baf5e114387c11b4fea9072d90c480168745a0f9
hartera
  Tue Apr 30 09:28:05 2013 -0700
Changed retrocopy to retrogene for consistency.
diff --git src/hg/hgc/retroClick.c src/hg/hgc/retroClick.c
index 5be10a0..e55dc88 100644
--- src/hg/hgc/retroClick.c
+++ src/hg/hgc/retroClick.c
@@ -557,33 +557,33 @@
     {
     printf("<TR><TH>Blocks in retro:gap%%/intronsSpliced <TD>\n");
     printBlocks(psl, MAXBLOCKGAP, pslList);
     printf("</td></TR>\n");  
     }
 if (pslList != NULL)
     {
     printf("<TR><TH>Exons in parent:gap%% <TD>\n");
     printBlocks(pslList, MAXBLOCKGAP, NULL);
     printf("</td></TR>\n");  
     pslFreeList(&pslList);
     }
 #endif
 printf("<TR><TH>Length of PolyA Tail<TD>%d As&nbsp;out&nbsp;of&nbsp;%d&nbsp;bp </TR><TR><TH>%% A's from Parent PolyA tail (Position)<TD>%5.1f&nbsp;%%\n",pg->polyA,pg->polyAlen, (float)pg->polyA*100/(float)pg->polyAlen);
 if (pg->polyAstart < 0)
-    printf("&nbsp;(%d&nbsp;bp&nbsp;before&nbsp;end&nbsp;of&nbsp;retrocopy)<br>\n",-(pg->polyAstart));
+    printf("&nbsp;(%d&nbsp;bp&nbsp;before&nbsp;end&nbsp;of&nbsp;retrogene)<br>\n",-(pg->polyAstart));
 else
-    printf("&nbsp;(%d&nbsp;bp&nbsp;past&nbsp;end&nbsp;of&nbsp;retrocopy)<br>\n",pg->polyAstart);
+    printf("&nbsp;(%d&nbsp;bp&nbsp;past&nbsp;end&nbsp;of&nbsp;retrogene)<br>\n",pg->polyAstart);
 
 printf("<tr><th>mRNA Expression Evidence<td>");
 if (!sameString(pg->overName, "none"))
     printf("%s&nbsp;(overlap:&nbsp;&nbsp;%d&nbsp;bp)\n", pg->overName, pg->maxOverlap);
 else
     printf("No&nbsp;overlapping");
 printf("<TR><TH>BESTORF Score (>50 is good)<TD>%4.0f</td></TR>\n",pg->posConf);
 #ifdef score
 printf("<TR><TH>score function<TD>1:xon %d %4.1f conSS %d 2: ax %4.1f 3: pA %4.1f 4: net + %4.1f max (%d, %d) 5: procIntrons %d %4.1f 6:in.cnt %d -%4.1f 7:overlap - %4.1f  8:cov %d*(qe %d- qsz %d)/%d=%4.1f 9:tRep - %4.1f 10:oldintron %d %4.1f </td></TR>\n",
                 pg->exonCover,
                 wt[1]*(log(pg->exonCover+1)/log(2))*200 , 
                 pg->conservedSpliceSites,
                 wt[2]*(((log(pg->axtScore>0?pg->axtScore:1)/log(2))*170)-1000),
                 wt[3]*(log(pg->polyAlen+2)*200) ,
                 wt[4]*overlapOrtholog*10 , pg->overlapMouse, pg->overlapDog,