// Returns a hash mapping from sequence header to sequence data. static stHash *readFastaFile(char *filename) { FILE *fasta = fopen(filename, "r"); if (fasta == NULL) { st_errnoAbort("Could not open fasta file %s", filename); } stHash *headerToData = stHash_construct3(stHash_stringKey, stHash_stringEqualKey, free, free); struct List *seqs = constructEmptyList(0, NULL); struct List *seqLengths = constructEmptyList(0, free); struct List *headers = constructEmptyList(0, free); fastaRead(fasta, seqs, seqLengths, headers); for (int64_t i = 0; i < seqs->length; i++) { char *fullHeader = headers->list[i]; stList *headerTokens = stString_splitByString(fullHeader, " "); char *usableHeader = stString_copy(stList_get(headerTokens, 0)); stHash_insert(headerToData, usableHeader, seqs->list[i]); stList_destruct(headerTokens); } destructList(seqs); destructList(seqLengths); destructList(headers); return headerToData; }
static void dumpBlockInfo(stPinchThreadSet *threadSet, const char *fileName) { stPinchThreadSetBlockIt blockIt = stPinchThreadSet_getBlockIt(threadSet); FILE *file = fopen(fileName, "w"); if (file == NULL) { st_errnoAbort("couldn't open debug file"); } stPinchBlock *block; while ((block = stPinchThreadSetBlockIt_getNext(&blockIt)) != NULL) { uint64_t supportingHomologies = stPinchBlock_getNumSupportingHomologies(block); uint64_t possibleSupportingHomologies = numPossibleSupportingHomologies(block, flower); double support = ((double) supportingHomologies) / possibleSupportingHomologies; fprintf(file, "%" PRIi64 "\t%" PRIi64 "\t%" PRIi64 "\t%" PRIi64 "\t%lf\n", stPinchBlock_getDegree(block), stPinchBlock_getLength(block), supportingHomologies, possibleSupportingHomologies, support); } fclose(file); }
int main(int argc, char *argv[]) { char * logLevelString = NULL; char * cactusDiskDatabaseString = NULL; int64_t i, j; int64_t spanningTrees = 10; int64_t maximumLength = 1500; bool useProgressiveMerging = 0; float matchGamma = 0.5; bool useBanding = 0; int64_t k; stList *listOfEndAlignmentFiles = NULL; char *endAlignmentsToPrecomputeOutputFile = NULL; bool calculateWhichEndsToComputeSeparately = 0; int64_t largeEndSize = 1000000; int64_t chainLengthForBigFlower = 1000000; int64_t longChain = 2; char *ingroupCoverageFilePath = NULL; int64_t minimumSizeToRescue = 1; double minimumCoverageToRescue = 0.0; PairwiseAlignmentParameters *pairwiseAlignmentBandingParameters = pairwiseAlignmentBandingParameters_construct(); /* * Setup the input parameters for cactus core. */ bool pruneOutStubAlignments = 0; /* * Parse the options. */ while (1) { static struct option long_options[] = { { "logLevel", required_argument, 0, 'a' }, { "cactusDisk", required_argument, 0, 'b' }, { "help", no_argument, 0, 'h' }, { "spanningTrees", required_argument, 0, 'i' }, { "maximumLength", required_argument, 0, 'j' }, { "useBanding", no_argument, 0, 'k' }, { "gapGamma", required_argument, 0, 'l' }, { "matchGamma", required_argument, 0, 'L' }, { "splitMatrixBiggerThanThis", required_argument, 0, 'o' }, { "anchorMatrixBiggerThanThis", required_argument, 0, 'p' }, { "repeatMaskMatrixBiggerThanThis", required_argument, 0, 'q' }, { "diagonalExpansion", required_argument, 0, 'r' }, { "constraintDiagonalTrim", required_argument, 0, 't' }, { "minimumDegree", required_argument, 0, 'u' }, { "alignAmbiguityCharacters", no_argument, 0, 'w' }, { "pruneOutStubAlignments", no_argument, 