e12ac8fea086d17ed824392a2bb3e425090ecb2d
jcasper
  Fri Sep 27 16:17:32 2019 -0700
Adding table browser selectors for normalization and resolution in .hic tracks, refs #18842

diff --git src/hg/hgTables/hic.c src/hg/hgTables/hic.c
index 2bc9253..14cde67 100644
--- src/hg/hgTables/hic.c
+++ src/hg/hgTables/hic.c
@@ -1,398 +1,423 @@
 /* hic - stuff to handle Hi-C stuff in table browser. */
 
 /* Copyright (C) 2019 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "localmem.h"
 #include "jksql.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "web.h"
 #include "bed.h"
 #include "hdb.h"
 #include "trackDb.h"
 #include "obscure.h"
 #include "hmmstats.h"
 #include "correlate.h"
 #include "asParse.h"
 #include "bbiFile.h"
 #include "bigBed.h"
 #include "hubConnect.h"
 #include "trackHub.h"
 #include "hgTables.h"
 #include "asFilter.h"
 #include "xmlEscape.h"
 #include "hic.h"
 #include "interact.h"
 #include "hgConfig.h"
 #include "chromAlias.h"
 #include "hicUi.h"
 
 boolean isHicTable(char *table)
 /* Return TRUE if table corresponds to a hic file. */
 {
 if (isHubTrack(table))
     {
     struct trackDb *tdb = hashFindVal(fullTableToTdbHash, table);
     return sameWord("hic", tdb->type);
     }
 else
     return trackIsType(database, table, curTrack, "hic", ctLookupName);
 }
 
 char *hicFileName(char *table, struct sqlConnection *conn)
 /* Return file name associated with hic.  This handles differences whether it's
  * a custom or built-in track.  Do a freeMem on returned string when done. */
 {
 char *fileName = bigFileNameFromCtOrHub(table, conn);
 // NB: Not planning to do hic tracks via filenames in tables.  If this changes,
 // add a check and a call to hicFileNameFromTable(), which will have to be written.
 return fileName;
 }
 
 struct hTableInfo *hicToHti(char *table)
 /* Get standard fields of hic into hti structure. */
 {
 struct hTableInfo *hti;
 AllocVar(hti);
 hti->rootName = cloneString(table);
 hti->isPos= TRUE;
 safecpy(hti->chromField, sizeof(hti->chromField), "chrom");
 safecpy(hti->startField, sizeof(hti->startField), "chromStart");
 safecpy(hti->endField, sizeof(hti->endField), "chromEnd");
 safecpy(hti->scoreField, sizeof(hti->scoreField), "value");
 hti->type = cloneString("hic");
 return hti;
 }
 
 struct slName *hicGetFields()
 /* Get fields of hic as simple name list.  We represent hic with an interact structure, so
  * this is really just an interact as object. */
 {
 struct asObject *as = interactAsObj();
 return asColNames(as);
 }
 
 struct sqlFieldType *hicListFieldsAndTypes()
 /* Get fields of hic as list of sqlFieldType (again, this is really just the list of interact fields. */
 {
 struct asObject *as = interactAsObj();
 return sqlFieldTypesFromAs(as);
 }
 
 #define HIC_NUM_BUF_SIZE 4096
 
 void hicRecordToRow(struct interact *sample, char *numBuf, char *row[INTERACT_NUM_COLS])
 /* Convert samAlignment data structure to an array of strings, using numBuf to store
  * ascii versions of numbers temporarily */
 {
 char *numPt = numBuf;
 char *numBufEnd = numBuf + HIC_NUM_BUF_SIZE;
 row[0] = sample->chrom;
 row[1] = numPt; numPt += sprintf(numPt, "%u", sample->chromStart); numPt += 1;
 row[2] = numPt; numPt += sprintf(numPt, "%u", sample->chromEnd); numPt += 1;
 row[3] = sample->name;
 row[4] = numPt; numPt += sprintf(numPt, "%u", sample->score); numPt += 1;
 row[5] = numPt; numPt += sprintf(numPt, "%f", sample->value); numPt += 1;
 row[6] = sample->exp;
 row[7] = numPt; numPt += sprintf(numPt, "%u", sample->color); numPt += 1;
 row[8] = sample->sourceChrom;
 row[9] = numPt; numPt += sprintf(numPt, "%u", sample->sourceStart); numPt += 1;
 row[10] = numPt; numPt += sprintf(numPt, "%u", sample->sourceEnd); numPt += 1;
 row[11] = sample->sourceName;
 row[12] = sample->sourceStrand;
 row[13] = sample->targetChrom;
 row[14] = numPt; numPt += sprintf(numPt, "%u", sample->targetStart); numPt += 1;
 row[15] = numPt; numPt += sprintf(numPt, "%u", sample->targetEnd); numPt += 1;
 row[16] = sample->targetName;
 row[17] = sample->targetStrand;
 assert(numPt < numBufEnd);
 }
 
