/* Parse XML string into a hash. This parses all attributes of all tags
* into values. st_kv_database_conf type is stored as conf_type,
* database tag is stores as db_tag. This does minimal error checking
* and is really lame.
*/
static stHash *hackParseXmlString(const char *xmlString) {
stHash *hash = stHash_construct3(stHash_stringKey, stHash_stringEqualKey, free, free);
char *toReplace[5] = { "</", "<", "/>", ">", "=" };
char *cA = stString_replace(xmlString, toReplace[0], " "), *cA2;
for (int64_t i = 1; i < 5; i++) {
cA2 = stString_replace(cA, toReplace[i], " ");
free(cA);
cA = cA2;
}
getExpectedToken(&cA2, "st_kv_database_conf");
stHash_insert(hash, stString_copy("conf_type"), getKeyValue(&cA2, "type"));
stHash_insert(hash, stString_copy("db_tag"), getNextToken(&cA2));
char *key;
while (((key = getNextToken(&cA2)) != NULL) && !stString_eq(key, "st_kv_database_conf")) {
char *value = getNextToken(&cA2);
if (value == NULL) {
stThrowNew(ST_KV_DATABASE_EXCEPTION_ID, "failed to to get value for key \"%s\"", key);
}
if (stHash_search(hash, key) != NULL) {
stThrowNew(ST_KV_DATABASE_EXCEPTION_ID, "got a duplicate entry in the database conf string \"%s\"", key);
}
stHash_insert(hash, key, value);
}
if(!stString_eq(key, "st_kv_database_conf")) {
stThrowNew(ST_KV_DATABASE_EXCEPTION_ID, "got an unexpected final entry \"%s\"", key);
}
free(key);
free(cA);
return hash;
}
static void test_addBlockToHash_3(CuTest *testCase) {
// concatenation with 2 bases of interstitial and a sequence length breakpoint
options_t *options = options_construct();
options->breakpointPenalty = 10;
options->interstitialSequence = 5;
stList *observedList = stList_construct3(0, free);
stList *expectedList = stList_construct3(0, free);
stHash *observedHash = createBlockHashFromString("a score=0\n"
"s reference.chr0 0 13 + 158545518 gcagctgaaaaca\n"
"s name.chr1 0 10 + 100 ATGT---ATGCCG\n"
"s name2.chr1 0 10 + 100 ATGT---ATGCCG\n"
"s name3.chr1 0 13 + 100 GCAGCTGAAAACA\n",
observedList
);
mafBlock_t *mb = maf_newMafBlockListFromString("a score=0 test\n"
"s reference.chr0 13 5 + 158545518 ACGTA\n"
"s name.chr1 12 5 + 100 gtcGG\n"
"s name2.chr1 10 5 + 100 ATGTg\n"
"s name3.chr1 50 5 + 100 CCCCC\n"
, 3);
stHash *expectedHash = NULL;
expectedHash = createBlockHashFromString("a score=0\n"
"s reference.chr0 0 18 + 158545518 gcagctgaaaaca------------ACGTA\n"
"s name.chr1 0 17 + 100 ATGT---ATGCCGac----------gtcGG\n"
"s name2.chr1 0 15 + 100 ATGT---ATGCCG------------ATGTg\n"
"s name3 0 28 + 28 GCAGCTGAAAACA--NNNNNNNNNNCCCCC\n",
expectedList
);
row_t *r = stHash_search(expectedHash, "name3");
r->prevRightPos = 54;
free(r->prevName);
r->prevName = stString_copy("name3.chr1");
r->multipleNames = true;
stHash *seqHash = createSeqHashFromString("name.chr1", "ATGTATGCCGacgtc"
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG"
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG");
mtfseq_t *mtfs = newMtfseqFromString("gcagctgaaaacaACGTA"
"tttttttttttttttttttttttttttttttt"
"tttttttttttttttttttttttttttttttttttttttttttttttttt");
stHash_insert(seqHash, stString_copy("reference.chr0"), mtfs);
mtfs = newMtfseqFromString("ATGTATGCCGATGTg"
"CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"
"CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC");
stHash_insert(seqHash, stString_copy("name2.chr1"), mtfs);
mtfs = newMtfseqFromString("GCAGCTGAAAACAggggggggggggggggggggggggggggggggggggg"
"CCCCCaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa"
);
stHash_insert(seqHash, stString_copy("name3.chr1"), mtfs);
addMafBlockToRowHash(observedHash, seqHash, observedList, mb, options);
CuAssertTrue(testCase, hashesAreEqual(observedHash, expectedHash));
CuAssertTrue(testCase, listsAreEqual(observedList, expectedList));
// clean up
stHash_destruct(observedHash);
stHash_destruct(expectedHash);
stHash_destruct(seqHash);
stList_destruct(observedList);
stList_destruct(expectedList);
maf_destroyMafBlockList(mb);
destroyOptions(options);
}
static char *tree_getNewickTreeStringP(stTree *tree) {
char *cA, *cA2;
if(stTree_getChildNumber(tree) > 0) {
int32_t i;
cA = stString_copy("(");
for(i=0; i<stTree_getChildNumber(tree); i++) {
cA2 = tree_getNewickTreeStringP(stTree_getChild(tree, i));
char *cA3 = stString_print((i+1 < stTree_getChildNumber(tree) ? "%s%s," : "%s%s"), cA, cA2);
free(cA);
free(cA2);
cA = cA3;
}
cA2 = stString_print("%s)", cA);
free(cA);
cA = cA2;
}
else {
cA = stString_copy("");
}
if(stTree_getLabel(tree) != NULL) {
cA2 = stString_print("%s%s", cA, stTree_getLabel(tree));
free(cA);
cA = cA2;
}
if(stTree_getBranchLength(tree) != INFINITY) {
char *cA2 = stString_print("%s:%g", cA, stTree_getBranchLength(tree));
free(cA);
cA = cA2;
}
return cA;
}
static void test_addMafLineToRow_1(CuTest *testCase) {
row_t *obs = newRow(20);
obs->name = stString_copy("seq1.chr0");
obs->prevName = stString_copy("seq1.amazing");
obs->multipleNames = true;
obs->start = 3;
obs->length = 10;
obs->prevRightPos = 20;
obs->strand = '+';
obs->prevStrand = '+';
obs->sourceLength = 100;
row_copyIn(obs, "acgtacgtac");
mafLine_t *ml = maf_newMafLineFromString("s seq1.chr_bleh 13 5 + 100 ACGTA", 10);
addMafLineToRow(obs, ml);
row_t *exp = newRow(20);
exp->name = stString_copy("seq1.chr0");
exp->prevName = stString_copy("seq1.chr_bleh");
exp->multipleNames = true;
exp->start = 3;
exp->length = 15;
exp->prevRightPos = 17;
exp->strand = '+';
exp->prevStrand = '+';
exp->sourceLength = 15;
row_copyIn(exp, "acgtacgtacACGTA");
CuAssertTrue(testCase, rowsAreEqual(obs, exp));
destroyRow(obs);
destroyRow(exp);
maf_destroyMafLineList(ml);
}
static stKVDatabaseConf *constructSql(stKVDatabaseType type, const char *host, unsigned port, const char *user, const char *password,
const char *databaseName, const char *tableName) {
stKVDatabaseConf *conf = stSafeCCalloc(sizeof(stKVDatabaseConf));
conf->type = type;
conf->host = stString_copy(host);
conf->port = port;
conf->user = stString_copy(user);
conf->password = stString_copy(password);
conf->databaseName = stString_copy(databaseName);
conf->tableName = stString_copy(tableName);
return conf;
}
static void test_addBlockToHash_2(CuTest *testCase) {
// concatenation with 2 bases of interstitial AND a previously unobserved sequence
options_t *options = options_construct();
options->breakpointPenalty = 10;
options->interstitialSequence = 5;
stList *observedList = stList_construct3(0, free);
stList *expectedList = stList_construct3(0, free);
stHash *observedHash = createBlockHashFromString("a score=0\n"
"s reference.chr0 0 13 + 158545518 gcagctgaaaaca\n"
"s name.chr1 0 10 + 100 ATGT---ATGCCG\n"
"s name2.chr1 0 10 + 100 ATGT---ATGCCG\n",
observedList);
mafBlock_t *mb = maf_newMafBlockListFromString("a score=0 test\n"
"s reference.chr0 13 5 + 158545518 ACGTA\n"
"s name.chr1 12 5 + 100 gTcGG\n"
"s name2.chr1 10 5 + 100 ATGTg\n"
"s name3.chr@ 0 5 + 20 aaccg\n"
, 3);
stHash *expectedHash = createBlockHashFromString("a score=0\n"
"s reference.chr0 0 18 + 158545518 gcagctgaaaaca--ACGTA\n"
"s name.chr1 0 17 + 100 ATGT---ATGCCGacgTcGG\n"
"s name2.chr1 0 15 + 100 ATGT---ATGCCG--ATGTg\n"
"s name3.chr@ 0 5 + 20 ---------------aaccg\n",
expectedList
);
stHash *seqHash = createSeqHashFromString("name.chr1", "ATGTATGCCGacgTc"