0, 'y' }, { "minimumIngroupDegree", required_argument, 0, 'A' }, { "minimumOutgroupDegree", required_argument, 0, 'B' }, { "precomputedAlignments", required_argument, 0, 'D' }, { "endAlignmentsToPrecomputeOutputFile", required_argument, 0, 'E' }, { "useProgressiveMerging", no_argument, 0, 'F' }, { "calculateWhichEndsToComputeSeparately", no_argument, 0, 'G' }, { "largeEndSize", required_argument, 0, 'I' }, {"ingroupCoverageFile", required_argument, 0, 'J'}, {"minimumSizeToRescue", required_argument, 0, 'K'}, {"minimumCoverageToRescue", required_argument, 0, 'M'}, { "minimumNumberOfSpecies", required_argument, 0, 'N' }, { 0, 0, 0, 0 } }; int option_index = 0; int key = getopt_long(argc, argv, "a:b:hi:j:kl:o:p:q:r:t:u:wy:A:B:D:E:FGI:J:K:L:M:N:", long_options, &option_index); if (key == -1) { break; } switch (key) { case 'a': logLevelString = stString_copy(optarg); st_setLogLevelFromString(logLevelString); break; case 'b': cactusDiskDatabaseString = stString_copy(optarg); break; case 'h': usage(); return 0; case 'i': i = sscanf(optarg, "%" PRIi64 "", &spanningTrees); (void) i; assert(i == 1); assert(spanningTrees >= 0); break; case 'j': i = sscanf(optarg, "%" PRIi64 "", &maximumLength); assert(i == 1); assert(maximumLength >= 0); break; case 'k': useBanding = !useBanding; break; case 'l': i = sscanf(optarg, "%f", &pairwiseAlignmentBandingParameters->gapGamma); assert(i == 1); assert(pairwiseAlignmentBandingParameters->gapGamma >= 0.0); break; case 'L': i = sscanf(optarg, "%f", &matchGamma); assert(i == 1); assert(matchGamma >= 0.0); break; case 'o': i = sscanf(optarg, "%" PRIi64 "", &k); assert(i == 1); assert(k >= 0); pairwiseAlignmentBandingParameters->splitMatrixBiggerThanThis = (int64_t) k * k; break; case 'p': i = sscanf(optarg, "%" PRIi64 "", &k); assert(i == 1); assert(k >= 0); pairwiseAlignmentBandingParameters->anchorMatrixBiggerThanThis = (int64_t) k * k; break; case 'q': i = sscanf(optarg, "%" PRIi64 "", &k); assert(i == 1); assert(k >= 0); pairwiseAlignmentBandingParameters->repeatMaskMatrixBiggerThanThis = (int64_t) k * k; break; case 'r': i = sscanf(optarg, "%" PRIi64 "", &pairwiseAlignmentBandingParameters->diagonalExpansion); assert(i == 1); assert(pairwiseAlignmentBandingParameters->diagonalExpansion >= 0); assert(pairwiseAlignmentBandingParameters->diagonalExpansion % 2 == 0); break; case 't': i = sscanf(optarg, "%" PRIi64 "", &pairwiseAlignmentBandingParameters->constraintDiagonalTrim); assert(i == 1); assert(pairwiseAlignmentBandingParameters->constraintDiagonalTrim >= 0); break; case 'u': i = sscanf(optarg, "%" PRIi64 "", &minimumDegree); assert(i == 1); break; case 'w': pairwiseAlignmentBandingParameters->alignAmbiguityCharacters = 1; break; case 'y': pruneOutStubAlignments = 1; break; case 'A': i = sscanf(optarg, "%" PRIi64 "", &minimumIngroupDegree); assert(i == 1); break; case 'B': i = sscanf(optarg, "%" PRIi64 "", &minimumOutgroupDegree); assert(i == 1); break; case 'D': listOfEndAlignmentFiles = stString_split(optarg); break; case 'E': endAlignmentsToPrecomputeOutputFile = stString_copy(optarg); break; case 'F': useProgressiveMerging = 1; break; case 'G': calculateWhichEndsToComputeSeparately = 1; break; case 'I': i = sscanf(optarg, "%" PRIi64 "", &largeEndSize); assert(i == 1); break; case 'J': ingroupCoverageFilePath = stString_copy(optarg); break; case 'K': i = sscanf(optarg, "%" PRIi64, &minimumSizeToRescue); assert(i == 1); break; case 'M': i = sscanf(optarg, "%lf", &minimumCoverageToRescue); assert(i == 1); break; case 'N': i = sscanf(optarg, "%" PRIi64, &minimumNumberOfSpecies); if (i != 1) { st_errAbort("Error parsing minimumNumberOfSpecies parameter"); } break; default: usage(); return 1; } } st_setLogLevelFromString(logLevelString); /* * Load the flowerdisk */ stKVDatabaseConf *kvDatabaseConf = stKVDatabaseConf_constructFromString(cactusDiskDatabaseString); CactusDisk *cactusDisk = cactusDisk_construct(kvDatabaseConf, 0); //We precache the sequences st_logInfo("Set up the flower disk\n"); /* * Load the hmm */ StateMachine *sM = stateMachine5_construct(fiveState); /* * For each flower. */ if (calculateWhichEndsToComputeSeparately) { stList *flowers = flowerWriter_parseFlowersFromStdin(cactusDisk); if (stList_length(flowers) != 1) { st_errAbort("We are breaking up a flower's end alignments for precomputation but we have %" PRIi64 " flowers.\n", stList_length(flowers)); } stSortedSet *endsToAlignSeparately = getEndsToAlignSeparately(stList_get(flowers, 0), maximumLength, largeEndSize); assert(stSortedSet_size(endsToAlignSeparately) != 1); stSortedSetIterator *it = stSortedSet_getIterator(endsToAlignSeparately); End *end; while ((end = stSortedSet_getNext(it)) != NULL) { fprintf(stdout, "%s\t%" PRIi64 "\t%" PRIi64 "\n", cactusMisc_nameToStringStatic(end_getName(end)), end_getInstanceNumber(end), getTotalAdjacencyLength(end)); } return 0; //avoid cleanup costs stSortedSet_destructIterator(it); stSortedSet_destruct(endsToAlignSeparately); } else if (endAlignmentsToPrecomputeOutputFile != NULL) { /* * In this case we will align a set of end and save the alignments in a file. */ stList *names = flowerWriter_parseNames(stdin); Flower *flower = cactusDisk_getFlower(cactusDisk, *((Name *)stList_get(names, 0))); FILE *fileHandle = fopen(endAlignmentsToPrecomputeOutputFile, "w"); for(int64_t i=1; i<stList_length(names); i++) { End *end = flower_getEnd(flower, *((Name *)stList_get(names, i))); if (end == NULL) { st_errAbort("The end %" PRIi64 " was not found in the flower\n", *((Name *)stList_get(names, i))); } stSortedSet *endAlignment = makeEndAlignment(sM, end, spanningTrees, maximumLength, useProgressiveMerging, matchGamma, pairwiseAlignmentBandingParameters); writeEndAlignmentToDisk(end, endAlignment, fileHandle); stSortedSet_destruct(endAlignment); } fclose(fileHandle); return 0; //avoid cleanup costs stList_destruct(names); st_logInfo("Finished precomputing end alignments\n"); } else { /* * Compute complete flower alignments, possibly loading some precomputed alignments. */ bedRegion *bedRegions = NULL; size_t numBeds = 0; if (ingroupCoverageFilePath != NULL) { // Pre-load the mmap for the coverage file. FILE *coverageFile = fopen(ingroupCoverageFilePath, "rb"); if (coverageFile == NULL) { st_errnoAbort("Opening coverage file %s failed", ingroupCoverageFilePath); } fseek(coverageFile, 0, SEEK_END); int64_t coverageFileLen = ftell(coverageFile); assert(coverageFileLen >= 0); assert(coverageFileLen % sizeof(bedRegion) == 0); if (coverageFileLen == 0) { // mmap doesn't like length-0 mappings, for obvious // reasons. Pretend that the coverage file doesn't // exist in this case, since it contains no data. ingroupCoverageFilePath = NULL; } else { // Establish a memory mapping for the file. bedRegions = mmap(NULL, coverageFileLen, PROT_READ, MAP_SHARED, fileno(coverageFile), 0); if (bedRegions == MAP_FAILED) { st_errnoAbort("Failure mapping coverage file"); } numBeds = coverageFileLen / sizeof(bedRegion); } fclose(coverageFile); } stList *flowers = flowerWriter_parseFlowersFromStdin(cactusDisk); if (listOfEndAlignmentFiles != NULL && stList_length(flowers) != 1) { st_errAbort("We have precomputed alignments but %" PRIi64 " flowers to align.