c20579fc7c537c1736650125c5d264357d2cfa78
angie
  Mon Sep 18 13:15:16 2017 -0700
Big search & replace: use https instead of http for NCBI URLs.  refs #17793

diff --git src/hg/hgVai/hgVai.c src/hg/hgVai/hgVai.c
index e9ac3b3..1945435 100644
--- src/hg/hgVai/hgVai.c
+++ src/hg/hgVai/hgVai.c
@@ -31,31 +31,31 @@
 #include "udc.h"
 #include "knetUdc.h"
 #include "md5.h"
 #include "regexHelper.h"
 #include "hAnno.h"
 #include "annoGratorQuery.h"
 #include "annoGratorGpVar.h"
 #include "annoFormatVep.h"
 #include "annoStreamBigBed.h"
 #include "annoStreamDb.h"
 
 #include "libifyMe.h"
 
 #define GENCODE_TAG_DOC_URL "\"http://www.gencodegenes.org/gencode_tags.html\""
 #define GENCODE_BASIC_DOC_URL "\"http://www.gencodegenes.org/faq.html\""
-#define REFSEQ_STATUS_DOC_URL "\"http://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_status_codes\""
+#define REFSEQ_STATUS_DOC_URL "\"https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_status_codes\""
 #define APPRIS_DOC_URL "\"http://appris.bioinfo.cnio.es/#/help/database\""
 
 /* Global Variables */
 struct cart *cart;		/* CGI and other variables */
 struct hash *oldVars = NULL;	/* The cart before new cgi stuff added. */
 char *genome = NULL;		/* Name of genome - mouse, human, etc. */
 char *database = NULL;		/* Current genome database - hg17, mm5, etc. */
 char *regionType = NULL;	/* genome, ENCODE pilot regions, or specific position range. */
 struct grp *fullGroupList = NULL;	/* List of all groups. */
 struct trackDb *fullTrackList = NULL;	/* List of all tracks in database. */
 static struct pipeline *compressPipeline = (struct pipeline *)NULL;
 
 
 // Null terminated list of CGI Variables we don't want to save permanently:
 char *excludeVars[] = {"Submit", "submit", "hgva_startQuery", NULL,};
@@ -633,31 +633,31 @@
 	errAbort("dbNsfpDescFromTableName: invalid PolyPhen2 subset type (%d)", subset);
     }
 else if (sameString(tableName, "dbNsfpMutationTaster"))
 	return formatDesc("http://www.mutationtaster.org/", "MutationTaster",
 			  "(A = disease causing automatic, D = disease causing, "
 			  "N = polymorphism, P = polymorphism automatic)", doHtml);
 else if (sameString(tableName, "dbNsfpMutationAssessor"))
 	return formatDesc("http://mutationassessor.org/", "MutationAssessor",
 			  "(high or medium: predicted functional; "
 			  "low or neutral: predicted non-functional)", doHtml);
 else if (sameString(tableName, "dbNsfpLrt"))
 	return formatDesc("http://www.genetics.wustl.edu/jflab/lrt_query.html",
 			  "Likelihood ratio test (LRT)",
 			  "(D = deleterious, N = Neutral, U = unknown)", doHtml);
 else if (sameString(tableName, "dbNsfpVest"))
-    return formatDesc("http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665549/",
+    return formatDesc("https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665549/",
                       "Variant Effect Scoring Tool (VEST)",
                       "(scores [0-1] predict confidence that a change is deleterious", doHtml);
 else if (sameString(tableName, "dbNsfpGerpNr"))
 	return formatDesc("http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html",
 			  "GERP++", "Neutral Rate (NR)", doHtml);
 else if (sameString(tableName, "dbNsfpGerpRs"))
 	return formatDesc("http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html",
 			  "GERP++", "Rejected Substitutions (RS)", doHtml);
 else if (sameString(tableName, "dbNsfpInterPro"))
 	return formatDesc("http://www.ebi.ac.uk/interpro/", "InterPro", "protein domains", doHtml);
 return NULL;
 }
 
 struct slName *findDbNsfpTables()
 /* See if this database contains dbNSFP tables. */
@@ -774,31 +774,31 @@
     }
 if (retTdb == NULL)
     return foundIt;
 else
     *retTdb = tdb;
 return TRUE;
 }
 
 void selectDbSnp(boolean gotSnp)
 /* Offer to include rsID (and other fields, or leave that for advanced output??) if available */
 {
 if (!gotSnp)
     return;
 startCollapsibleSection("dbSnp", "Known variation", TRUE);
 cartMakeCheckBox(cart, "hgva_rsId", TRUE);
-printf("Include <A HREF='http://www.ncbi.nlm.nih.gov/projects/SNP/' TARGET=_BLANK>dbSNP</A> "
+printf("Include <A HREF='https://www.ncbi.nlm.nih.gov/projects/SNP/' TARGET=_BLANK>dbSNP</A> "
        "rs# ID if one exists<BR>\n");
 puts("<BR>");
 endCollapsibleSection();
 }
 
 #define GENCODE_PREFIX "wgEncodeGencode"
 
 struct slName *getGencodeTagVersions()
 /* Return a list of version strings from the ends of wgEncodeGencodeTag% tables. */
 {
 static struct slName *tagVersions = NULL;
 if (tagVersions == NULL)
     {
     struct sqlConnection *conn = hAllocConn(database);
     struct slName *tagTables = sqlQuickList(conn,