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG"
"GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG");
mtfseq_t *mtfs = newMtfseqFromString("gcagctgaaaacaACGTA"
"tttttttttttttttttttttttttttttttt"
"tttttttttttttttttttttttttttttttttttttttttttttttttt");
stHash_insert(seqHash, stString_copy("reference.chr0"), mtfs);
mtfs = newMtfseqFromString("ATGTATGCCGATGTg"
"CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"
"CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC");
stHash_insert(seqHash, stString_copy("name2.chr1"), mtfs);
mtfs = newMtfseqFromString("aaccgTTTTTTTTTTTTTTT");
stHash_insert(seqHash, stString_copy("name3.chr@"), mtfs);
addMafBlockToRowHash(observedHash, seqHash, observedList, mb, options);
CuAssertTrue(testCase, hashesAreEqual(observedHash, expectedHash));
CuAssertTrue(testCase, listsAreEqual(observedList, expectedList));
// clean up
stHash_destruct(observedHash);
stHash_destruct(expectedHash);
stHash_destruct(seqHash);
stList_destruct(observedList);
stList_destruct(expectedList);
maf_destroyMafBlockList(mb);
destroyOptions(options);
}
stKVDatabaseConf *stKVDatabaseConf_constructKyotoTycoon(const char *host, unsigned port, int timeout,
int64_t maxRecordSize, int64_t maxBulkSetSize,
int64_t maxBulkSetNumRecords,
const char *databaseDir, const char* databaseName) {
stKVDatabaseConf *conf = stSafeCCalloc(sizeof(stKVDatabaseConf));
conf->type = stKVDatabaseTypeKyotoTycoon;
conf->databaseDir = stString_copy(databaseDir);
conf->host = stString_copy(host);
conf->port = port;
conf->timeout = timeout;
conf->maxKTRecordSize = maxRecordSize;
conf->maxKTBulkSetSize = maxBulkSetSize;
conf->maxKTBulkSetNumRecords = maxBulkSetNumRecords;
conf->databaseName = stString_copy(databaseName);
return conf;
}
// 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 stHash *createSeqHashFromString(char *name, char *input) {
mtfseq_t *mtfs = newMtfseq(strlen(input));
stHash *hash = stHash_construct3(stHash_stringKey, stHash_stringEqualKey, free, destroyMtfseq);
seq_copyIn(mtfs, input);
stHash_insert(hash, stString_copy(name), mtfs);
return hash;
}
char *makeAlphaNumeric(const char *string) {
char *cA = stString_copy(string);
int64_t j = 0;
for (int64_t i = 0; i < strlen(string); i++) {
if (isalpha(string[i]) || isdigit(string[i])) {
cA[j++] = string[i];
}
}
cA[j] = '\0';
return cA;
}
static int64_t *getInts(const char *string, int64_t *arrayLength) {
int64_t *iA = st_malloc(sizeof(int64_t) * strlen(string));
char *cA = stString_copy(string);
char *cA2 = cA;
char *cA3;
*arrayLength = 0;
while ((cA3 = stString_getNextWord(&cA)) != NULL) {
int64_t i = sscanf(cA3, "%" PRIi64 "", &iA[(*arrayLength)++]);
(void) i;
assert(i == 1);
free(cA3);
}
free(cA2);
return iA;
}
int main(int argc, char *argv[])
{
char *cactusDiskString = NULL;
stKVDatabaseConf *kvDatabaseConf;
CactusDisk *cactusDisk;
Flower *flower;
Flower_SequenceIterator *flowerIt;
Sequence *sequence;
struct option longopts[] = { {"cactusDisk", required_argument, NULL, 'c' },
{0, 0, 0, 0} };
int flag;
while((flag = getopt_long(argc, argv, "", longopts, NULL)) != -1) {
switch(flag) {
case 'c':
cactusDiskString = stString_copy(optarg);
break;
case '?':
default:
usage();
return 1;
}
}
if (cactusDiskString == NULL) {
st_errAbort("--cactusDisk option must be provided");
}
kvDatabaseConf = stKVDatabaseConf_constructFromString(cactusDiskString);
cactusDisk = cactusDisk_construct(kvDatabaseConf, 0);
// Get top-level flower.
flower = cactusDisk_getFlower(cactusDisk, 0);
flowerIt = flower_getSequenceIterator(flower);
while((sequence = flower_getNextSequence(flowerIt)) != NULL) {
MetaSequence *metaSequence = sequence_getMetaSequence(sequence);
const char *header;
char *firstToken, *newHeader;
stList *tokens;
// Strip the ID token from the header (should be the first
// |-separated token) and complain if there isn't one.
header = metaSequence_getHeader(metaSequence);
tokens = fastaDecodeHeader(header);
assert(stList_length(tokens) > 1);
firstToken = stList_removeFirst(tokens);
assert(!strncmp(firstToken, "id=", 3));
free(firstToken);
newHeader = fastaEncodeHeader(tokens);
metaSequence_setHeader(metaSequence, newHeader);
}
cactusDisk_write(cactusDisk);
}
Event *event_construct(Name name, const char *header, float branchLength, Event *parentEvent,
EventTree *eventTree) {
assert(eventTree_getEvent(eventTree, name) == NULL); //the event must not already exist in the tree.
Event *event;
event = st_malloc(sizeof(Event));
event->name = name;
event->parent = parentEvent;
event->children = constructEmptyList(0, NULL);
event->header = stString_copy(header == NULL ? "" : header);
event->branchLength = branchLength < 0.0 ? 0.0 : branchLength;
event->isOutgroup = 0;
if (parentEvent != NULL) {
listAppend(parentEvent->children, event);
}
event->eventTree = eventTree;
eventTree_addEvent(eventTree, event);
return event;
}
MetaSequence *metaSequence_construct2(Name name, int64_t start,
int64_t length, Name stringName, const char *header,
Name eventName, bool isTrivialSequence, CactusDisk *cactusDisk) {
MetaSequence *metaSequence;
metaSequence = st_malloc(sizeof(MetaSequence));
metaSequence->name = name;
assert(length >= 0);
metaSequence->start = start;
metaSequence->length = length;
metaSequence->stringName = stringName;
metaSequence->eventName = eventName;
metaSequence->cactusDisk = cactusDisk;
metaSequence->header = stString_copy(header != NULL ? header : "");
metaSequence->isTrivialSequence = isTrivialSequence;
cactusDisk_addMetaSequence(cactusDisk, metaSequence);
return metaSequence;
}
char *getTerminalAdjacencySubString(Cap *cap) {
if(getTerminalAdjacencyLength_ignoreAdjacencies) {
return stString_copy("");
}
cap = getTerminalCap(cap);
cap = cap_getStrand(cap) ? cap : cap_getReverse(cap); //This ensures the asserts are as expected.
Cap *adjacentCap = cap_getAdjacency(cap);
int64_t i = cap_getCoordinate(cap) - cap_getCoordinate(adjacentCap);
assert(i != 0);
if (i > 0) {
assert(cap_getSide(cap));
assert(!cap_getSide(adjacentCap));
return sequence_getString(cap_getSequence(cap),
cap_getCoordinate(adjacentCap) + 1, i - 1, 1);
} else {
assert(cap_getSide(adjacentCap));
assert(!cap_getSide(cap));
return sequence_getString(cap_getSequence(cap), cap_getCoordinate(cap) + 1, -i - 1, 1);
}
}
stKVDatabaseConf *stKVDatabaseConf_constructClone(stKVDatabaseConf *srcConf) {
stKVDatabaseConf *conf = stSafeCCalloc(sizeof(stKVDatabaseConf));
conf->type = srcConf->type;
conf->databaseDir = stString_copy(srcConf->databaseDir);
conf->host = stString_copy(srcConf->host);
conf->port = srcConf->port;
conf->timeout = srcConf->timeout;
conf->maxKTRecordSize = srcConf->maxKTRecordSize;
conf->maxKTBulkSetSize = srcConf->maxKTBulkSetSize;
conf->maxKTBulkSetNumRecords = srcConf->maxKTBulkSetNumRecords;
conf->user = stString_copy(srcConf->user);
conf->password = stString_copy(srcConf->password);
conf->databaseName = stString_copy(srcConf->databaseName);
conf->tableName = stString_copy(srcConf->tableName);
return conf;
}
char *cactusDisk_getString(CactusDisk *cactusDisk, Name name, int64_t start, int64_t length, int64_t strand,
int64_t totalSequenceLength) {
/*
* Gets a string from the database.
