5ac37dc9ecaeba30c49c34d0a2d0883bc45d3276
max
  Fri Mar 27 05:57:38 2015 +0100
Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"

This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.

diff --git src/hg/hgc/vcfClick.c src/hg/hgc/vcfClick.c
index bb65d7a..c1d23ac 100644
--- src/hg/hgc/vcfClick.c
+++ src/hg/hgc/vcfClick.c
@@ -1,479 +1,482 @@
 /* vcfTrack -- handlers for Variant Call Format data. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "dystring.h"
 #include "errCatch.h"
 #include "hCommon.h"
 #include "hdb.h"
 #include "hgc.h"
 #include "htmshell.h"
 #include "jsHelper.h"
 #include "pgSnp.h"
 #include "regexHelper.h"
 #include "trashDir.h"
 #include "knetUdc.h"
 #include "udc.h"
 #include "vcf.h"
 #include "vcfUi.h"
 
 #define NA "<em>n/a</em>"
 
 static void printKeysWithDescriptions(struct vcfFile *vcff, int wordCount, char **words,
 				      struct vcfInfoDef *infoDefs, boolean stripToSymbol)
 /* Given an array of keys, print out a list of values with descriptions if descriptions are
  * available.  If stripToSymbol, when searching infoDefs, pick the actual key out of
  * <>'s and other extraneous stuff (e.g. "(C)<DEL>" --> "DEL"). */
 {
 int i;
 for (i = 0;  i < wordCount; i++)
     {
     if (i > 0)
 	printf(", ");
     char *displayKey = words[i];
     char *descKey = displayKey;
     if (stripToSymbol)
         {
         char *p = strchr(displayKey, '<');
         if (p)
             {
             descKey = cloneString(p+1);
             p = strchr(descKey, '>');
             if (p)
                 *p = '\0';
             }
         }
     char *description = NULL;
     struct vcfInfoDef *def;
     for (def = infoDefs;  def != NULL;  def = def->next)
         if (sameString(descKey, def->key))
             {
             description = def->description;
             break;
             }
     char *htmlKey = htmlEncode(displayKey);
     if (description)
 	printf("%s (%s)", htmlKey, description);
     else
 	printf("%s", htmlKey);
     }
 printf("<BR>\n");
 }
 
 static void vcfAltAlleleDetails(struct vcfRecord *rec, char **displayAls)
 /* If VCF header specifies any symbolic alternate alleles, pull in descriptions. */
 {
 printf("<B>Alternate allele(s):</B> ");
 if (rec->alleleCount < 2 || sameString(rec->alleles[1], "."))
     {
     printf(NA"<BR>\n");
     return;
     }
 struct vcfFile *vcff = rec->file;
 printKeysWithDescriptions(vcff, rec->alleleCount-1, &(displayAls[1]), vcff->altDefs, TRUE);
 }
 
 static void vcfQualDetails(struct vcfRecord *rec)
 /* If VCF header specifies a quality/confidence score (not "."), print it out. */
 {
 printf("<B>Quality/confidence score:</B> %s<BR>\n", sameString(rec->qual, ".") ? NA : rec->qual);
 }
 
 static void vcfFilterDetails(struct vcfRecord *rec)
 /* If VCF header specifies any filters, pull in descriptions. */
 {
 if (rec->filterCount == 0 || sameString(rec->filters[0], "."))
     printf("<B>Filter:</B> "NA"<BR>\n");
 else if (rec->filterCount == 1 && sameString(rec->filters[0], "PASS"))
     printf("<B>Filter:</B> PASS<BR>\n");
 else
     {
     printf("<B>Filter failures:</B> ");
     printf("<font style='font-weight: bold; color: #FF0000;'>\n");
     struct vcfFile *vcff = rec->file;
     printKeysWithDescriptions(vcff, rec->filterCount, rec->filters, vcff->filterDefs, FALSE);
     printf("</font>\n");
     }
 }
 