 int hicCompare(const void *elem1, const void *elem2)
 /* Simple comparison function for sorting hic data in interact structures,
  * since it is not always returned in sorted order. */
 {
 const struct interact *first = *((struct interact **)elem1);
 const struct interact *second = *((struct interact **)elem2);
 int dif = strcmp(first->chrom, second->chrom);
 if (dif == 0)
     dif = first->chromStart - second->chromStart;
 return dif;
 }
 
 void hicTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f)
 /* Print out selected fields from hic.  If fields is NULL, then print out all fields. */
 {
 if (f == NULL)
     f = stdout;
 
 /* Convert comma separated list of fields to array. */
 int fieldCount = chopByChar(fields, ',', NULL, 0);
 char **fieldArray;
 AllocArray(fieldArray, fieldCount);
 chopByChar(fields, ',', fieldArray, fieldCount);
 
 /* Get list of all fields in hic and turn it into a hash of column indexes keyed by
  * column name. */
 struct hash *fieldHash = hashNew(0);
 struct slName *field, *fieldList = hicGetFields();
 int i;
 for (field = fieldList, i=0; field != NULL; field = field->next, ++i)
     {
     hashAddInt(fieldHash, field->name, i);
     }
 
 /* Create an array of column indexes corresponding to the selected field list. */
 int *columnArray;
 AllocArray(columnArray, fieldCount);
 for (i=0; i<fieldCount; ++i)
     {
     columnArray[i] = hashIntVal(fieldHash, fieldArray[i]);
     }
 
 /* Output row of labels */
 fprintf(f, "#%s", fieldArray[0]);
 for (i=1; i<fieldCount; ++i)
     fprintf(f, "\t%s", fieldArray[i]);
 fprintf(f, "\n");
 
 struct asObject *as = interactAsObj();
 struct asFilter *filter = NULL;
 
 if (anyFilter())
     {
     filter = asFilterFromCart(cart, db, table, as);
     if (filter)
         {
 	fprintf(f, "# Filtering on %d columns\n", slCount(filter->columnList));
 	}
     }
 
 /* Loop through outputting each region */
 struct region *region, *regionList = getRegions();
 
 int maxOut = bigFileMaxOutput();
 
 char *fileName = hicFileName(table, conn);
 struct hicMeta *fileInfo;
 char *errMsg = hicLoadHeader(fileName, &fileInfo, database);
 if (errMsg != NULL)
     errAbort("%s", errMsg);
 struct trackDb *tdb = hashFindVal(fullTableToTdbHash, table);
 char *norm = hicUiFetchNormalization(cart, tdb, fileInfo);
 
 for (region = regionList; region != NULL && (maxOut > 0); region = region->next)
     {
     struct interact *results = NULL, *result = NULL;
     int res = hicUiFetchResolutionAsInt(cart, tdb, fileInfo, region->end-region->start);
     char *errMsg = hicLoadData(fileInfo, res, norm, region->chrom, region->start, region->end,
             region->chrom, region->start, region->end, &results);
     if (errMsg != NULL)
         warn("%s", errMsg);
     slSort(&results, &hicCompare);
     char *row[INTERACT_NUM_COLS];
     char numBuf[HIC_NUM_BUF_SIZE];
     for (result = results; result != NULL && (maxOut > 0); result = result->next)
         {
 	hicRecordToRow(result, numBuf, row);
 	if (asFilterOnRow(filter, row))
 	    {
 	    int i;
 	    fprintf(f, "%s", row[columnArray[0]]);
 	    for (i=1; i<fieldCount; ++i)
 		fprintf(f, "\t%s", row[columnArray[i]]);
 	    fprintf(f, "\n");
 	    maxOut --;
 	    }
 	}
     }
 freeMem(fileName);
 
