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checking .//homerTools.h vs. /home/cbenner/data/data/homer/homer//homerTools.h
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checking .//Makefile vs. /home/cbenner/data/data/homer/homer//Makefile
1c1
< DEBUG = -O3 -Wall
---
> DEBUG = -O3 -Wall -g
14c14
< homer2 homer getMappableRegions makeTagDirectory getPeakTags makeUCSCfile getDifferentialPeaks mergePeaks genomeOntology homerTools analyzeHiC getGenomeTilingPeaks : Hashtable.o Motif.o statistics.o CommandLine.o homer.o getMappableRegions.o SeqTag.o makeTagDirectory.o getPeakTags.o findPeaks.o makeUCSCfile.o getDifferentialPeaks.o assignGenomeAnnotation.o mergePeaks.o genomeOntology.o homerTools.o analyzeHiC.o Motif2.o homer2.o Clustering.o getGenomeCorrelation.o
---
> findTADs homer2 homer getMappableRegions makeTagDirectory getPeakTags makeUCSCfile getDifferentialPeaks mergePeaks genomeOntology homerTools analyzeHiC getGenomeTilingPeaks : Hashtable.o Motif.o statistics.o CommandLine.o homer.o getMappableRegions.o SeqTag.o makeTagDirectory.o getPeakTags.o findPeaks.o makeUCSCfile.o getDifferentialPeaks.o assignGenomeAnnotation.o mergePeaks.o genomeOntology.o homerTools.o analyzeHiC.o Motif2.o homer2.o Clustering.o getGenomeCorrelation.o findTADsFromRelativeMatrix.o
19a20
> 	$(COMPILER) findTADsFromRelativeMatrix.o SeqTag.o Motif2.o Clustering.o Hashtable.o statistics.o $(LIBRARIES) $(DEBUG) -o findTADs
29,42d29
< 	cp findPeaks ../bin/
< 	cp mergePeaks ../bin/
< 	cp genomeOntology ../bin/
< 	cp getPeakTags ../bin/
< 	cp makeUCSCfile ../bin/
< 	cp getDifferentialPeaks ../bin/
< 	cp assignGenomeAnnotation ../bin/
< 	cp homerTools ../bin/
< 	cp analyzeHiC ../bin/
< 	cp homer ../bin/
< 	cp makeTagDirectory ../bin/
< 	cp homer2 ../bin/
< 	cp getMappableRegions ../bin/
< 	cp getGenomeTilingPeaks ../bin/getGenomeTilingPeaks
43a31,32
> findTADsFromRelativeMatrix.o : findTADsFromRelativeMatrix.cpp
> 	$(COMPILER) findTADsFromRelativeMatrix.cpp -c $(DEBUG)
89c78
< 	rm -f getMappableRegions makeTagDirectory findPeaks mergePeaks genomeOntology getPeakTags makeUCSCfile getDifferentialPeaks assignGenomeAnnotation homerTools homer homer2 analyzeHiC getGenomeTilingPeaks;
---
> 	rm -f getMappableRegions makeTagDirectory findPeaks mergePeaks genomeOntology getPeakTags makeUCSCfile getDifferentialPeaks assignGenomeAnnotation homerTools homer homer2 analyzeHiC getGenomeTilingPeaks findTADs;
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287a288,289
> 				} else if (strcmp(argv[i],"pe") == 0 || strcmp(argv[i],"PE") == 0) {
> 					fragLength = FRAGMENT_LEN_PE;
425a428,429
> 
> 		if (fragLength == FRAGMENT_LEN_PE) tags->setFragLength(FRAGMENT_LEN_AUTO);
571c575
< 	fprintf(stderr, "\t\t-fragLength <# | given> (Set estimated fragment length - given: use read lengths)\n");
---
> 	fprintf(stderr, "\t\t-fragLength <# | given | pe> (Set estimated fragment length or use PE length - given: use read lengths)\n");
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checking .//rwrappers.cpp vs. /home/cbenner/data/data/homer/homer//rwrappers.cpp
checking .//rwrappers.h vs. /home/cbenner/data/data/homer/homer//rwrappers.h
