/* 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 "regexHelper.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);
    char *htmlKey = htmlEncode(key);
    if (def != NULL)
	printf("%s (%s)", htmlKey, def->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);
}

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(", ");
	if (el->missingData[j])
	    printf(".");
	else
	    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 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, char *track, 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)
	printf("<B>Hardy-Weinberg equilibrium:</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);
    }
vcfGenotypeTable(rec, 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);
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);
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->track, displayAls);
}

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);
char *fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, tdb->table, seqName);
hFreeConn(&conn);
int vcfMaxErr = -1;
struct vcfFile *vcff = NULL;
/* protect against temporary network error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
    {
    vcff = vcfTabixFileMayOpen(fileOrUrl, seqName, start, end, vcfMaxErr, -1);
    }
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