 if (maxOut == 0)
     errAbort("Reached output limit of %d data values, please make region smaller,\n\tor set a higher output line limit with the filter settings.", bigFileMaxOutput());
 /* Clean up and exit. */
 hashFree(&fieldHash);
 freeMem(fieldArray);
 freeMem(columnArray);
 }
 
 static void addFilteredBedsOnRegion(char *fileName, struct region *region,
 	char *table, struct asFilter *filter, struct lm *bedLm, struct bed **pBedList,
 	struct hash *idHash, int *pMaxOut)
 /* Add relevant beds in reverse order to pBedList */
 {
 struct hicMeta *fileInfo = NULL;
 char *errMsg = hicLoadHeader(fileName, &fileInfo, database);
 
 if (errMsg != NULL)
     {
     warn("%s", errMsg);
     }
 else
     {
     struct trackDb *tdb = hashFindVal(fullTableToTdbHash, table);
     int res = hicUiFetchResolutionAsInt(cart, tdb, fileInfo, region->end-region->start);
     char *norm = hicUiFetchNormalization(cart, tdb, fileInfo);
 
     struct interact *results = NULL, *result = NULL;
     errMsg = hicLoadData(fileInfo, res, norm, region->chrom, region->start, region->end,
             region->chrom, region->start, region->end, &results);
     if (errMsg != NULL)
         warn("%s", errMsg);
     slSort(&results, &hicCompare);
     char *row[INTERACT_NUM_COLS];
     char numBuf[HIC_NUM_BUF_SIZE];
     for (result=results; result != NULL; result = result->next)
         {
         hicRecordToRow(result, numBuf, row);
         if (asFilterOnRow(filter, row))
             {
             struct bed *bed;
             lmAllocVar(bedLm, bed);
             bed->chrom = lmCloneString(bedLm, result->chrom);
             bed->chromStart = result->chromStart;
             bed->chromEnd = result->chromEnd;
             bed->name = NULL;
             slAddHead(pBedList, bed);
             }
         (*pMaxOut)--;
         if (*pMaxOut <= 0)
             break;
         }
     }
 }
 
 struct bed *hicGetFilteredBedsOnRegions(struct sqlConnection *conn,
 	char *db, char *table, struct region *regionList, struct lm *lm,
 	int *retFieldCount)
 /* Get list of beds from HIC, in all regions, that pass filtering. */
 {
 int maxOut = bigFileMaxOutput();
 /* Figure out hic file name get column info and filter. */
 struct asObject *as = interactAsObj();
 struct asFilter *filter = asFilterFromCart(cart, db, table, as);
 struct hash *idHash = identifierHash(db, table);
 
 /* Get beds a region at a time. */
 struct bed *bedList = NULL;
 struct region *region;
 for (region = regionList; region != NULL; region = region->next)
     {
     char *fileName = hicFileName(table, conn);
     addFilteredBedsOnRegion(fileName, region, table, filter, lm, &bedList, idHash, &maxOut);
     freeMem(fileName);
     if (maxOut <= 0)
 	{
 	errAbort("Reached output limit of %d data values, please make region smaller,\n"
 	     "\tor set a higher output line limit with the filter settings.", bigFileMaxOutput());
 	}
     }
 slReverse(&bedList);
 return bedList;
 }
 
 
 void showSchemaHic(char *table, struct trackDb *tdb)
 /* Show schema on hic. */
 {
 struct sqlConnection *conn = NULL;
 if (!trackHubDatabase(database))
     conn = hAllocConn(database);
 char *fileName = hicFileName(table, conn);
 
 struct asObject *as = interactAsObj();
 hPrintf("<B>Database:</B> %s", database);
 hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;<B>Primary Table:</B> %s<br>", table);
 hPrintf("<B>HI-C File:</B> %s", fileName);
 hPrintf("<BR>\n");
 hPrintf("<B>Format description:</B> %s<BR>", as->comment);
 hPrintf("See the <A HREF=\"%s\" target=_blank>Interact Format Specification</A> for more details on "
         "the interact format, which is available for output here.  For details on the .hic format by "
         "the Aiden Lab, please see <a href=\"%s\" target=_blank>this page</a>.<BR>\n",
 	"../goldenPath/help/interact.html", "https://www.aidenlab.org/documentation.html");
 