*
*/
assert(length >= 0);
if (length == 0) {
return stString_copy("");
}
//First try getting it from the cache
char *string = cactusDisk_getStringFromCache(cactusDisk, name, start, length, strand);
if (string == NULL) { //If not in the cache, add it to the cache and then get it from the cache.
stList *list = stList_construct3(0, (void (*)(void *)) substring_destruct);
stList_append(list, substring_construct(name, start, length));
cacheSubstringsFromDB(cactusDisk, list);
stList_destruct(list);
string = cactusDisk_getStringFromCache(cactusDisk, name, start, length, strand);
}
assert(string != NULL);
return string;
}
/* connect to a database server */
static MySqlDb *connect(stKVDatabaseConf *conf) {
MySqlDb *dbImpl = stSafeCCalloc(sizeof(MySqlDb));
if ((dbImpl->conn = mysql_init(NULL)) == NULL) {
disconnect(dbImpl);
stThrowNew(ST_KV_DATABASE_EXCEPTION_ID, "mysql_init failed");
}
if (mysql_real_connect(dbImpl->conn, stKVDatabaseConf_getHost(conf), stKVDatabaseConf_getUser(conf), stKVDatabaseConf_getPassword(conf), stKVDatabaseConf_getDatabaseName(conf), stKVDatabaseConf_getPort(conf), NULL, 0) == NULL) {
stExcept *ex = createMySqlExcept(dbImpl, "failed to connect to MySql database: %s on %s as user %s",
stKVDatabaseConf_getDatabaseName(conf), stKVDatabaseConf_getHost(conf), stKVDatabaseConf_getUser(conf));
disconnect(dbImpl);
stThrow(ex);
}
dbImpl->table = stString_copy(stKVDatabaseConf_getTableName(conf));
// disable report of notes, so only warnings and errors come back
sqlExec(dbImpl, "set sql_notes=0");
// set max sizes of an sql statment to 1G. This must also be specified
// for the server by adding "max_allowed_packet = 1G" to the [mysqld]
// section of my.cnf
sqlExec(dbImpl, "set global max_allowed_packet=1073741824");
// set the idle timeout to a week
int waitTimeout = 7 * 24 * 60 * 60; // 1 week
sqlExec(dbImpl, "set wait_timeout=%d", waitTimeout);
// set the read timeout to an hour
int readTimeout = 60 * 60; // 1 hour
sqlExec(dbImpl, "set net_read_timeout=%d", readTimeout);
// NOTE: commit will not return an error, this does row-level locking on
// the select done before the update
sqlExec(dbImpl, "set autocommit = 0;");
sqlExec(dbImpl, "set session transaction isolation level serializable;");
return dbImpl;
}
static CactusDisk *cactusDisk_constructPrivate(stKVDatabaseConf *conf, bool create, const char *sequencesFileName) {
//sequencesFileName = NULL; //Disable the ability to store the sequences on disk.
CactusDisk *cactusDisk = st_calloc(1, sizeof(CactusDisk));
//construct lists of in memory objects
cactusDisk->metaSequences = stSortedSet_construct3(cactusDisk_constructMetaSequencesP, NULL);
cactusDisk->flowers = stSortedSet_construct3(cactusDisk_constructFlowersP, NULL);
cactusDisk->flowerNamesMarkedForDeletion = stSortedSet_construct3((int (*)(const void *, const void *)) strcmp,
free);
cactusDisk->updateRequests = stList_construct3(0, (void (*)(void *)) stKVDatabaseBulkRequest_destruct);
//Now open the database
cactusDisk->database = stKVDatabase_construct(conf, create);
cactusDisk->cache = stCache_construct();
cactusDisk->stringCache = stCache_construct();
//initialise the unique ids.
int64_t seed = (clock() << 24) | (time(NULL) << 16) | (getpid() & 65535); //Likely to be unique
st_logDebug("The cactus disk is seeding the random number generator with the value %" PRIi64 "\n", seed);
st_randomSeed(seed);
cactusDisk->uniqueNumber = 0;
cactusDisk->maxUniqueNumber = 0;
//Now load any stuff..
if (containsRecord(cactusDisk, CACTUS_DISK_PARAMETER_KEY)) {
if (create) {
stThrowNew(CACTUS_DISK_EXCEPTION_ID, "Tried to create a cactus disk, but the cactus disk already exists");
}
if (sequencesFileName != NULL) {
stThrowNew(CACTUS_DISK_EXCEPTION_ID,
"A sequences file name is specified, but the cactus disk is not being created");
}
void *record = getRecord(cactusDisk, CACTUS_DISK_PARAMETER_KEY, "cactus_disk parameters");
void *record2 = record;
cactusDisk_loadFromBinaryRepresentation(&record, cactusDisk, conf);
free(record2);
} else {
assert(create);
if (sequencesFileName == NULL) {
cactusDisk->storeSequencesInAFile = 0;
cactusDisk->sequencesFileName = NULL;
cactusDisk->sequencesReadFileHandle = NULL;
cactusDisk->sequencesWriteFileHandle = NULL;
cactusDisk->absSequencesFileName = NULL;
} else {
if (stKVDatabaseConf_getDir(conf) == NULL) {
stThrowNew(CACTUS_DISK_EXCEPTION_ID,
"The database conf does not contain a directory in which the sequence file is to be found!\n");
}
cactusDisk->storeSequencesInAFile = 1;
cactusDisk->sequencesFileName = stString_copy(sequencesFileName);
cactusDisk->absSequencesFileName = stString_print("%s/%s", stKVDatabaseConf_getDir(conf),
cactusDisk->sequencesFileName);
//Make sure the file exists
cactusDisk->sequencesReadFileHandle = fopen(cactusDisk->absSequencesFileName, "w");
assert(cactusDisk->sequencesReadFileHandle != NULL);
fclose(cactusDisk->sequencesReadFileHandle); //Flush it first time.
cactusDisk->sequencesReadFileHandle = NULL;
cactusDisk->sequencesWriteFileHandle = NULL;
}
}
return cactusDisk;
}
int main(int argc, char *argv[]) {
/*
* Script for adding alignments to cactus tree.
*/
int64_t startTime;
stKVDatabaseConf *kvDatabaseConf;
CactusDisk *cactusDisk;
int key, k;
bool (*filterFn)(stPinchSegment *, stPinchSegment *) = NULL;
stSet *outgroupThreads = NULL;
/*
* Arguments/options
*/
char * logLevelString = NULL;
char * alignmentsFile = NULL;
char * constraintsFile = NULL;
char * cactusDiskDatabaseString = NULL;
char * lastzArguments = "";
int64_t minimumSequenceLengthForBlast = 1;
//Parameters for annealing/melting rounds
int64_t *annealingRounds = NULL;
int64_t annealingRoundsLength = 0;
int64_t *meltingRounds = NULL;
int64_t meltingRoundsLength = 0;
//Parameters for melting
float maximumAdjacencyComponentSizeRatio = 10;
int64_t blockTrim = 0;
int64_t alignmentTrimLength = 0;
int64_t *alignmentTrims = NULL;
int64_t chainLengthForBigFlower = 1000000;
int64_t longChain = 2;
int64_t minLengthForChromosome = 1000000;
float proportionOfUnalignedBasesForNewChromosome = 0.8;
bool breakChainsAtReverseTandems = 1;
int64_t maximumMedianSequenceLengthBetweenLinkedEnds = INT64_MAX;
bool realign = 0;
char *realignArguments = "";
bool removeRecoverableChains = false;
bool (*recoverableChainsFilter)(stCactusEdgeEnd *, Flower *) = NULL;
int64_t maxRecoverableChainsIterations = 1;
int64_t maxRecoverableChainLength = INT64_MAX;
//Parameters for removing ancient homologies
bool doPhylogeny = false;
int64_t phylogenyNumTrees = 1;
enum stCaf_RootingMethod phylogenyRootingMethod = BEST_RECON;
enum stCaf_ScoringMethod phylogenyScoringMethod = COMBINED_LIKELIHOOD;
double breakpointScalingFactor = 1.0;
bool phylogenySkipSingleCopyBlocks = 0;
int64_t phylogenyMaxBaseDistance = 1000;
int64_t phylogenyMaxBlockDistance = 100;
bool phylogenyKeepSingleDegreeBlocks = 0;
stList *phylogenyTreeBuildingMethods = stList_construct();
enum stCaf_TreeBuildingMethod defaultMethod = GUIDED_NEIGHBOR_JOINING;
stList_append(phylogenyTreeBuildingMethods, &defaultMethod);
double phylogenyCostPerDupPerBase = 0.2;
double phylogenyCostPerLossPerBase = 0.2;
const char *debugFileName = NULL;
const char *referenceEventHeader = NULL;
double phylogenyDoSplitsWithSupportHigherThanThisAllAtOnce = 1.0;
int64_t numTreeBuildingThreads = 2;
int64_t minimumBlockDegreeToCheckSupport = 10;
double minimumBlockHomologySupport = 0.7;
double nucleotideScalingFactor = 1.0;
HomologyUnitType phylogenyHomologyUnitType = BLOCK;
enum stCaf_DistanceCorrectionMethod phylogenyDistanceCorrectionMethod = JUKES_CANTOR;
bool sortAlignments = false;
///////////////////////////////////////////////////////////////////////////
// (0) Parse the inputs handed by genomeCactus.py / setup stuff.
