where:\n"
+    "    in.psl is an alignment file generated by psLayout and sorted by pslSort\n" 
+    "    out.psl is the best alignment output\n"
+    "    out.psr contains repeat info\n"
     "options:\n"
-    "    -nohead don't add PSL header\n"
-    "    -ignoreSize Will not weigh in favor of larger alignments so much\n"
+    "    -nohead            Don't add PSL header.\n"
+    "    -ignoreSize        Will not weigh as much in favor of larger alignments.\n"
     "    -noIntrons         Will not penalize for not having introns when calculating\n"
-    "              size factor\n"
-    "    -singleHit  Takes single best hit, not splitting into parts\n"
-    "    -minCover=0.N minimum coverage to output.  Default is 0.\n"
-    "    -ignoreNs Ignore 'N's when calculating minCover.\n"
-    "    -minAli=0.N minimum alignment ratio\n"
-    "               default is 0.93\n"
-    "    -nearTop=0.N how much can deviate from top and be taken\n"
-    "               default is 0.01\n"
+    "                       size factor.\n"
+    "    -singleHit         Takes single best hit, not splitting into parts.\n"
+    "    -minCover=0.N      Minimum coverage to output.  Default is 0.\n"
+    "    -ignoreNs          Ignore Ns when calculating minCover.\n"
+    "    -minAli=0.N        Minimum alignment ratio.  Default is 0.93.\n"
+    "    -nearTop=0.N       How much can deviate from top and be taken.\n"
+    "                       Default is 0.01.\n"
     "    -minNearTopSize=N  Minimum size of alignment that is near top\n"
     "                       for alignment to be kept.  Default 30.\n"
     "    -coverQSizes=file  Tab-separate file with effective query sizes.\n"
     "                       When used with -minCover, this allows polyAs\n"
-    "                     to be excluded from the coverage calculation\n");
+    "                       to be excluded from the coverage calculation.\n");
 }
 
 /* hash table of query name to sizes */
 struct hash* coverQSizes = NULL;
 
 void loadCoverQSizes(char* coverQSizeFile)
 /* load coverage query sizes */
 {
 struct lineFile *lf = lineFileOpen(coverQSizeFile, TRUE);
 char *row[2];
 coverQSizes = hashNew(0);
 
 while (lineFileNextRowTab(lf, row, ArraySize(row)))
     {
     int qSize = sqlSigned(row[1]);