 static void vcfInfoDetails(struct vcfRecord *rec)
 /* Expand info keys to descriptions, then print out keys and values. */
 {
 if (rec->infoCount == 0)
     return;
 struct vcfFile *vcff = rec->file;
 puts("<B>INFO column annotations:</B><BR>");
 puts("<TABLE border=0 cellspacing=0 cellpadding=2>");
 int i;
 for (i = 0;  i < rec->infoCount;  i++)
     {
     struct vcfInfoElement *el = &(rec->infoElements[i]);
     const struct vcfInfoDef *def = vcfInfoDefForKey(vcff, el->key);
     printf("<TR valign='top'><TD align=\"right\"><B>%s:</B></TD><TD style=width:15%%;'>",
            el->key);
     int j;
     enum vcfInfoType type = def ? def->type : vcfInfoString;
     if (type == vcfInfoFlag && el->count == 0)
 	printf("Yes"); // no values, so we can't call vcfPrintDatum...
     // However, if this is older VCF, type vcfInfoFlag might have a value.
     for (j = 0;  j < el->count;  j++)
 	{
 	if (j > 0)
 	    printf(", ");
 	if (el->missingData[j])
 	    printf(".");
 	else
 	    vcfPrintDatum(stdout, el->values[j], type);
 	}
     if (def != NULL)
 	printf("&nbsp;&nbsp;</TD><TD>%s", def->description);
     else
 	printf("</TD><TD>");
     printf("</TD></TR>\n");
     }
 puts("</TABLE>");
 }
 
 static void vcfGenotypeTable(struct vcfRecord *rec, char *track, char **displayAls)
 /* Put the table containing details about each genotype into a collapsible section. */
 {
 static struct dyString *tmp1 = NULL;
 if (tmp1 == NULL)
     tmp1 = dyStringNew(0);
 jsBeginCollapsibleSection(cart, track, "genotypes", "Detailed genotypes", FALSE);
 dyStringClear(tmp1);
 dyStringAppend(tmp1, rec->format);
 struct vcfFile *vcff = rec->file;
 enum vcfInfoType formatTypes[256];
 char *formatKeys[256];
 int formatCount = chopString(tmp1->string, ":", formatKeys, ArraySize(formatKeys));
 puts("<B>Genotype info key:</B><BR>");
 int i;
 for (i = 0;  i < formatCount;  i++)
     {
     if (sameString(formatKeys[i], vcfGtGenotype))
 	continue;
     const struct vcfInfoDef *def = vcfInfoDefForGtKey(vcff, formatKeys[i]);
     char *desc = def ? def->description : "<em>not described in VCF header</em>";
     printf("&nbsp;&nbsp;<B>%s:</B> %s<BR>\n", formatKeys[i], desc);
     formatTypes[i] = def->type;
     }
 hTableStart();
 puts("<TR><TH>Sample ID</TH><TH>Genotype</TH><TH>Phased?</TH>");
 for (i = 0;  i < formatCount;  i++)
     {
     if (sameString(formatKeys[i], vcfGtGenotype))
 	continue;
     printf("<TH>%s</TH>", formatKeys[i]);
     }
 puts("</TR>\n");
 for (i = 0;  i < vcff->genotypeCount;  i++)
     {
     struct vcfGenotype *gt = &(rec->genotypes[i]);
     char *hapA = ".", *hapB = ".";
     if (gt->hapIxA >= 0)
 	hapA = displayAls[(unsigned char)gt->hapIxA];
     if (gt->isHaploid)
 	hapB = "";
     else if (gt->hapIxB >= 0)
 	hapB = displayAls[(unsigned char)gt->hapIxB];
     char sep = gt->isHaploid ? ' ' : gt->isPhased ? '|' : '/';
     char *phasing = gt->isHaploid ? NA : gt->isPhased ? "Y" : "n";
     printf("<TR><TD>%s</TD><TD>%s%c%s</TD><TD>%s</TD>", vcff->genotypeIds[i],
 	   hapA, sep, hapB, phasing);
     int j;
     for (j = 0;  j < gt->infoCount;  j++)
 	{
 	if (sameString(formatKeys[j], vcfGtGenotype))
 	    continue;
 	printf("<TD>");
 	struct vcfInfoElement *el = &(gt->infoElements[j]);
 	int k;
 	for (k = 0;  k < el->count;  k++)
 	    {
 	    if (k > 0)
 		printf(", ");
 	    if (el->missingData[k])
 		printf(".");
 	    else
 		vcfPrintDatum(stdout, el->values[k], formatTypes[j]);
 	    }
 	printf("</TD>");
 	}
     puts("</TR>");
     }
 hTableEnd();
 jsEndCollapsibleSection();
 }
 