///////////////////////////////////////////////////////////////////////////
while (1) {
static struct option long_options[] = { { "logLevel", required_argument, 0, 'a' }, { "alignments", required_argument, 0, 'b' }, {
"cactusDisk", required_argument, 0, 'c' }, { "lastzArguments", required_argument, 0, 'd' },
{ "help", no_argument, 0, 'h' }, { "annealingRounds", required_argument, 0, 'i' }, { "trim", required_argument, 0, 'k' }, {
"trimChange", required_argument, 0, 'l', }, { "minimumTreeCoverage", required_argument, 0, 'm' }, { "blockTrim",
required_argument, 0, 'n' }, { "deannealingRounds", required_argument, 0, 'o' }, { "minimumDegree",
required_argument, 0, 'p' }, { "minimumIngroupDegree", required_argument, 0, 'q' }, {
"minimumOutgroupDegree", required_argument, 0, 'r' }, { "alignmentFilter", required_argument, 0, 't' }, {
"minimumSequenceLengthForBlast", required_argument, 0, 'v' }, { "maxAdjacencyComponentSizeRatio",
required_argument, 0, 'w' }, { "constraints", required_argument, 0, 'x' }, { "minLengthForChromosome",
required_argument, 0, 'y' }, { "proportionOfUnalignedBasesForNewChromosome", required_argument, 0, 'z' },
{ "maximumMedianSequenceLengthBetweenLinkedEnds", required_argument, 0, 'A' },
{ "realign", no_argument, 0, 'B' }, { "realignArguments", required_argument, 0, 'C' },
{ "phylogenyNumTrees", required_argument, 0, 'D' },
{ "phylogenyRootingMethod", required_argument, 0, 'E' },
{ "phylogenyScoringMethod", required_argument, 0, 'F' },
{ "phylogenyBreakpointScalingFactor", required_argument, 0, 'G' },
{ "phylogenySkipSingleCopyBlocks", no_argument, 0, 'H' },
{ "phylogenyMaxBaseDistance", required_argument, 0, 'I' },
{ "phylogenyMaxBlockDistance", required_argument, 0, 'J' },
{ "phylogenyDebugFile", required_argument, 0, 'K' },
{ "phylogenyKeepSingleDegreeBlocks", no_argument, 0, 'L' },
{ "phylogenyTreeBuildingMethod", required_argument, 0, 'M' },
{ "phylogenyCostPerDupPerBase", required_argument, 0, 'N' },
{ "phylogenyCostPerLossPerBase", required_argument, 0, 'O' },
{ "referenceEventHeader", required_argument, 0, 'P' },
{ "phylogenyDoSplitsWithSupportHigherThanThisAllAtOnce", required_argument, 0, 'Q' },
{ "numTreeBuildingThreads", required_argument, 0, 'R' },
{ "phylogeny", no_argument, 0, 'S' },
{ "minimumBlockHomologySupport", required_argument, 0, 'T' },
{ "phylogenyNucleotideScalingFactor", required_argument, 0, 'U' },
{ "minimumBlockDegreeToCheckSupport", required_argument, 0, 'V' },
{ "removeRecoverableChains", required_argument, 0, 'W' },
{ "minimumNumberOfSpecies", required_argument, 0, 'X' },
{ "phylogenyHomologyUnitType", required_argument, 0, 'Y' },
{ "phylogenyDistanceCorrectionMethod", required_argument, 0, 'Z' },
{ "maxRecoverableChainsIterations", required_argument, 0, '1' },
{ "maxRecoverableChainLength", required_argument, 0, '2' },
{ 0, 0, 0, 0 } };
int option_index = 0;
key = getopt_long(argc, argv, "a:b:c:hi:k:m:n:o:p:q:r:stv:w:x:y:z:A:BC:D:E:", long_options, &option_index);
if (key == -1) {
break;
}
switch (key) {
case 'a':
logLevelString = stString_copy(optarg);
st_setLogLevelFromString(logLevelString);
break;
case 'b':
alignmentsFile = stString_copy(optarg);
break;
case 'c':
cactusDiskDatabaseString = stString_copy(optarg);
break;
case 'd':
lastzArguments = stString_copy(optarg);
break;
case 'h':
usage();
return 0;
case 'i':
annealingRounds = getInts(optarg, &annealingRoundsLength);
break;
case 'o':
meltingRounds = getInts(optarg, &meltingRoundsLength);
break;
case 'k':
alignmentTrims = getInts(optarg, &alignmentTrimLength);
break;
case 'm':
k = sscanf(optarg, "%f", &minimumTreeCoverage);
assert(k == 1);
break;
case 'n':
k = sscanf(optarg, "%" PRIi64 "", &blockTrim);
assert(k == 1);
break;
case 'p':
k = sscanf(optarg, "%" PRIi64 "", &minimumDegree);
assert(k == 1);
break;
case 'q':
k = sscanf(optarg, "%" PRIi64 "", &minimumIngroupDegree);
assert(k == 1);
break;
case 'r':
k = sscanf(optarg, "%" PRIi64 "", &minimumOutgroupDegree);
assert(k == 1);
break;
case 't':
if (strcmp(optarg, "singleCopyOutgroup") == 0) {
sortAlignments = true;
filterFn = stCaf_filterByOutgroup;
} else if (strcmp(optarg, "relaxedSingleCopyOutgroup") == 0) {
sortAlignments = true;
filterFn = stCaf_relaxedFilterByOutgroup;
} else if (strcmp(optarg, "singleCopy") == 0) {
sortAlignments = true;
filterFn = stCaf_filterByRepeatSpecies;
} else if (strcmp(optarg, "relaxedSingleCopy") == 0) {
sortAlignments = true;
filterFn = stCaf_relaxedFilterByRepeatSpecies;
} else if (strcmp(optarg, "singleCopyChr") == 0) {
sortAlignments = true;
filterFn = stCaf_singleCopyChr;
} else if (strcmp(optarg, "singleCopyIngroup") == 0) {
sortAlignments = true;
filterFn = stCaf_singleCopyIngroup;
} else if (strcmp(optarg, "relaxedSingleCopyIngroup") == 0) {
sortAlignments = true;
filterFn = stCaf_relaxedSingleCopyIngroup;
} else if (strcmp(optarg, "none") == 0) {
sortAlignments = false;
filterFn = NULL;
} else {
st_errAbort("Could not recognize alignmentFilter option %s", optarg);
}
break;
case 'v':
k = sscanf(optarg, "%" PRIi64 "", &minimumSequenceLengthForBlast);
assert(k == 1);
break;
case 'w':
k = sscanf(optarg, "%f", &maximumAdjacencyComponentSizeRatio);
assert(k == 1);
break;
case 'x':
constraintsFile = stString_copy(optarg);
break;
case 'y':
k = sscanf(optarg, "%" PRIi64 "", &minLengthForChromosome);
assert(k == 1);
break;
case 'z':
k = sscanf(optarg, "%f", &proportionOfUnalignedBasesForNewChromosome);
assert(k == 1);
break;
case 'A':
k = sscanf(optarg, "%" PRIi64 "", &maximumMedianSequenceLengthBetweenLinkedEnds);
assert(k == 1);
break;
case 'B':
realign = 1;
break;
case 'C':
realignArguments = stString_copy(optarg);
break;
case 'D':
k = sscanf(optarg, "%" PRIi64, &phylogenyNumTrees);
assert(k == 1);
break;
case 'E':
if (!strcmp(optarg, "outgroupBranch")) {
phylogenyRootingMethod = OUTGROUP_BRANCH;
} else if (!strcmp(optarg, "longestBranch")) {
phylogenyRootingMethod = LONGEST_BRANCH;
} else if (!strcmp(optarg, "bestRecon")) {
phylogenyRootingMethod = BEST_RECON;
} else {
st_errAbort("Invalid tree rooting method: %s", optarg);
}
break;
case 'F':
if (!strcmp(optarg, "reconCost")) {
phylogenyScoringMethod = RECON_COST;
} else if (!strcmp(optarg, "nucLikelihood")) {
phylogenyScoringMethod = NUCLEOTIDE_LIKELIHOOD;
} else if (!strcmp(optarg, "reconLikelihood")) {
phylogenyScoringMethod = RECON_LIKELIHOOD;
} else if (!strcmp(optarg, "combinedLikelihood")) {
phylogenyScoringMethod = COMBINED_LIKELIHOOD;
} else {
st_errAbort("Invalid tree scoring method: %s", optarg);
}
break;
case 'G':
k = sscanf(optarg, "%lf", &breakpointScalingFactor);
assert(k == 1);
break;
case 'H':
phylogenySkipSingleCopyBlocks = true;
break;
case 'I':
k = sscanf(optarg, "%" PRIi64, &phylogenyMaxBaseDistance);
assert(k == 1);
break;
case 'J':
k = sscanf(optarg, "%" PRIi64, &phylogenyMaxBlockDistance);
assert(k == 1);
break;
case 'K':
debugFileName = stString_copy(optarg);
break;
case 'L':
phylogenyKeepSingleDegreeBlocks = true;
break;
case 'M':
// clear the default setting of the list
stList_destruct(phylogenyTreeBuildingMethods);
phylogenyTreeBuildingMethods = stList_construct();
stList *methodStrings = stString_splitByString(optarg, ",");
for (int64_t i = 0; i < stList_length(methodStrings); i++) {
char *methodString = stList_get(methodStrings, i);
enum stCaf_TreeBuildingMethod *method = st_malloc(sizeof(enum stCaf_TreeBuildingMethod));
if (strcmp(methodString, "neighborJoining") == 0) {
*method = NEIGHBOR_JOINING;
} else if (strcmp(methodString, "guidedNeighborJoining") == 0) {
*method = GUIDED_NEIGHBOR_JOINING;
} else if (strcmp(methodString, "splitDecomposition") == 0) {
*method = SPLIT_DECOMPOSITION;
} else if (strcmp(methodString, "strictSplitDecomposition") == 0) {
*method = STRICT_SPLIT_DECOMPOSITION;
} else if (strcmp(methodString, "removeBadChains") == 0) {
*method = REMOVE_BAD_CHAINS;
} else {
st_errAbort("Unknown tree building method: %s", methodString);
}
stList_append(phylogenyTreeBuildingMethods, method);
}
stList_destruct(methodStrings);
break;
case 'N':
k = sscanf(optarg, "%lf", &phylogenyCostPerDupPerBase);
assert(k == 1);
break;
case 'O':
k = sscanf(optarg, "%lf", &phylogenyCostPerLossPerBase);
assert(k == 1);
break;
case 'P':
referenceEventHeader = stString_copy(optarg);
break;
case 'Q':
k = sscanf(optarg, "%lf", &phylogenyDoSplitsWithSupportHigherThanThisAllAtOnce);
assert(k == 1);
break;
case 'R':
k = sscanf(optarg, "%" PRIi64, &numTreeBuildingThreads);
assert(k == 1);
break;
case 'S':
doPhylogeny = true;
break;
case 'T':
k = sscanf(optarg, "%lf", &minimumBlockHomologySupport);
assert(k == 1);
assert(minimumBlockHomologySupport <= 1.0);
assert(minimumBlockHomologySupport >= 0.0);
break;
case 'U':
k = sscanf(optarg, "%lf", &nucleotideScalingFactor);
assert(k == 1);
break;
case 'V':
k = sscanf(optarg, "%" PRIi64, &minimumBlockDegreeToCheckSupport);
assert(k == 1);
break;
case 'W':
if (strcmp(optarg, "1") == 0) {
removeRecoverableChains = true;
recoverableChainsFilter = NULL;
} else if (strcmp(optarg, "unequalNumberOfIngroupCopies") == 0) {
removeRecoverableChains = true;
recoverableChainsFilter = stCaf_chainHasUnequalNumberOfIngroupCopies;
} else if (strcmp(optarg, "unequalNumberOfIngroupCopiesOrNoOutgroup") == 0) {
removeRecoverableChains = true;
recoverableChainsFilter = stCaf_chainHasUnequalNumberOfIngroupCopiesOrNoOutgroup;
} else if (strcmp(optarg, "0") == 0) {
removeRecoverableChains = false;
} else {
st_errAbort("Could not parse removeRecoverableChains argument");
}
break;
case 'X':
k = sscanf(optarg, "%" PRIi64, &minimumNumberOfSpecies);
if (k != 1) {
st_errAbort("Error parsing the minimumNumberOfSpecies argument");
}
break;
case 'Y':
if (strcmp(optarg, "chain") == 0) {
phylogenyHomologyUnitType = CHAIN;
} else if (strcmp(optarg, "block") == 0) {
phylogenyHomologyUnitType = BLOCK;
} else {
st_errAbort("Could not parse the phylogenyHomologyUnitType argument");
}
break;
case 'Z':
if (strcmp(optarg, "jukesCantor") == 0) {
phylogenyDistanceCorrectionMethod = JUKES_CANTOR;
} else if (strcmp(optarg, "none") == 0 ) {
phylogenyDistanceCorrectionMethod = NONE;
} else {
st_errAbort("Could not parse the phylogenyDistanceCorrectionMethod argument");
}
break;
case '1':
k = sscanf(optarg, "%" PRIi64, &maxRecoverableChainsIterations);
if (k != 1) {
st_errAbort("Error parsing the maxRecoverableChainsIterations argument");
}
break;
case '2':
k = sscanf(optarg, "%" PRIi64, &maxRecoverableChainLength);
if (k != 1) {
st_errAbort("Error parsing the maxRecoverableChainLength argument");
}
break;
default:
usage();
return 1;
}
}
///////////////////////////////////////////////////////////////////////////
// (0) Check the inputs.