checking .//SeqTag.cpp vs. /home/cbenner/data/data/homer/homer//SeqTag.cpp
1973a1974,1976
> 	for (int i=0;i<numPeaks;i++) {
> 		fprintf(stderr, "\t%d\t%s\n", i, keys[i]);
> 	}
1981a1985,2004
> 
> void PeakLibrary::printBED2D(FILE* fp) {
> 	char** keys = peaks->keys();
> 	for (int i=0;i<numPeaks;i++) {
> 		//fprintf(stderr, "\t%d\t%s\n", i, keys[i]);
> 	}
> 	sortKeys(keys);
> 	for (int i=0;i<peaks->total;i++) {
> 		Peak* p = (Peak*) peaks->search(keys[i]);
> 		p->printBED2D(fp);
> 		delete [](keys[i]);
> 	}	
> 	delete []keys;
> }
> 
> void PeakLibrary::printCurrentPeakOrder(FILE* fp) {
> 	for (int i=0;i<numPeaks;i++) {
> 		peakOrder[i]->print(fp);
> 	}	
> }
2500a2524,2547
> void PeakLibrary::setDefaultPeakOrder(int mode) {
> 	if (peakOrder != NULL) {
> 		delete []peakOrder;
> 	}
> 	if (numPeaks < 1) return;
> 	peakOrder = new Peak*[numPeaks];
> 	char** keys = peaks->keys();
> 	for (int i=0;i<peaks->total;i++) {
> 		peakOrder[i] = (Peak*) peaks->search(keys[i]);
> 		delete [](keys[i]);
> 	}
> 	delete []keys;
> 
> 	if (mode == PEAK_SORT_BY_CHR_START_COORDINATE) { //0
> 		qsort(peakOrder,numPeaks,sizeof(Peak*),&cmpPeaks);
> 	} else if (mode == PEAK_SORT_BY_CHR_END_POS_COORDINATE) {
> 		qsort(peakOrder,numPeaks,sizeof(Peak*),&cmpPeaksEndPos);
> 	}
> 	for (int i=0;i<numPeaks;i++) {
> 		peakOrder[i]->index = i;
> 	}
> 
> }
> 
4337d4383
< 	//xxxxxxxxxxxxxxxxxxxxxxxx
4455a4502,4521
> int cmpPeaksEndPos(const void* a, const void* b) {
> 	char* ac = (*(Peak**)a)->chr;
> 	char* bc = (*(Peak**)b)->chr;
> 	int cc = chrcmp(&ac,&bc);
> 	if (cc != 0) return cc;
> 	int ad = (*(Peak**)a)->end;
> 	int bd = (*(Peak**)b)->end;
> 	if (ad < bd) return -1;
> 	if (ad > bd) return 1;
> 	int ap = (*(Peak**)a)->start;
> 	int bp = (*(Peak**)b)->start;
> 	if (ap < bp) return -1;
> 	if (ap > bp) return 1;
> 	char al = (*(Peak**)a)->strand;
> 	char bl = (*(Peak**)b)->strand;
> 	if (al < bl) return -1;
> 	if (al > bl) return 1;
> 	return 0;
> }
> 
5352a5419,5424
> 
> void Peak::printBED2D(FILE* fp) {
> 	fprintf(fp, "%s\t%d\t%d\t%s\t%d\t%d",chr,start,end,chr,start,end);
> 	fprintf(fp, "\t255,255,0\t%.3f\t%.3f", v, focusRatio);
> 	fprintf(fp, "\n");
> }
6954a7027,7036
> 
> 			if (fragmentLengthSetting == FRAGMENT_LEN_PE && numCols > 8) {
> 				int pelen = 0;
> 				sscanf(line[8],"%d",&pelen);
> 				if (pelen < 0) pelen *= -1;
> 				if (pelen > 0) {
> 					len = pelen;
> 				}
> 			}
> 
7045c7127,7129
< 			len = initLen;
---
> 			if (fragmentLengthSetting != FRAGMENT_LEN_PE) {
> 				len = initLen;
> 			}
checking .//SeqTag.h vs. /home/cbenner/data/data/homer/homer//SeqTag.h
102a103
> #define FRAGMENT_LEN_PE -123456
266a268,270
> #define PEAK_SORT_BY_CHR_START_COORDINATE 0 
> #define PEAK_SORT_BY_CHR_END_POS_COORDINATE 1
> 
1107a1112
> 	void printBED2D(FILE*);
1110a1116
> 	void printCurrentPeakOrder(FILE*);
1114a1121
> 	void setDefaultPeakOrder(int);
1261a1269
> 	void printBED2D(FILE* fp);
1461a1470
> int cmpPeaksEndPos(const void*, const void*);
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Files Not found in directory .//


Files Not found in directory /home/cbenner/data/data/homer/homer//
	findTADs
	findTADsFromRelativeMatrix.cpp
	findTADsFromRelativeMatrix.o