\n", stList_length(flowers)); } cactusDisk_preCacheStrings(cactusDisk, flowers); for (j = 0; j < stList_length(flowers); j++) { flower = stList_get(flowers, j); st_logInfo("Processing a flower\n"); stSortedSet *alignedPairs = makeFlowerAlignment3(sM, flower, listOfEndAlignmentFiles, spanningTrees, maximumLength, useProgressiveMerging, matchGamma, pairwiseAlignmentBandingParameters, pruneOutStubAlignments); st_logInfo("Created the alignment: %" PRIi64 " pairs\n", stSortedSet_size(alignedPairs)); stPinchIterator *pinchIterator = stPinchIterator_constructFromAlignedPairs(alignedPairs, getNextAlignedPairAlignment); /* * Run the cactus caf functions to build cactus. */ stPinchThreadSet *threadSet = stCaf_setup(flower); stCaf_anneal(threadSet, pinchIterator, NULL); if (minimumDegree < 2) { stCaf_makeDegreeOneBlocks(threadSet); } if (minimumIngroupDegree > 0 || minimumOutgroupDegree > 0 || minimumDegree > 1) { stCaf_melt(flower, threadSet, blockFilterFn, 0, 0, 0, INT64_MAX); } if (ingroupCoverageFilePath != NULL) { // Rescue any sequence that is covered by outgroups // but currently unaligned into single-degree blocks. stPinchThreadSetIt pinchIt = stPinchThreadSet_getIt(threadSet); stPinchThread *thread; while ((thread = stPinchThreadSetIt_getNext(&pinchIt)) != NULL) { Cap *cap = flower_getCap(flower, stPinchThread_getName(thread)); assert(cap != NULL); Sequence *sequence = cap_getSequence(cap); assert(sequence != NULL); rescueCoveredRegions(thread, bedRegions, numBeds, sequence_getName(sequence), minimumSizeToRescue, minimumCoverageToRescue); } stCaf_joinTrivialBoundaries(threadSet); } stCaf_finish(flower, threadSet, chainLengthForBigFlower, longChain, INT64_MAX, INT64_MAX); //Flower now destroyed. stPinchThreadSet_destruct(threadSet); st_logInfo("Ran the cactus core script.\n"); /* * Cleanup */ //Clean up the sorted set after cleaning up the iterator stPinchIterator_destruct(pinchIterator); stSortedSet_destruct(alignedPairs); st_logInfo("Finished filling in the alignments for the flower\n"); } stList_destruct(flowers); //st_errAbort("Done\n"); /* * Write and close the cactusdisk. */ cactusDisk_write(cactusDisk); return 0; //Exit without clean up is quicker, enable cleanup when doing memory leak detection. if (bedRegions != NULL) { // Clean up our mapping. munmap(bedRegions, numBeds * sizeof(bedRegion)); } } /////////////////////////////////////////////////////////////////////////// // Cleanup /////////////////////////////////////////////////////////////////////////// stateMachine_destruct(sM); cactusDisk_destruct(cactusDisk); stKVDatabaseConf_destruct(kvDatabaseConf); //destructCactusCoreInputParameters(cCIP); free(cactusDiskDatabaseString); if (listOfEndAlignmentFiles != NULL) { stList_destruct(listOfEndAlignmentFiles); } if (logLevelString != NULL) { free(logLevelString); } st_logInfo("Finished with the flower disk for this flower.\n"); //while(1); return 0; }