8504d7cd72e01e7a28601edb5d4c98c7c87a7849 braney Thu Nov 16 20:16:51 2017 -0800 add filtering to bigNarrowPeak diff --git src/hg/hgTracks/encode.c src/hg/hgTracks/encode.c index f09a61a..1fcbf41 100644 --- src/hg/hgTracks/encode.c +++ src/hg/hgTracks/encode.c @@ -164,78 +164,164 @@ boolean and = FALSE; extraWhere = dyAddFilterAsInt(cart,tdb,extraWhere,SCORE_FILTER,"0:1000","score",&and); extraWhere = dyAddFilterAsDouble(cart,tdb,extraWhere,SIGNAL_FILTER,NULL,"signalValue",&and); extraWhere = dyAddFilterAsDouble(cart,tdb,extraWhere,PVALUE_FILTER,NULL,"pValue",&and); extraWhere = dyAddFilterAsDouble(cart,tdb,extraWhere,QVALUE_FILTER,NULL,"qValue",&and); if (sameString(extraWhere->string, "")) return NULL; return dyStringCannibalize(&extraWhere); } struct bigBedFilter /* Filter on a field in a bigBed file. */ { struct bigBedFilter *next; -int field; // the field number -enum {COMPARE_DOUBLE, COMPARE_INT} comparisonType; // the type of the comparison -union // the value to compare to - { - double dvalue; - int ivalue; - }; +int fieldNum; // the field number +enum {COMPARE_LESS, COMPARE_MORE, COMPARE_BETWEEN} comparisonType; // the type of the comparison +double value1, value2; }; -struct bigBedFilter *bigBedMakeFilter(struct cart *cart, struct trackDb *tdb, char *tdbName, char *fieldName) +struct bigBedFilter *bigBedMakeFilter(struct cart *cart, struct bbiFile *bbi, struct trackDb *tdb, char *filter, char *defaultLimits, char *field) /* Make a filter on this column if the trackDb or cart wants us to. */ { -return NULL; +struct bigBedFilter *ret = NULL; +char *setting = trackDbSettingClosestToHome(tdb, filter); +int fieldNum = bbExtraFieldIndex(bbi, field) + 3; +if (setting) + { + boolean invalid = FALSE; + double minValueTdb = 0,maxValueTdb = NO_VALUE; + colonPairToDoubles(setting,&minValueTdb,&maxValueTdb); + double minLimit=NO_VALUE,maxLimit=NO_VALUE,min=minValueTdb,max=maxValueTdb; + colonPairToDoubles(defaultLimits,&minLimit,&maxLimit); + getScoreFloatRangeFromCart(cart,tdb,FALSE,filter,&minLimit,&maxLimit,&min,&max); + if ((int)minLimit != NO_VALUE || (int)maxLimit != NO_VALUE) + { + // assume tdb default values within range! + // (don't give user errors that have no consequence) + if ((min != minValueTdb && (((int)minLimit != NO_VALUE && min < minLimit) + || ((int)maxLimit != NO_VALUE && min > maxLimit))) + || (max != maxValueTdb && (((int)minLimit != NO_VALUE && max < minLimit) + || ((int)maxLimit != NO_VALUE && max > maxLimit)))) + { + invalid = TRUE; + char value[64]; + if ((int)max == NO_VALUE) // min only is allowed, but max only is not + safef(value, sizeof(value), "entered minimum (%g)", min); + else + safef(value, sizeof(value), "entered range (min:%g and max:%g)", min, max); + char limits[64]; + if ((int)minLimit != NO_VALUE && (int)maxLimit != NO_VALUE) + safef(limits, sizeof(limits), "violates limits (%g to %g)", minLimit, maxLimit); + else if ((int)minLimit != NO_VALUE) + safef(limits, sizeof(limits), "violates lower limit (%g)", minLimit); + else //if ((int)maxLimit != NO_VALUE) + safef(limits, sizeof(limits), "violates uppper limit (%g)", maxLimit); + warn("invalid filter by %s: %s %s for track %s", field, value, limits, tdb->track); + } + } + if (invalid) + { + char