 /* Put up table that describes fields. */
 hTableStart();
 hPrintf("<TR><TH>field</TH>");
 hPrintf("<TH>description</TH> ");
 puts("</TR>\n");
 struct asColumn *col;
 int colCount = 0;
 for (col = as->columnList; col != NULL; col = col->next)
     {
     hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
     hPrintf("<TD>%s</TD></TR>", col->comment);
     ++colCount;
     }
 hTableEnd();
 
 /* Put up another section with sample rows. */
 webNewSection("Sample Rows");
 hTableStart();
 
 /* Print field names as column headers for example */
 hPrintf("<TR>");
 int colIx = 0;
 for (col = as->columnList; col != NULL; col = col->next)
     {
     hPrintf("<TH>%s</TH>", col->name);
     ++colIx;
     }
 hPrintf("</TR>\n");
 
 struct hicMeta *fileInfo = NULL;
 char *errMsg = hicLoadHeader(fileName, &fileInfo, database);
 
 if (errMsg != NULL)
     {
     warn("%s", errMsg);
     }
 else
     {
     /* Print sample lines. */
     struct hash *chromAliasHash = chromAliasMakeLookupTable(database);
     char *chrName = fileInfo->chromNames[1]; // Skip 0, which is "All"
     struct chromAlias *a = hashFindVal(chromAliasHash, chrName);
     char *ucscChrName = NULL;
     if (a != NULL)
         ucscChrName = a->chrom;
     else
         ucscChrName = chrName;
 
     int maxRes = atoi(fileInfo->resolutions[0]);
 
     struct interact *sampleList = NULL, *sample = NULL;
     errMsg = hicLoadData(fileInfo, maxRes, "NONE", ucscChrName, 0, hChromSize(database, ucscChrName),
             ucscChrName, 0, hChromSize(database, ucscChrName), &sampleList);
     if (errMsg != NULL)
         warn("%s", errMsg);
     slSort(&sampleList, &hicCompare);
     char *row[INTERACT_NUM_COLS];
     char numBuf[HIC_NUM_BUF_SIZE];
     int count = 0;
     for (sample=sampleList; sample != NULL && count < 10; sample = sample->next, count++)
         {
         hicRecordToRow(sample, numBuf, row);
         hPrintf("<TR>");
         for (colIx=0; colIx<colCount; ++colIx)
             {
             hPrintf("<TD>");
             xmlEscapeStringToFile(row[colIx], stdout);
             hPrintf("</TD>");
             }
         hPrintf("</TR>\n");
         }
     }
 hTableEnd();
 printTrackHtml(tdb);
 
 /* Clean up and go home. */
 freeMem(fileName);
 hFreeConn(&conn);
 }
 
+void hicMainPageConfig(struct cart *cart, struct trackDb *tdb)
+/* Display Hi-C-specific track configuration options (resolution, normalization) on
+ * the main page. */
+{
+char *filename = trackDbSettingOrDefault(tdb, "bigDataUrl", NULL);
+struct hicMeta *meta = NULL;
+if (filename == NULL)
+    {
+    warn("Missing bigDataUrl setting for track %s", tdb->shortLabel);
+    return;
+    }
+char *errMsg = hicLoadHeader(filename, &meta, NULL);
+if (errMsg != NULL)
+    {
+    warn("Error fetching header for track %s: %s", tdb->shortLabel, errMsg);
+    return;
+    }
+hPrintf("<TR><TD><B>track options:</B> ");
+hPrintf("resolution ");
+hicUiResolutionDropDown(cart, tdb, meta);
+hPrintf("&nbsp;&nbsp;&nbsp;");
+hPrintf("score normalization ");
+hicUiNormalizationDropDown(cart, tdb, meta);
+hPrintf("</TD></TR>\n");
+}