///////////////////////////////////////////////////////////////////////////
assert(cactusDiskDatabaseString != NULL);
assert(minimumTreeCoverage >= 0.0);
assert(minimumTreeCoverage <= 1.0);
assert(blockTrim >= 0);
assert(annealingRoundsLength >= 0);
for (int64_t i = 0; i < annealingRoundsLength; i++) {
assert(annealingRounds[i] >= 0);
}
assert(meltingRoundsLength >= 0);
for (int64_t i = 1; i < meltingRoundsLength; i++) {
assert(meltingRounds[i - 1] < meltingRounds[i]);
assert(meltingRounds[i - 1] >= 1);
}
assert(alignmentTrimLength >= 0);
for (int64_t i = 0; i < alignmentTrimLength; i++) {
assert(alignmentTrims[i] >= 0);
}
assert(minimumOutgroupDegree >= 0);
assert(minimumIngroupDegree >= 0);
//////////////////////////////////////////////
//Set up logging
//////////////////////////////////////////////
st_setLogLevelFromString(logLevelString);
//////////////////////////////////////////////
//Log (some of) the inputs
//////////////////////////////////////////////
st_logInfo("Flower disk name : %s\n", cactusDiskDatabaseString);
//////////////////////////////////////////////
//Load the database
//////////////////////////////////////////////
kvDatabaseConf = stKVDatabaseConf_constructFromString(cactusDiskDatabaseString);
cactusDisk = cactusDisk_construct(kvDatabaseConf, 0);
st_logInfo("Set up the flower disk\n");
///////////////////////////////////////////////////////////////////////////
// Sort the constraints
///////////////////////////////////////////////////////////////////////////
stPinchIterator *pinchIteratorForConstraints = NULL;
if (constraintsFile != NULL) {
pinchIteratorForConstraints = stPinchIterator_constructFromFile(constraintsFile);
st_logInfo("Created an iterator for the alignment constaints from file: %s\n", constraintsFile);
}
///////////////////////////////////////////////////////////////////////////
// Do the alignment
///////////////////////////////////////////////////////////////////////////
startTime = time(NULL);
stList *flowers = flowerWriter_parseFlowersFromStdin(cactusDisk);
if (alignmentsFile == NULL) {
cactusDisk_preCacheStrings(cactusDisk, flowers);
}
char *tempFile1 = NULL;
for (int64_t i = 0; i < stList_length(flowers); i++) {
flower = stList_get(flowers, i);
if (!flower_builtBlocks(flower)) { // Do nothing if the flower already has defined blocks
st_logDebug("Processing flower: %lli\n", flower_getName(flower));
stCaf_setFlowerForAlignmentFiltering(flower);
//Set up the graph and add the initial alignments
stPinchThreadSet *threadSet = stCaf_setup(flower);
//Build the set of outgroup threads
outgroupThreads = stCaf_getOutgroupThreads(flower, threadSet);
//Setup the alignments
stPinchIterator *pinchIterator;
stList *alignmentsList = NULL;
if (alignmentsFile != NULL) {
assert(i == 0);
assert(stList_length(flowers) == 1);
if (sortAlignments) {
tempFile1 = getTempFile();
stCaf_sortCigarsFileByScoreInDescendingOrder(alignmentsFile, tempFile1);
pinchIterator = stPinchIterator_constructFromFile(tempFile1);
} else {
pinchIterator = stPinchIterator_constructFromFile(alignmentsFile);
}
} else {
if (tempFile1 == NULL) {
tempFile1 = getTempFile();
}
alignmentsList = stCaf_selfAlignFlower(flower, minimumSequenceLengthForBlast, lastzArguments, realign, realignArguments, tempFile1);
if (sortAlignments) {
stCaf_sortCigarsByScoreInDescendingOrder(alignmentsList);
}
st_logDebug("Ran lastz and have %" PRIi64 " alignments\n", stList_length(alignmentsList));
pinchIterator = stPinchIterator_constructFromList(alignmentsList);
}
for (int64_t annealingRound = 0; annealingRound < annealingRoundsLength; annealingRound++) {
int64_t minimumChainLength = annealingRounds[annealingRound];
int64_t alignmentTrim = annealingRound < alignmentTrimLength ? alignmentTrims[annealingRound] : 0;
st_logDebug("Starting annealing round with a minimum chain length of %" PRIi64 " and an alignment trim of %" PRIi64 "\n", minimumChainLength, alignmentTrim);
stPinchIterator_setTrim(pinchIterator, alignmentTrim);
//Add back in the constraints
if (pinchIteratorForConstraints != NULL) {
stCaf_anneal(threadSet, pinchIteratorForConstraints, filterFn);
}
//Do the annealing
if (annealingRound == 0) {
stCaf_anneal(threadSet, pinchIterator, filterFn);
} else {
stCaf_annealBetweenAdjacencyComponents(threadSet, pinchIterator, filterFn);
}
// Dump the block degree and length distribution to a file
if (debugFileName != NULL) {
dumpBlockInfo(threadSet, stString_print("%s-blockStats-preMelting", debugFileName));
}
printf("Sequence graph statistics after annealing:\n");
printThreadSetStatistics(threadSet, flower, stdout);
// Check for poorly-supported blocks--those that have
// been transitively aligned together but with very
// few homologies supporting the transitive
// alignment. These "megablocks" can snarl up the
// graph so that a lot of extra gets thrown away in
// the first melting step.
stPinchThreadSetBlockIt blockIt = stPinchThreadSet_getBlockIt(threadSet);
stPinchBlock *block;
while ((block = stPinchThreadSetBlockIt_getNext(&blockIt)) != NULL) {
if (stPinchBlock_getDegree(block) > minimumBlockDegreeToCheckSupport) {
uint64_t supportingHomologies = stPinchBlock_getNumSupportingHomologies(block);
uint64_t possibleSupportingHomologies = numPossibleSupportingHomologies(block, flower);
double support = ((double) supportingHomologies) / possibleSupportingHomologies;
if (support < minimumBlockHomologySupport) {
fprintf(stdout, "Destroyed a megablock with degree %" PRIi64
" and %" PRIi64 " supporting homologies out of a maximum "
"of %" PRIi64 " (%lf%%).\n", stPinchBlock_getDegree(block),
supportingHomologies, possibleSupportingHomologies, support);
stPinchBlock_destruct(block);
}
}
}
//Do the melting rounds
for (int64_t meltingRound = 0; meltingRound < meltingRoundsLength; meltingRound++) {
int64_t minimumChainLengthForMeltingRound = meltingRounds[meltingRound];
st_logDebug("Starting melting round with a minimum chain length of %" PRIi64 " \n", minimumChainLengthForMeltingRound);
if (minimumChainLengthForMeltingRound >= minimumChainLength) {
break;
}
stCaf_melt(flower, threadSet, NULL, 0, minimumChainLengthForMeltingRound, 0, INT64_MAX);
} st_logDebug("Last melting round of cycle with a minimum chain length of %" PRIi64 " \n", minimumChainLength);
stCaf_melt(flower, threadSet, NULL, 0, minimumChainLength, breakChainsAtReverseTandems, maximumMedianSequenceLengthBetweenLinkedEnds);
//This does the filtering of blocks that do not have the required species/tree-coverage/degree.