 static void ignoreEm(char *format, va_list args)
 /* Ignore warnings from genotype parsing -- when there's one, there
  * are usually hundreds more just like it. */
 {
 }
 
 static void vcfGenotypesDetails(struct vcfRecord *rec, struct trackDb *tdb, char **displayAls)
 /* Print summary of allele and genotype frequency, plus collapsible section
  * with table of genotype details. */
 {
 struct vcfFile *vcff = rec->file;
 if (vcff->genotypeCount == 0)
     return;
 // Wrapper table for collapsible section:
 puts("<TABLE>");
 pushWarnHandler(ignoreEm);
 vcfParseGenotypes(rec);
 popWarnHandler();
 // Tally genotypes and alleles for summary:
 int refs = 0, alts = 0, unks = 0;
 int refRefs = 0, refAlts = 0, altAlts = 0, gtUnk = 0, gtOther = 0, phasedGts = 0;
 int i;
 for (i = 0;  i < vcff->genotypeCount;  i++)
     {
     struct vcfGenotype *gt = &(rec->genotypes[i]);
     if (gt->isPhased)
 	phasedGts++;
     if (gt->hapIxA == 0)
 	refs++;
     else if (gt->hapIxA > 0)
 	alts++;
     else
 	unks++;
     if (!gt->isHaploid)
 	{
 	if (gt->hapIxB == 0)
 	    refs++;
 	else if (gt->hapIxB > 0)
 	    alts++;
 	else
 	    unks++;
 	if (gt->hapIxA == 0 && gt->hapIxB == 0)
 	    refRefs++;
 	else if (gt->hapIxA == 1 && gt->hapIxB == 1)
 	    altAlts++;
 	else if ((gt->hapIxA == 1 && gt->hapIxB == 0) ||
 		 (gt->hapIxA == 0 && gt->hapIxB == 1))
 	    refAlts++;
 	else if (gt->hapIxA < 0 || gt->hapIxB < 0)
 	    gtUnk++;
 	else
 	    gtOther++;
 	}
     }
 printf("<B>Genotype count:</B> %d", vcff->genotypeCount);
 if (differentString(seqName, "chrY"))
     printf(" (%d phased)", phasedGts);
 else
     printf(" (haploid)");
 puts("<BR>");
 int totalAlleles = refs + alts + unks;
 double refAf = (double)refs/totalAlleles;
 double altAf = (double)alts/totalAlleles;
 printf("<B>Alleles:</B> %s: %d (%.3f%%); %s: %d (%.3f%%)",
        displayAls[0], refs, 100*refAf, displayAls[1], alts, 100*altAf);
 if (unks > 0)
     printf("; unknown: %d (%.3f%%)", unks, 100 * (double)unks/totalAlleles);
 puts("<BR>");
 // Should be a better way to detect haploid chromosomes than comparison with "chrY":
 if (vcff->genotypeCount > 1 && differentString(seqName, "chrY"))
     {
     printf("<B>Genotypes:</B> %s/%s: %d (%.3f%%); %s/%s: %d (%.3f%%); %s/%s: %d (%.3f%%)",
 	   displayAls[0], displayAls[0], refRefs, 100*(double)refRefs/vcff->genotypeCount,
 	   displayAls[0], displayAls[1], refAlts, 100*(double)refAlts/vcff->genotypeCount,
 	   displayAls[1], displayAls[1], altAlts, 100*(double)altAlts/vcff->genotypeCount);
     if (gtUnk > 0)
 	printf("; unknown: %d (%.3f%%)", gtUnk, 100*(double)gtUnk/vcff->genotypeCount);
     if (gtOther > 0)
 	printf("; other: %d (%.3f%%)", gtOther, 100*(double)gtOther/vcff->genotypeCount);
     printf("<BR>\n");
     if (rec->alleleCount == 2)
 	{
 	boolean showHW = cartOrTdbBoolean(cart, tdb, VCF_SHOW_HW_VAR, FALSE);
 	if (showHW)
 	    printf("<B><A HREF=\"http://en.wikipedia.org/wiki/Hardy%%E2%%80%%93Weinberg_principle\" "
 		   "TARGET=_BLANK>Hardy-Weinberg equilibrium</A>:</B> "
 		   "P(%s/%s) = %.3f%%; P(%s/%s) = %.3f%%; P(%s/%s) = %.3f%%<BR>",
 		   displayAls[0], displayAls[0], 100*refAf*refAf,
 		   displayAls[0], displayAls[1], 100*2*refAf*altAf,
 		   displayAls[1], displayAls[1], 100*altAf*altAf);
 	}
     }
 puts("<BR>");
 vcfGenotypeTable(rec, tdb->track, displayAls);
 puts("</TABLE>");
 }
 
