519e0946826199d1d9792fa8df5972843fce021c
angie
  Tue Aug 9 14:39:38 2011 -0700
Feature #2821 (VCF parser): improved representation of alleles:parse ref and comma-sep'd alt allele string into count and array
inside record, so callers don't all have to parse the comma-sep'd
alternate allele string.

diff --git src/hg/hgc/vcfClick.c src/hg/hgc/vcfClick.c
index 1ad1a7c..a26df9d 100644
--- src/hg/hgc/vcfClick.c
+++ src/hg/hgc/vcfClick.c
@@ -1,325 +1,303 @@
 /* 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 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. */
 {
 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, "."))
+if (rec->alleleCount < 2 || sameString(rec->alleles[1], "."))
     {
     printf(NA"<BR>\n");
     return;
     }
 struct vcfFile *vcff = rec->file;
-printListWithDescriptions(vcff, rec->alt, ",", vcff->altDefs);
+printKeysWithDescriptions(vcff, rec->alleleCount-1, &(rec->alleles[1]), 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 (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);
     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);
     if (def == NULL)
 	continue;
     printf("<TR><TD align=\"right\"><B>%s:</B></TD><TD>&nbsp;", el->key);
     int j;
     enum vcfInfoType type = def->type;
     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(", ");
 	vcfPrintDatum(stdout, el->values[j], type);
 	}
     if (def != NULL)
 	printf("</TD><TD>&nbsp;%s", def->description);
     else
 	printf("</TD><TD>");
     printf("</TD></TR>\n");
     }
 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, 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;
+static struct dyString *tmp1 = NULL;
 if (tmp1 == NULL)
-    {
     tmp1 = dyStringNew(0);
-    tmp2 = dyStringNew(0);
-    }
 vcfParseGenotypes(rec);
 // Tally genotypes and alleles for summary:
-// Note: this lumps all alternate alleles together.
-int refs = 0, alts = 0, refRefs = 0, refAlts = 0, altAlts = 0, phasedGts = 0;
+int refs = 0, alts = 0, refRefs = 0, refAlts = 0, altAlts = 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
 	alts++;
     if (!gt->isHaploid)
 	{
 	if (gt->hapIxB == 0)
 	    refs++;
 	else
 	    alts++;
 	if (gt->hapIxA == 0 && gt->hapIxB == 0)
 	    refRefs++;
-	else if (gt->hapIxA != 0 && gt->hapIxB != 0)
+	else if (gt->hapIxA == 1 && gt->hapIxB == 1)
 	    altAlts++;
-	else
+	else if ((gt->hapIxA == 1 && gt->hapIxB == 0) ||
+		 (gt->hapIxA == 0 && gt->hapIxB == 1))
 	    refAlts++;
+	else
+	    gtOther++;
 	}
     }
 printf("<B>Genotype count:</B> %d (%d phased)<BR>\n", vcff->genotypeCount, phasedGts);
 printf("<B>Alleles:</B> %s: %d (%.2f); %s: %d (%.2f)<BR>\n",
-       rec->ref, refs, (double)refs/(2*vcff->genotypeCount),
-       rec->alt, alts, (double)alts/(2*vcff->genotypeCount));
+       rec->alleles[0], refs, (double)refs/(2*vcff->genotypeCount),
+       rec->alleles[1], alts, (double)alts/(2*vcff->genotypeCount));
 if (vcff->genotypeCount > 1)
-    printf("<B>Genotypes:</B> %s/%s: %d (%.2f); %s/%s: %d (%.2f); %s/%s: %d (%.2f)<BR>\n",
-	   rec->ref, rec->ref, refRefs, (double)refRefs/vcff->genotypeCount,
-	   rec->ref, rec->alt, refAlts, (double)refAlts/vcff->genotypeCount,
-	   rec->alt, rec->alt, altAlts, (double)altAlts/vcff->genotypeCount);
+    {
+    printf("<B>Genotypes:</B> %s/%s: %d (%.2f); %s/%s: %d (%.2f); %s/%s: %d (%.2f)",
+	   rec->alleles[0], rec->alleles[0], refRefs, (double)refRefs/vcff->genotypeCount,
+	   rec->alleles[0], rec->alleles[1], refAlts, (double)refAlts/vcff->genotypeCount,
+	   rec->alleles[1], rec->alleles[1], altAlts, (double)altAlts/vcff->genotypeCount);
+    if (gtOther > 0)
+	printf("; other: %d (%.2f)", gtOther, (double)gtOther/vcff->genotypeCount);
+    printf("<BR>\n");
+    }
 jsBeginCollapsibleSection(cart, track, "genotypes", "Detailed genotypes", FALSE);
 dyStringClear(tmp1);
 dyStringAppend(tmp1, rec->format);
 enum vcfInfoType formatTypes[256];
 char *formatKeys[256];
 int formatCount = chopString(tmp1->string, ":", formatKeys, ArraySize(formatKeys));
 puts("<B>Genotype info key:</B><BR>");
 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");
-dyStringClear(tmp2);
-dyStringAppend(tmp2, rec->alt);
-char *altAlleles[256];
-unsigned char altCount = chopCommas(tmp2->string, altAlleles);
 for (i = 0;  i < vcff->genotypeCount;  i++)
     {
     struct vcfGenotype *gt = &(rec->genotypes[i]);
-    char *hapA = hapFromIx(rec->ref, altAlleles, altCount, gt->hapIxA);
-    char *hapB = gt->isHaploid ? NA : hapFromIx(rec->ref, altAlleles, altCount, gt->hapIxB);
+    char *hapA = rec->alleles[gt->hapIxA];
+    char *hapB = gt->isHaploid ? NA : rec->alleles[gt->hapIxB];
     char sep = 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 < formatCount;  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(", ");
 	    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);
 printCustomUrl(tdb, rec->name, TRUE);
 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);
+printf("<B>Reference allele:</B> %s<BR>\n", rec->alleles[0]);
 vcfAltAlleleDetails(rec);
 vcfQualDetails(rec);
 vcfFilterDetails(rec);
 vcfInfoDetails(rec);
 pgSnpCodingDetail(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);
 hFreeConn(&conn);
 int vcfMaxErr = 100;
 struct vcfFile *vcff = NULL;
 /* protect against temporary network error */
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     vcff = vcfTabixFileMayOpen(fileOrUrl, seqName, start, end, vcfMaxErr);
     }
 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);
 }
 
 
 #endif // no USE_TABIX