stCaf_melt(flower, threadSet, blockFilterFn, blockTrim, 0, 0, INT64_MAX);
}
if (removeRecoverableChains) {
stCaf_meltRecoverableChains(flower, threadSet, breakChainsAtReverseTandems, maximumMedianSequenceLengthBetweenLinkedEnds, recoverableChainsFilter, maxRecoverableChainsIterations, maxRecoverableChainLength);
}
if (debugFileName != NULL) {
dumpBlockInfo(threadSet, stString_print("%s-blockStats-postMelting", debugFileName));
}
printf("Sequence graph statistics after melting:\n");
printThreadSetStatistics(threadSet, flower, stdout);
// Build a tree for each block, then use each tree to
// partition the homologies between the ingroups sequences
// into those that occur before the speciation with the
// outgroup and those which occur late.
if (stSet_size(outgroupThreads) > 0 && doPhylogeny) {
st_logDebug("Starting to build trees and partition ingroup homologies\n");
stHash *threadStrings = stCaf_getThreadStrings(flower, threadSet);
st_logDebug("Got sets of thread strings and set of threads that are outgroups\n");
stCaf_PhylogenyParameters params;
params.distanceCorrectionMethod = phylogenyDistanceCorrectionMethod;
params.treeBuildingMethods = phylogenyTreeBuildingMethods;
params.rootingMethod = phylogenyRootingMethod;
params.scoringMethod = phylogenyScoringMethod;
params.breakpointScalingFactor = breakpointScalingFactor;
params.nucleotideScalingFactor = nucleotideScalingFactor;
params.skipSingleCopyBlocks = phylogenySkipSingleCopyBlocks;
params.keepSingleDegreeBlocks = phylogenyKeepSingleDegreeBlocks;
params.costPerDupPerBase = phylogenyCostPerDupPerBase;
params.costPerLossPerBase = phylogenyCostPerLossPerBase;
params.maxBaseDistance = phylogenyMaxBaseDistance;
params.maxBlockDistance = phylogenyMaxBlockDistance;
params.numTrees = phylogenyNumTrees;
params.ignoreUnalignedBases = 1;
params.onlyIncludeCompleteFeatureBlocks = 0;
params.doSplitsWithSupportHigherThanThisAllAtOnce = phylogenyDoSplitsWithSupportHigherThanThisAllAtOnce;
params.numTreeBuildingThreads = numTreeBuildingThreads;
assert(params.numTreeBuildingThreads >= 1);
stCaf_buildTreesToRemoveAncientHomologies(
threadSet, phylogenyHomologyUnitType, threadStrings, outgroupThreads, flower, ¶ms,
debugFileName == NULL ? NULL : stString_print("%s-phylogeny", debugFileName), referenceEventHeader);
stHash_destruct(threadStrings);
st_logDebug("Finished building trees\n");
if (removeRecoverableChains) {
// We melt recoverable chains after splitting, as
// well as before, to alleviate coverage loss
// caused by bad splits.
stCaf_meltRecoverableChains(flower, threadSet, breakChainsAtReverseTandems, maximumMedianSequenceLengthBetweenLinkedEnds, recoverableChainsFilter, maxRecoverableChainsIterations, maxRecoverableChainLength);
}
// Enforce the block constraints on minimum degree,
// etc. after splitting.
stCaf_melt(flower, threadSet, blockFilterFn, 0, 0, 0, INT64_MAX);
}
//Sort out case when we allow blocks of degree 1
if (minimumDegree < 2) {
st_logDebug("Creating degree 1 blocks\n");
stCaf_makeDegreeOneBlocks(threadSet);
stCaf_melt(flower, threadSet, blockFilterFn, blockTrim, 0, 0, INT64_MAX);
} else if (maximumAdjacencyComponentSizeRatio < INT64_MAX) { //Deal with giant components
st_logDebug("Breaking up components greedily\n");
stCaf_breakupComponentsGreedily(threadSet, maximumAdjacencyComponentSizeRatio);
}
//Finish up
stCaf_finish(flower, threadSet, chainLengthForBigFlower, longChain, minLengthForChromosome,
proportionOfUnalignedBasesForNewChromosome); //Flower is then destroyed at this point.
st_logInfo("Ran the cactus core script\n");
//Cleanup
stPinchThreadSet_destruct(threadSet);
stPinchIterator_destruct(pinchIterator);
stSet_destruct(outgroupThreads);
if (alignmentsList != NULL) {
stList_destruct(alignmentsList);
}
st_logInfo("Cleaned up from main loop\n");
} else {
st_logInfo("We've already built blocks / alignments for this flower\n");
}
}
stList_destruct(flowers);
if (tempFile1 != NULL) {
st_system("rm %s", tempFile1);
}
if (constraintsFile != NULL) {
stPinchIterator_destruct(pinchIteratorForConstraints);
}
///////////////////////////////////////////////////////////////////////////
// Write the flower to disk.
///////////////////////////////////////////////////////////////////////////
st_logDebug("Writing the flowers to disk\n");
cactusDisk_write(cactusDisk);
st_logInfo("Updated the flower on disk and %" PRIi64 " seconds have elapsed\n", time(NULL) - startTime);
///////////////////////////////////////////////////////////////////////////
// Clean up.
///////////////////////////////////////////////////////////////////////////
cactusDisk_destruct(cactusDisk);
}
//============================== MAIN =========================================
int main(int argc, char *argv[]) {
Flower *flower;
/*
* Arguments/options
*/
char * st_logLevelString = NULL;
char * cactusDiskDatabaseString = NULL;
char * flowerName = "0";
char * outputFile = NULL;
char * species = NULL;
char * geneFile = NULL;
///////////////////////////////////////////////////////////////////////////
// (0) Parse the inputs handed by genomeCactus.py / setup stuff.
///////////////////////////////////////////////////////////////////////////
while(1) {
static struct option long_options[] = {
{ "genePslFile", required_argument, 0, 'g' },
{ "species", required_argument, 0, 's' },
{ "st_logLevel", required_argument, 0, 'a' },
{ "cactusDisk", required_argument, 0, 'c' },
{ "outputFile", required_argument, 0, 'o' },
{ "help", no_argument, 0, 'h' },
{ 0, 0, 0, 0 }
};
int option_index = 0;
int key = getopt_long(argc, argv, "s:g:o:a:c:h", long_options, &option_index);
if(key == -1) {
break;
}
switch(key) {
case 'a':
st_logLevelString = stString_copy(optarg);
break;
case 'c':
cactusDiskDatabaseString = stString_copy(optarg);
break;
case 'o':
outputFile = stString_copy(optarg);
break;
case 's':
species = stString_copy(optarg);
break;
case 'g':
geneFile = stString_copy(optarg);
break;
case 'h':
usage();
return 0;
default:
usage();
return 1;
}
}
///////////////////////////////////////////////////////////////////////////
// (0) Check the inputs.
///////////////////////////////////////////////////////////////////////////
assert(cactusDiskDatabaseString != NULL);
assert(outputFile != NULL);
assert(species != NULL);
assert(geneFile != NULL);
//////////////////////////////////////////////
//Set up st_logging
//////////////////////////////////////////////
st_setLogLevelFromString(st_logLevelString);
//////////////////////////////////////////////
//Log (some of) the inputs
//////////////////////////////////////////////
st_logInfo("Flower disk name : %s\n", cactusDiskDatabaseString);
st_logInfo("Output file : %s\n", outputFile);
st_logInfo("Species: %s\n", species);
st_logInfo("GenePslFile: %s\n", geneFile);
//////////////////////////////////////////////
//Load the database
//////////////////////////////////////////////
stKVDatabaseConf *kvDatabaseConf = stKVDatabaseConf_constructFromString(cactusDiskDatabaseString);
CactusDisk *cactusDisk = cactusDisk_construct(kvDatabaseConf, 0);
st_logInfo("Set up the flower disk\n");
///////////////////////////////////////////////////////////////////////////
// Parse the basic reconstruction problem
///////////////////////////////////////////////////////////////////////////
flower = cactusDisk_getFlower(cactusDisk, cactusMisc_stringToName(flowerName));
st_logInfo("Parsed the top level flower of the cactus tree to check\n");
///////////////////////////////////////////////////////////////////////////
// Recursive check the flowers.
///////////////////////////////////////////////////////////////////////////
int64_t startTime = time(NULL);
FILE *fileHandle = fopen(outputFile, "w");
struct bed *gene = bedLoadAll(geneFile);
mapGenes(flower, fileHandle, gene, species);
fclose(fileHandle);
st_logInfo("Map genes in %" PRIi64 " seconds/\n", time(NULL) - startTime);
///////////////////////////////////////////////////////////////////////////
// Clean up.
