void testEnd_getOtherBlockEnd(CuTest *testCase) { cactusEndTestSetup(); Block *block = block_construct(10, flower); End *leftEnd = block_get5End(block); End *rightEnd = block_get3End(block); CuAssertTrue(testCase, end_getOtherBlockEnd(end) == NULL); CuAssertTrue(testCase, end_getOtherBlockEnd(end_getReverse(end)) == NULL); CuAssertTrue(testCase, end_getOtherBlockEnd(leftEnd) == rightEnd); CuAssertTrue(testCase, end_getOtherBlockEnd(rightEnd) == leftEnd); CuAssertTrue(testCase, end_getOtherBlockEnd(end_getReverse(leftEnd)) == end_getReverse(rightEnd)); CuAssertTrue(testCase, end_getOtherBlockEnd(end_getReverse(rightEnd)) == end_getReverse(leftEnd)); cactusEndTestTeardown(); }
int mapGene(Cap *cap, int level, int exon, struct bed *gene, FILE *fileHandle){ /* *Following cactus adjacencies, starting from 'cap', find regions that overlap with *exons of input gene. Report chain relations of these regions with the exons. *cap: current cap. Level = chain level. exon = exon number. gene = bed record of gene */ int64_t exonStart, exonEnd; if(isStubCap(cap)){ Group *group = end_getGroup(cap_getEnd(cap)); Flower *nestedFlower = group_getNestedFlower(group); if(nestedFlower != NULL){//recursive call Cap *childCap = flower_getCap(nestedFlower, cap_getName(cap)); assert(childCap != NULL); exon = mapGene(childCap, level + 1, exon, gene, fileHandle); exonStart = gene->chromStarts->list[exon] + gene->chromStart; exonEnd = exonStart + gene->blockSizes->list[exon]; } } cap = cap_getAdjacency(cap); Cap *nextcap; int64_t capCoor; exonStart = gene->chromStarts->list[exon] + gene->chromStart; exonEnd = exonStart + gene->blockSizes->list[exon]; Block *block = end_getBlock(cap_getEnd(cap)); if(block == NULL){ moveCapToNextBlock(&cap); } while(!isStubCap(cap) && exon < gene->blockCount){ End *cend = cap_getEnd(cap); capCoor = cap_getCoordinate(cap);//Cap coordinate is always the coordinate on + strand nextcap = cap_getAdjacency(cap_getOtherSegmentCap(cap)); st_logInfo("capCoor: %d, nextCap: %d, eStart: %d, eEnd: %d. Exon: %d\n", capCoor, cap_getCoordinate(nextcap), exonStart, exonEnd, exon); //keep moving if nextBlock Start is still upstream of current exon if(cap_getCoordinate(nextcap) <= exonStart){ moveCapToNextBlock(&cap); st_logInfo("Still upstream, nextcap <= exonStart. Move to next chainBlock\n"); }else if(capCoor >= exonEnd){//Done with current exon, move to next st_logInfo("Done with current exon, move to next one\n\n"); fprintf(fileHandle, "\t\t</exon>\n");//end previous exon exon++; if(exon < gene->blockCount){ exonStart = gene->chromStarts->list[exon] + gene->chromStart; exonEnd = exonStart + gene->blockSizes->list[exon]; fprintf(fileHandle, "\t\t<exon id=\"%d\" start=\"%" PRIi64 "\" end=\"%" PRIi64 "\">\n", exon, exonStart, exonEnd); } }else{//current exon overlaps with current block Or with lower level flower Cap *oppcap = cap_getOtherSegmentCap(cap); st_logInfo("Current exon overlaps with current block or with lower flower\n"); if(cap_getCoordinate(oppcap) >= exonStart && exonEnd > capCoor){ mapBlockToExon(cap, level, fileHandle); if(exonEnd <= cap_getCoordinate(oppcap) + 1){ st_logInfo("Done with current exon, move to next one\n\n"); fprintf(fileHandle, "\t\t</exon>\n");//end previous exon exon++; if(exon < gene->blockCount){ exonStart = gene->chromStarts->list[exon] + gene->chromStart; exonEnd = exonStart + gene->blockSizes->list[exon]; fprintf(fileHandle, "\t\t<exon id=\"%d\" start=\"%" PRIi64 "\" end=\"%" PRIi64 "\">\n", exon, exonStart, exonEnd); } continue; } } //Traverse lower level flowers if exists Group *group = end_getGroup(end_getOtherBlockEnd(cend)); Flower *nestedFlower = group_getNestedFlower(group); if(nestedFlower != NULL){//recursive call Cap *childCap = flower_getCap(nestedFlower, cap_getName(cap_getOtherSegmentCap(cap))); assert(childCap != NULL); exon = mapGene(childCap, level + 1, exon, gene, fileHandle); exonStart = gene->chromStarts->list[exon] + gene->chromStart; exonEnd = exonStart + gene->blockSizes->list[exon]; } moveCapToNextBlock(&cap); } } return exon; }