 static void pgSnpCodingDetail(struct vcfRecord *rec)
 /* Translate rec into pgSnp (with proper chrom name) and call Belinda's
  * coding effect predictor from pgSnp details. */
 {
 char *genePredTable = "knownGene";
 if (hTableExists(database, genePredTable))
     {
     struct pgSnp *pgs = pgSnpFromVcfRecord(rec);
     if (!sameString(rec->chrom, seqName))
 	// rec->chrom might be missing "chr" prefix:
 	pgs->chrom = seqName;
     printSeqCodDisplay(database, pgs, genePredTable);
     }
 }
 
 static void abbreviateLongSeq(char *seqIn, int endLength, boolean showLength, struct dyString *dy)
 /* If seqIn is longer than 2*endLength plus abbreviation fudge, abbreviate it
  * to its first endLength bases, ellipsis that says how many bases are skipped,
  * and its last endLength bases; add result to dy. */
 {
 int threshold = 2*endLength + 30;
 int seqInLen = strlen(seqIn);
 if (seqInLen > threshold)
     {
     dyStringAppendN(dy, seqIn, endLength);
     dyStringAppend(dy, "...");
     if (showLength)
 	{
 	int skippedLen = seqInLen-2*endLength;
 	dyStringPrintf(dy, "<%d bases>...", skippedLen);
 	}
     dyStringAppend(dy, seqIn+seqInLen-endLength);
     }
 else
     dyStringAppend(dy, seqIn);
 }
 
 static void makeDisplayAlleles(struct vcfRecord *rec, boolean showLeftBase, char leftBase,
 			       int endLength, boolean showLength, boolean encodeHtml,
 			       char **displayAls)
 /* If necessary, show the left base that we trimmed and/or abbreviate long sequences. */
 {
 struct dyString *dy = dyStringNew(128);
 int i;
 for (i = 0;  i < rec->alleleCount; i++)
     {
     dyStringClear(dy);
     if (showLeftBase)
 	dyStringPrintf(dy, "(%c)", leftBase);
     abbreviateLongSeq(rec->alleles[i], endLength, showLength, dy);
     if (encodeHtml)
 	displayAls[i] = htmlEncode(dy->string);
     else
 	displayAls[i] = cloneString(dy->string);
     }
 }
 
