0d6f83aa38e1a6ee04952a36ce1e03e8591199c5
braney
  Tue Jan 31 12:32:39 2017 -0800
turn on indel and query gap annotation for BLAT custom tracks

diff --git src/hg/hgBlat/hgBlat.c src/hg/hgBlat/hgBlat.c
index f3524be..fbb2ec7 100644
--- src/hg/hgBlat/hgBlat.c
+++ src/hg/hgBlat/hgBlat.c
@@ -624,31 +624,31 @@
 trashDirDateFile(&bigBedTn, "hgBlat", "bp", ".bb");
 char *bigBedFile = bigBedTn.forCgi;
 makeBigPsl(pslFilename, faFilename, db, bigBedFile);
 char *customTextFile = replaceSuffix(bigBedFile, "txt");
 FILE *fp = fopen(customTextFile, "w");
 char* host = getenv("HTTP_HOST");
 char* reqUrl = getenv("REQUEST_URI");
 // remove everything after / in URL
 char *e = strrchr(reqUrl, '/');
 if (e) *e = 0;
 
 char *trackName = NULL;
 char *trackDescription = NULL;
 
 getCustomName(db, cart, pslList, &trackName, &trackDescription);
-char *customTextTemplate = "track type=bigPsl pslFile=%s visibility=pack showAll=on htmlUrl=http://%s/goldenPath/help/hgUserPsl.html %s bigDataUrl=http://%s%s/%s name=\"%s\" description=\"%s\"\n";
+char *customTextTemplate = "track type=bigPsl indelDoubleInsert=on indelQueryInsert=on  pslFile=%s visibility=pack showAll=on htmlUrl=http://%s/goldenPath/help/hgUserPsl.html %s bigDataUrl=http://%s%s/%s name=\"%s\" description=\"%s\"\n";
 char *extraForMismatch = "showDiffBasesAllScales=. baseColorUseSequence=lfExtra baseColorDefault=diffBases"; 
 
 if (isProt)
     extraForMismatch = "";
 fprintf(fp, customTextTemplate, bigBedTn.forCgi, host, extraForMismatch, host, reqUrl, bigBedTn.forCgi, trackName, trackDescription);
 fclose(fp);
 
 char buffer[4096];
 safef(buffer, sizeof buffer, "http://%s%s/%s", host, reqUrl, customTextFile);
 
 return cloneString(buffer);
 }
     
 void blatSeq(char *userSeq, char *organism, char *database)
 /* Blat sequence user pasted in. */