4cab7f311cadce7428c1d7e1c4dfdcb0d3a43033
angie
  Wed Jul 27 10:32:19 2011 -0700
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting.  Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.

diff --git src/hg/hgc/vcfClick.c src/hg/hgc/vcfClick.c
index 4a1565d..4339481 100644
--- src/hg/hgc/vcfClick.c
+++ src/hg/hgc/vcfClick.c
@@ -1,83 +1,102 @@
 /* vcfTrack -- handlers for Variant Call Format data. */
 
 #ifdef USE_TABIX
 
 #include "common.h"
 #include "dystring.h"
 #include "errCatch.h"
 #include "hCommon.h"
 #include "hdb.h"
 #include "hgc.h"
 #include "htmshell.h"
+#include "jsHelper.h"
 #if (defined USE_TABIX && defined KNETFILE_HOOKS)
 #include "knetUdc.h"
 #include "udc.h"
 #endif//def USE_TABIX && KNETFILE_HOOKS
 #include "pgSnp.h"
 #include "trashDir.h"
 #include "vcf.h"
-
+#include "vcfUi.h"
 
 #define NA "<em>n/a</em>"
 
-static void printListWithDescriptions(struct vcfFile *vcff, char *str, char *sep, struct vcfInfoDef *infoDefs)
-/* Given a VCF field, its separator char and a list of vcfInfoDefs, print out a list
- * of values with descriptions if descriptions are available. */
+static void printKeysWithDescriptions(struct vcfFile *vcff, int wordCount, char **words,
+				      struct vcfInfoDef *infoDefs)
+/* Given an array of keys, print out a list of values with
+ * descriptions if descriptions are available. */
 {
-char *copy = cloneString(str);
-char *words[256];
-int i, wordCount = chopString(copy, sep, words, ArraySize(words));
+int i;
 for (i = 0;  i < wordCount; i++)
     {
     if (i > 0)
 	printf(", ");
     char *key = words[i];
     const struct vcfInfoDef *def = vcfInfoDefForKey(vcff, key);
     if (def != NULL)
 	printf("%s (%s)", htmlEncode(key), def->description);
     else
 	printf("%s", htmlEncode(key));
     }
 printf("<BR>\n");
 }
 
+static void printListWithDescriptions(struct vcfFile *vcff, char *str, char *sep, struct vcfInfoDef *infoDefs)
+/* Given a VCF field, its separator char and a list of vcfInfoDefs, print out a list
+ * of values with descriptions if descriptions are available. */
+{
+char *copy = cloneString(str);
+char *words[256];
+int wordCount = chopString(copy, sep, words, ArraySize(words));
+printKeysWithDescriptions(vcff, wordCount, words, infoDefs);
+}
+
 static void vcfAltAlleleDetails(struct vcfRecord *rec)
 /* If VCF header specifies any symbolic alternate alleles, pull in descriptions. */
 {
 printf("<B>Alternate allele(s):</B> ");
 if (sameString(rec->alt, "."))
     {
     printf(NA"<BR>\n");
     return;
     }
 struct vcfFile *vcff = rec->file;
 printListWithDescriptions(vcff, rec->alt, ",", vcff->altDefs);
 }
 
+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 (sameString(rec->filter, "PASS"))
-    printf("<B>Filter:</B> ");
+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;
-if (sameString(rec->filter, "."))
-    printf(NA"<BR>\n");
-else
-    printListWithDescriptions(vcff, rec->filter, ",", vcff->filterDefs);
+    printKeysWithDescriptions(vcff, rec->filterCount, rec->filters, vcff->filterDefs);
+    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=0>");
 int i;
 for (i = 0;  i < rec->infoCount;  i++)
     {
     struct vcfInfoElement *el = &(rec->infoElements[i]);
     const struct vcfInfoDef *def = vcfInfoDefForKey(vcff, el->key);
@@ -104,50 +123,50 @@
 puts("</TABLE>");
 }
 
 static char *hapFromIx(char *ref, char *altAlleles[], unsigned char altAlCount, unsigned char hapIx)
 /* Look up the allele specified by hapIx: 0 = ref, 1 & up = offset index into altAlleles */
 {
 if (hapIx == 0)
     return ref;
 else if (hapIx-1 < altAlCount)
     return altAlleles[hapIx-1];
 else
     errAbort("hapFromIx: index %d is out of range (%d alleles specified)", hapIx, altAlCount+1);
 return NULL;
 }
 