 static void vcfRecordDetails(struct trackDb *tdb, struct vcfRecord *rec)
 /* Display the contents of a single line of VCF, assumed to be from seqName
  * (using seqName instead of rec->chrom because rec->chrom might lack "chr"). */
 {
 printf("<B>Name:</B> %s<BR>\n", rec->name);
 // Since these are variants, if it looks like a dbSNP or dbVar ID, provide a link:
 if (regexMatch(rec->name, "^rs[0-9]+$"))
     {
     printf("<B>dbSNP:</B> ");
     printDbSnpRsUrl(rec->name, "%s", rec->name);
     puts("<BR>");
     }
 else if (regexMatch(rec->name, "^[en]ss?v[0-9]+$"))
     {
     printf("<B>dbVar:</B> ");
     printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/dbvar/variants/%s/\" "
 	   "TARGET=_BLANK>%s</A><BR>\n", rec->name, rec->name);
     }
 printCustomUrl(tdb, rec->name, TRUE);
 boolean hapClustEnabled = cartOrTdbBoolean(cart, tdb, VCF_HAP_ENABLED_VAR, TRUE);
 if (hapClustEnabled)
     {
     static char *formName = "vcfCfgHapCenter";
     printf("<FORM NAME=\"%s\" ACTION=\"%s\">\n", formName, hgTracksName());
     cartSaveSession(cart);
     vcfCfgHaplotypeCenter(cart, tdb, tdb->track, FALSE, rec->file, rec->name,
 			  seqName, rec->chromStart, formName);
     printf("</FORM>\n");
     }
 char leftBase = rec->alleles[0][0];
 unsigned int vcfStart = vcfRecordTrimIndelLeftBase(rec);
 boolean showLeftBase = (rec->chromStart == vcfStart+1);
 (void)vcfRecordTrimAllelesRight(rec);
 char *displayAls[rec->alleleCount];
 makeDisplayAlleles(rec, showLeftBase, leftBase, 20, TRUE, FALSE, displayAls);
 printPosOnChrom(seqName, rec->chromStart, rec->chromEnd, NULL, FALSE, rec->name);
 printf("<B>Reference allele:</B> %s<BR>\n", displayAls[0]);
 vcfAltAlleleDetails(rec, displayAls);
 vcfQualDetails(rec);
 vcfFilterDetails(rec);
 vcfInfoDetails(rec);
 pgSnpCodingDetail(rec);
 makeDisplayAlleles(rec, showLeftBase, leftBase, 5, FALSE, TRUE, displayAls);
 vcfGenotypesDetails(rec, tdb, displayAls);
 }
 
 void doVcfDetailsCore(struct trackDb *tdb, char *fileOrUrl, boolean isTabix)
 /* Show item details using fileOrUrl. */
 {
 genericHeader(tdb, NULL);
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 int vcfMaxErr = -1;
 struct vcfFile *vcff = NULL;
 /* protect against temporary network or parsing error */
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     if (isTabix)
 	vcff = vcfTabixFileMayOpen(fileOrUrl, seqName, start, end, vcfMaxErr, -1);
     else
 	vcff = vcfFileMayOpen(fileOrUrl, seqName, start, end, vcfMaxErr, -1, TRUE);
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     if (isNotEmpty(errCatch->message->string))
 	warn("%s", errCatch->message->string);
     }
 errCatchFree(&errCatch);
 if (vcff != NULL)
     {
     struct vcfRecord *rec;
     for (rec = vcff->records;  rec != NULL;  rec = rec->next)
 	if (rec->chromStart == start && rec->chromEnd == end) // in pgSnp mode, don't get name
 	    vcfRecordDetails(tdb, rec);
     }
 else
     printf("Sorry, unable to open %s<BR>\n", fileOrUrl);
 printTrackHtml(tdb);
 }
 
 
 #ifdef USE_TABIX
 
 void doVcfTabixDetails(struct trackDb *tdb, char *item)
 /* Show details of an alignment from a VCF file compressed and indexed by tabix. */
 {
+knetUdcInstall();
+if (udcCacheTimeout() < 300)
+    udcSetCacheTimeout(300);
 struct sqlConnection *conn = hAllocConnTrack(database, tdb);
 char *fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, tdb->table, seqName);
 hFreeConn(&conn);
 doVcfDetailsCore(tdb, fileOrUrl, TRUE);
 }
 
 
 #endif // no USE_TABIX
 
 
 void doVcfDetails(struct trackDb *tdb, char *item)
 /* Show details of an alignment from an uncompressed VCF file. */
 {
 struct customTrack *ct = lookupCt(tdb->track);
 struct sqlConnection *conn = NULL;
 char *table = tdb->table;
 if (ct)
     {
     conn = hAllocConn(CUSTOM_TRASH);
     table = ct->dbTableName;
     }
 else
     conn = hAllocConnTrack(database, tdb);
 char *fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, table, seqName);
 hFreeConn(&conn);
 doVcfDetailsCore(tdb, fileOrUrl, FALSE);
 }