filterLimitName[64]; + safef(filterLimitName, sizeof(filterLimitName), "%s%s", filter, _MIN); + cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName); + safef(filterLimitName, sizeof(filterLimitName), "%s%s", filter, _MAX); + cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName); + } + else if (((int)min != NO_VALUE && ((int)minLimit == NO_VALUE || minLimit != min)) + || ((int)max != NO_VALUE && ((int)maxLimit == NO_VALUE || maxLimit != max))) + // Assumes min==NO_VALUE or min==minLimit is no filter + // Assumes max==NO_VALUE or max==maxLimit is no filter! + { + AllocVar(ret); + ret->fieldNum = fieldNum; + if ((int)max == NO_VALUE || ((int)maxLimit != NO_VALUE && maxLimit == max)) + { + ret->comparisonType = COMPARE_MORE; + ret->value1 = min; + } + else if ((int)min == NO_VALUE || ((int)minLimit != NO_VALUE && minLimit == min)) + { + ret->comparisonType = COMPARE_LESS; + ret->value1 = max; + } + else + { + ret->comparisonType = COMPARE_BETWEEN; + ret->value1 = min; + ret->value2 = max; + } + } + } +return ret; } boolean bigBedFilterInterval(char **bedRow, struct bigBedFilter *filters) /* Go through a row and filter based on filters. Return TRUE if all filters are passed. */ { +struct bigBedFilter *filter; +for(filter = filters; filter; filter = filter->next) + { + double val = atof(bedRow[filter->fieldNum]); + + switch(filter->comparisonType) + { + case COMPARE_LESS: + if (!(val <= filter->value1)) + return FALSE; + break; + case COMPARE_MORE: + if (!(val >= filter->value1)) + return FALSE; + break; + case COMPARE_BETWEEN: + if (!((val >= filter->value1) && (val <= filter->value2))) + return FALSE; + break; + } + } return TRUE; } void bigNarrowPeakLoadItems(struct track *tg) /* Load a set of narrowPeaks from a bigNarrowPeak file. */ { struct linkedFeatures *lfList = NULL; enum encodePeakType pt = 0; int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMin", "0")); int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMax", "1000")); pt = narrowPeak; tg->customInt = pt; struct bbiFile *bbi = fetchBbiForTrack(tg); struct lm *lm = lmInit(0); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chromName, winStart, winEnd, 0, lm); int fieldCount = 10; char *bedRow[fieldCount]; char startBuf[16], endBuf[16]; struct bigBedFilter *filters = NULL; struct bigBedFilter *filter; -if ((filter = bigBedMakeFilter(cart, tg->tdb, SCORE_FILTER, "score")) != NULL) +if ((filter = bigBedMakeFilter(cart, bbi, tg->tdb, SCORE_FILTER, "0:1000", "score")) != NULL) slAddHead(&filters, filter); -if ((filter = bigBedMakeFilter(cart, tg->tdb, SIGNAL_FILTER, "signalValue")) != NULL) +if ((filter = bigBedMakeFilter(cart, bbi, tg->tdb, SIGNAL_FILTER, NULL, "signalValue")) != NULL) slAddHead(&filters, filter); -if ((filter = bigBedMakeFilter(cart, tg->tdb, PVALUE_FILTER, "pValue")) != NULL) +if ((filter = bigBedMakeFilter(cart, bbi, tg->tdb, PVALUE_FILTER, NULL, "pValue")) != NULL) slAddHead(&filters, filter); -if ((filter = bigBedMakeFilter(cart, tg->tdb, QVALUE_FILTER, "qValue")) != NULL) +if ((filter = bigBedMakeFilter(cart, bbi, tg->tdb, QVALUE_FILTER, NULL, "qValue")) != NULL) slAddHead(&filters, filter); for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow)); if (bigBedFilterInterval(bedRow, filters)) { struct encodePeak *peak = encodePeakGeneralLoad(bedRow, pt); struct linkedFeatures *lf = lfFromEncodePeak((struct slList *)peak, tg->tdb, scoreMin, scoreMax); if (lf) slAddHead(&lfList, lf); } }