///////////////////////////////////////////////////////////////////////////
cactusDisk_destruct(cactusDisk);
return 0;
}
void stTree_setLabel(stTree *tree, const char *label) {
if(tree->label != NULL) {
free(tree->label);
}
tree->label = label == NULL ? NULL : stString_copy(label);
}
struct bed *bedLoadAll(char *fileName){
struct bed *list = NULL;
struct bed *currbed = NULL;
struct bed *prevbed = NULL;
FILE *fp;
char *line = st_malloc(sizeof(char)*LINEMAXSIZE);
char *lend;
struct List *lineList;
fp = fopen(fileName, "r");
assert(fp != NULL);
while( fgets(line, LINEMAXSIZE, fp) != NULL ){//each line
//catch if not enough buffer
if ( (lend = strstr(line, "\n")) == NULL ){
fprintf(stderr, "Input line is too long for buffer: \n*%s*\n", line);
exit(0);
}else{//trim \n
*lend = '\0';
}
//skip header line
if(strstr(line, "track") == line){ continue; }
lineList = splitString(line, "\t");
//empty lines, skip
if(lineList->length == 0){ continue; }
if(lineList->length < 12){
fprintf(stderr, "Wrong input format. Need at least 12 fields for each bed\n");
exit(0);
}else{
currbed = constructbed();
currbed->chrom = stString_copy(lineList->list[0]);
assert( sscanf(lineList->list[1], "%" PRIi64, &(currbed->chromStart)) == 1);
assert( sscanf(lineList->list[2], "%" PRIi64, &(currbed->chromEnd)) == 1);
currbed->name = stString_copy(lineList->list[3]);
assert( sscanf(lineList->list[4], "%d", &(currbed->score)) == 1);
currbed->strand = stString_copy(lineList->list[5]);
assert( sscanf(lineList->list[6], "%" PRIi64, &(currbed->thickStart)) == 1);
assert( sscanf(lineList->list[7], "%" PRIi64, &(currbed->thickEnd)) == 1);
assert( sscanf(lineList->list[8], "%" PRIi64, &(currbed->itemRgb)) == 1);
assert( sscanf(lineList->list[9], "%" PRIi64, &(currbed->blockCount)) == 1);
currbed->blockSizes = splitIntString(stString_copy(lineList->list[10]), ",");
assert(currbed->blockSizes->length == currbed->blockCount);
currbed->chromStarts = splitIntString(stString_copy(lineList->list[11]), ",");
assert(currbed->chromStarts->length == currbed->blockCount);
//destructList(lineList);
if(list == NULL){
list = currbed;
prevbed = currbed;
}else{
prevbed->next = currbed;
prevbed = currbed;
}
}
st_logInfo("Gene: %s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%d\t%d\n",
currbed->chrom, currbed->chromStart, currbed->chromEnd, currbed->name,
currbed->score, currbed->strand, currbed->thickStart, currbed->thickEnd,
currbed->itemRgb, currbed->blockCount);
}
fclose(fp);
return list;
}
int main(int argc, char *argv[]) {
/*
* Script for adding a reference genome to a flower.
*/
/*
* Arguments/options
*/
char * logLevelString = NULL;
char * cactusDiskDatabaseString = NULL;
char *referenceEventString =
(char *) cactusMisc_getDefaultReferenceEventHeader();
char *outputFile = NULL;
Name flowerName = NULL_NAME;
///////////////////////////////////////////////////////////////////////////
// (0) Parse the inputs handed by genomeCactus.py / setup stuff.
///////////////////////////////////////////////////////////////////////////
while (1) {
static struct option long_options[] = { { "logLevel",
required_argument, 0, 'a' }, { "cactusDisk", required_argument,
0, 'c' }, { "flowerName", required_argument,
0, 'd' },
{ "referenceEventString", required_argument, 0, 'g' }, {
"help", no_argument, 0, 'h' }, { "outputFile",
required_argument, 0, 'k' },
{ 0, 0, 0, 0 } };
int option_index = 0;
int key = getopt_long(argc, argv, "a:c:d:g:hk:", long_options,
&option_index);
if (key == -1) {
break;
}
switch (key) {
case 'a':
logLevelString = stString_copy(optarg);
break;
case 'c':
cactusDiskDatabaseString = stString_copy(optarg);
break;
case 'd':
flowerName = cactusMisc_stringToName(optarg);
break;
case 'g':
referenceEventString = stString_copy(optarg);
break;
case 'h':
usage();
return 0;
case 'k':
outputFile = stString_copy(optarg);
break;
default:
usage();
return 1;
}
}
///////////////////////////////////////////////////////////////////////////
// (0) Check the inputs.
///////////////////////////////////////////////////////////////////////////
assert(cactusDiskDatabaseString != NULL);
//////////////////////////////////////////////
//Set up logging
//////////////////////////////////////////////
st_setLogLevelFromString(logLevelString);
//////////////////////////////////////////////
//Load the database
//////////////////////////////////////////////
stKVDatabaseConf *kvDatabaseConf = stKVDatabaseConf_constructFromString(
cactusDiskDatabaseString);
CactusDisk *cactusDisk = cactusDisk_construct(kvDatabaseConf, 0);
stKVDatabaseConf_destruct(kvDatabaseConf);
st_logInfo("Set up the flower disk\n");
///////////////////////////////////////////////////////////////////////////
// Get the set of flowers to manipulate
///////////////////////////////////////////////////////////////////////////
Flower *flower = cactusDisk_getFlower(cactusDisk, flowerName);
///////////////////////////////////////////////////////////////////////////
// Get the reference event name
///////////////////////////////////////////////////////////////////////////
Event *referenceEvent = eventTree_getEventByHeader(
flower_getEventTree(flower), referenceEventString);
assert(referenceEvent != NULL);
Name referenceEventName = event_getName(referenceEvent);
///////////////////////////////////////////////////////////////////////////
// Now process each flower in turn.
///////////////////////////////////////////////////////////////////////////
if(outputFile == NULL) {
st_errAbort("No output file specified\n");
}
FILE *fileHandle = fopen(outputFile, "w");
printFastaSequences(flower, fileHandle, referenceEventName);
if(fileHandle != NULL) {
fclose(fileHandle);
}
///////////////////////////////////////////////////////////////////////////
//Clean up memory
///////////////////////////////////////////////////////////////////////////
cactusDisk_destruct(cactusDisk);
//return 0; //Exit without clean up is quicker, enable cleanup when doing memory leak detection.
free(cactusDiskDatabaseString);
free(referenceEventString);
free(logLevelString);
st_logInfo("Cleaned stuff up and am finished\n");
//while(1);
return 0;
}
static char *terminalAdjacencyWriteFn(Cap *cap) {
return stString_copy("");
}
int main(int argc, char *argv[]) {
Flower *flower;
FILE *fileHandle;
/*
* Arguments/options
*/
char * logLevelString = NULL;
char * cactusDiskDatabaseString = NULL;
char * flowerName = NULL;
char * outputFile = NULL;
///////////////////////////////////////////////////////////////////////////
// (0) Parse the inputs handed by genomeCactus.py / setup stuff.
///////////////////////////////////////////////////////////////////////////
while (1) {
static struct option long_options[] = { { "logLevel",
required_argument, 0, 'a' }, { "cactusDisk", required_argument, 0,
'c' }, { "flowerName", required_argument, 0, 'd' }, {
"outputFile", required_argument, 0, 'e' }, { "scaleNodeSizes",
no_argument, 0, 'f' }, { "nameLabels", no_argument, 0, 'g' }, {
"help", no_argument, 0, 'h' }, { 0, 0, 0, 0 } };
int option_index = 0;
int key = getopt_long(argc, argv, "a:c:d:e:fgh", long_options,
&option_index);
if (key == -1) {
break;
}
switch (key) {
case 'a':
logLevelString = stString_copy(optarg);
break;
case 'c':
cactusDiskDatabaseString = stString_copy(optarg);
break;
case 'd':
flowerName = stString_copy(optarg);
break;
case 'e':
outputFile = stString_copy(optarg);
break;
case 'f':
scaleNodeSizes = !scaleNodeSizes;
break;
case 'g':
nameLabels = !nameLabels;
break;
case 'h':
usage();
return 0;
default:
usage();
return 1;
}
}
///////////////////////////////////////////////////////////////////////////
// (0) Check the inputs.
///////////////////////////////////////////////////////////////////////////
assert(cactusDiskDatabaseString != NULL);
assert(flowerName != NULL);
assert(outputFile != NULL);
//////////////////////////////////////////////
//Set up logging
//////////////////////////////////////////////
st_setLogLevelFromString(logLevelString);
//////////////////////////////////////////////
//Log (some of) the inputs
//////////////////////////////////////////////
st_logInfo("Flower name : %s\n", flowerName);
st_logInfo("Output graph file : %s\n", outputFile);
//////////////////////////////////////////////
//Load the database
//////////////////////////////////////////////
stKVDatabaseConf *kvDatabaseConf = stKVDatabaseConf_constructFromString(cactusDiskDatabaseString);
CactusDisk *cactusDisk = cactusDisk_construct(kvDatabaseConf, 0);
st_logInfo("Set up the flower disk\n");
///////////////////////////////////////////////////////////////////////////
// Parse the basic reconstruction problem
///////////////////////////////////////////////////////////////////////////
flower = cactusDisk_getFlower(cactusDisk, cactusMisc_stringToName(flowerName));
st_logInfo("Parsed the top level flower of the cactus tree to build\n");
///////////////////////////////////////////////////////////////////////////
// Build the graph.