-static void vcfGenotypesDetails(struct vcfRecord *rec)
+static void vcfGenotypesDetails(struct vcfRecord *rec, char *track)
 /* Print genotypes in some kind of table... */
 {
 struct vcfFile *vcff = rec->file;
 if (vcff->genotypeCount == 0)
     return;
 static struct dyString *tmp1 = NULL, *tmp2 = NULL;
 if (tmp1 == NULL)
     {
     tmp1 = dyStringNew(0);
     tmp2 = dyStringNew(0);
     }
-// TODO: make this a collapsible section
+jsBeginCollapsibleSection(cart, track, "genotypes", "Detailed genotypes", FALSE);
 vcfParseGenotypes(rec);
 dyStringClear(tmp1);
 dyStringAppend(tmp1, rec->format);
 enum vcfInfoType formatTypes[256];
 char *formatKeys[256];
 int formatCount = chopString(tmp1->string, ":", formatKeys, ArraySize(formatKeys));
-puts("<BR><B>Genotype info key:</B><BR>");
+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))
@@ -175,67 +194,67 @@
 	    continue;
 	printf("<TD>");
 	struct vcfInfoElement *el = &(gt->infoElements[j]);
 	int k;
 	for (k = 0;  k < el->count;  k++)
 	    {
 	    if (k > 0)
 		printf(", ");
 	    vcfPrintDatum(stdout, el->values[k], formatTypes[j]);
 	    }
 	printf("</TD>");
 	}
     puts("</TR>");
     }
 hTableEnd();
+jsEndCollapsibleSection();
 }
 
 static void pgSnpCodingDetail(struct vcfRecord *rec)
 /* Translate rec into pgSnp (with proper chrom name) and call Belinda's
  * coding effect predictor from pgSnp details. */
 {
 if (hTableExists(database, "knownGene"))
     {
     struct pgSnp *pgs = pgSnpFromVcfRecord(rec);
     if (!sameString(rec->chrom, seqName))
 	// rec->chrom might be missing "chr" prefix:
 	pgs->chrom = seqName;
     printSeqCodDisplay(database, pgs);
     }
 }
 
 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);
-if (rec->file->genotypeCount > 0)
-    {
-    char cartVar[512];
-    safef(cartVar, sizeof(cartVar), "%s.centerVariantPos", tdb->track);
-    printf("<A HREF=\"%s&%s=%s:%d\">View haplotypes sorted by variants at this position</A><BR>\n",
-	   hgTracksPathAndSettings(), cartVar, seqName, rec->chromStart);
-    }
+static char *formName = "vcfCfgHapCenter";
+printf("<FORM NAME=\"%s\" ACTION=\"%s\">\n", formName, hgTracksName());
+vcfCfgHaplotypeCenter(cart, tdb, rec->file, rec->name, seqName, rec->chromStart, formName);
+printf("</FORM>\n");
 printPosOnChrom(seqName, rec->chromStart, rec->chromEnd, NULL, FALSE, rec->name);
 printf("<B>Reference allele:</B> %s<BR>\n", rec->ref);
 vcfAltAlleleDetails(rec);
-if (rec->qual != 0.0)
-    printf("<B>Call quality:</B> %.1f<BR>\n", rec->qual);
+vcfQualDetails(rec);
 vcfFilterDetails(rec);
 vcfInfoDetails(rec);
 pgSnpCodingDetail(rec);
-vcfGenotypesDetails(rec);
+// Wrapper table for collapsible section:
+puts("<TABLE>");
+vcfGenotypesDetails(rec, tdb->track);
+puts("</TABLE>");
 }
 
 void doVcfTabixDetails(struct trackDb *tdb, char *item)
 /* Show details of an alignment from a VCF file compressed and indexed by tabix. */
 {
 #if (defined USE_TABIX && defined KNETFILE_HOOKS)
 knetUdcInstall();
 if (udcCacheTimeout() < 300)
     udcSetCacheTimeout(300);
 #endif//def USE_TABIX && KNETFILE_HOOKS
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 struct sqlConnection *conn = hAllocConnTrack(database, tdb);
 // TODO: will need to handle per-chrom files like bam, maybe fold bamFileNameFromTable into this::
 char *fileOrUrl = bbiNameFromSettingOrTable(tdb, conn, tdb->table);