///////////////////////////////////////////////////////////////////////////
totalProblemSize = flower_getTotalBaseLength(flower);
fileHandle = fopen(outputFile, "w");
graphViz_setupGraphFile(fileHandle);
makeCactusTree_flower(flower, fileHandle, NULL, NULL);
graphViz_finishGraphFile(fileHandle);
fclose(fileHandle);
st_logInfo("Written the tree to file\n");
///////////////////////////////////////////////////////////////////////////
// Clean up.
///////////////////////////////////////////////////////////////////////////
cactusDisk_destruct(cactusDisk);
stKVDatabaseConf_destruct(kvDatabaseConf);
return 0;
}
int main(int argc, char *argv[]) {
/*
* Open the database.
* Construct a flower.
* Construct an event tree representing the species tree.
* For each sequence contruct two ends each containing an cap.
* Make a file for the sequence.
* Link the two caps.
* Finish!
*/
int64_t key, j;
Group *group;
Flower_EndIterator *endIterator;
End *end;
bool makeEventHeadersAlphaNumeric = 0;
/*
* Arguments/options
*/
char * logLevelString = NULL;
char * speciesTree = NULL;
char * outgroupEvents = NULL;
///////////////////////////////////////////////////////////////////////////
// (0) Parse the inputs handed by genomeCactus.py / setup stuff.
///////////////////////////////////////////////////////////////////////////
while (1) {
static struct option long_options[] = { { "logLevel", required_argument, 0, 'a' }, { "cactusDisk", required_argument, 0, 'b' }, {
"speciesTree", required_argument, 0, 'f' }, { "outgroupEvents", required_argument, 0, 'g' },
{ "help", no_argument, 0, 'h' }, { "makeEventHeadersAlphaNumeric", no_argument, 0, 'i' }, { 0, 0, 0, 0 } };
int option_index = 0;
key = getopt_long(argc, argv, "a:b:f:hg:i", long_options, &option_index);
if (key == -1) {
break;
}
switch (key) {
case 'a':
logLevelString = optarg;
break;
case 'b':
cactusDiskDatabaseString = optarg;
break;
case 'f':
speciesTree = optarg;
break;
case 'g':
outgroupEvents = optarg;
break;
case 'h':
usage();
return 0;
case 'i':
makeEventHeadersAlphaNumeric = 1;
break;
default:
usage();
return 1;
}
}
///////////////////////////////////////////////////////////////////////////
// (0) Check the inputs.
///////////////////////////////////////////////////////////////////////////
//assert(logLevelString == NULL || strcmp(logLevelString, "CRITICAL") == 0 || strcmp(logLevelString, "INFO") == 0 || strcmp(logLevelString, "DEBUG") == 0);
assert(cactusDiskDatabaseString != NULL);
assert(speciesTree != NULL);
//////////////////////////////////////////////
//Set up logging
//////////////////////////////////////////////
st_setLogLevelFromString(logLevelString);
//////////////////////////////////////////////
//Log (some of) the inputs
//////////////////////////////////////////////
st_logInfo("Flower disk name : %s\n", cactusDiskDatabaseString);
for (j = optind; j < argc; j++) {
st_logInfo("Sequence file/directory %s\n", argv[j]);
}
//////////////////////////////////////////////
//Load the database
//////////////////////////////////////////////
stKVDatabaseConf *kvDatabaseConf = kvDatabaseConf = stKVDatabaseConf_constructFromString(cactusDiskDatabaseString);
if (stKVDatabaseConf_getType(kvDatabaseConf) == stKVDatabaseTypeTokyoCabinet || stKVDatabaseConf_getType(kvDatabaseConf)
== stKVDatabaseTypeKyotoTycoon) {
assert(stKVDatabaseConf_getDir(kvDatabaseConf) != NULL);
cactusDisk = cactusDisk_construct2(kvDatabaseConf, "cactusSequences");
} else {
cactusDisk = cactusDisk_construct(kvDatabaseConf, 1);
}
st_logInfo("Set up the flower disk\n");
//////////////////////////////////////////////
//Construct the flower
//////////////////////////////////////////////
if (cactusDisk_getFlower(cactusDisk, 0) != NULL) {
cactusDisk_destruct(cactusDisk);
st_logInfo("The first flower already exists\n");
return 0;
}
flower = flower_construct2(0, cactusDisk);
assert(flower_getName(flower) == 0);
st_logInfo("Constructed the flower\n");
//////////////////////////////////////////////
//Construct the event tree
//////////////////////////////////////////////
st_logInfo("Going to build the event tree with newick string: %s\n", speciesTree);
stTree *tree = stTree_parseNewickString(speciesTree);
st_logInfo("Parsed the tree\n");
if (makeEventHeadersAlphaNumeric) {
makeEventHeadersAlphaNumericFn(tree);
}
stTree_setBranchLength(tree, INT64_MAX);
checkBranchLengthsAreDefined(tree);
eventTree = eventTree_construct2(flower); //creates the event tree and the root even
totalEventNumber = 1;
st_logInfo("Constructed the basic event tree\n");
// Construct a set of outgroup names so that ancestral outgroups
// get recognized.
stSet *outgroupNameSet = stSet_construct3(stHash_stringKey,
stHash_stringEqualKey,
free);
if(outgroupEvents != NULL) {
stList *outgroupNames = stString_split(outgroupEvents);
for(int64_t i = 0; i < stList_length(outgroupNames); i++) {
char *outgroupName = stList_get(outgroupNames, i);
stSet_insert(outgroupNameSet, stString_copy(outgroupName));
}
stList_destruct(outgroupNames);
}
//now traverse the tree
j = optind;
assignEventsAndSequences(eventTree_getRootEvent(eventTree), tree,
outgroupNameSet, argv, &j);
char *eventTreeString = eventTree_makeNewickString(eventTree);
st_logInfo(
"Constructed the initial flower with %" PRIi64 " sequences and %" PRIi64 " events with string: %s\n",
totalSequenceNumber, totalEventNumber, eventTreeString);
assert(event_getSubTreeBranchLength(eventTree_getRootEvent(eventTree)) >= 0.0);
free(eventTreeString);
//assert(0);
//////////////////////////////////////////////
//Label any outgroup events.
//////////////////////////////////////////////
if (outgroupEvents != NULL) {
stList *outgroupEventsList = stString_split(outgroupEvents);
for (int64_t i = 0; i < stList_length(outgroupEventsList); i++) {
char *outgroupEvent = makeEventHeadersAlphaNumeric ? makeAlphaNumeric(stList_get(outgroupEventsList, i)) : stString_copy(stList_get(outgroupEventsList, i));
Event *event = eventTree_getEventByHeader(eventTree, outgroupEvent);
if (event == NULL) {
st_errAbort("Got an outgroup string that does not match an event, outgroup string %s", outgroupEvent);
}
assert(!event_isOutgroup(event));
event_setOutgroupStatus(event, 1);
assert(event_isOutgroup(event));
free(outgroupEvent);
}
stList_destruct(outgroupEventsList);
}
//////////////////////////////////////////////
//Construct the terminal group.
//////////////////////////////////////////////
if (flower_getEndNumber(flower) > 0) {
group = group_construct2(flower);
endIterator = flower_getEndIterator(flower);
while ((end = flower_getNextEnd(endIterator)) != NULL) {
end_setGroup(end, group);
}
flower_destructEndIterator(endIterator);
assert(group_isLeaf(group));
// Create a one link chain if there is only one pair of attached ends..
group_constructChainForLink(group);
assert(!flower_builtBlocks(flower));
} else {
flower_setBuiltBlocks(flower, 1);
}
///////////////////////////////////////////////////////////////////////////
// Write the flower to disk.
///////////////////////////////////////////////////////////////////////////
//flower_check(flower);
cactusDisk_write(cactusDisk);
st_logInfo("Updated the flower on disk\n");
///////////////////////////////////////////////////////////////////////////
// Cleanup.
///////////////////////////////////////////////////////////////////////////
cactusDisk_destruct(cactusDisk);
return 0; //Exit without clean up is quicker, enable cleanup when doing memory leak detection.
stSet_destruct(outgroupNameSet);
stTree_destruct(tree);
stKVDatabaseConf_destruct(kvDatabaseConf);
return 0;
}
int main(int argc, char *argv[]) {
char * logLevelString = NULL;
char * cactusDiskDatabaseString = NULL;
char * flowerName = NULL;
char * outputFile = NULL;
char *referenceEventString = NULL;
///////////////////////////////////////////////////////////////////////////
// (0) Parse the inputs handed by genomeCactus.py / setup stuff.
///////////////////////////////////////////////////////////////////////////
while (1) {
static struct option long_options[] = {
{ "logLevel", required_argument, 0, 'a' },
{ "referenceEventString", required_argument, 0, 'b' },
{ "cactusDisk", required_argument, 0, 'c' },
{ "flowerName", required_argument, 0, 'e' },
{ "outputFile", required_argument, 0, 'f' },
{ "help", no_argument, 0, 'h' }, { 0, 0, 0, 0 } };
int option_index = 0;
int key = getopt_long(argc, argv, "a:b:c:d:e:f:h", long_options,
&option_index);
if (key == -1) {
break;
}
switch (key) {
case 'a':
logLevelString = stString_copy(optarg);
break;
case 'b':
referenceEventString = stString_copy(optarg);
break;
case 'c':
cactusDiskDatabaseString = stString_copy(optarg);
break;
case 'e':
flowerName = stString_copy(optarg);
break;
case 'f':
outputFile = stString_copy(optarg);
break;
case 'h':
usage();
return 0;
default:
usage();
return 1;
}
}
///////////////////////////////////////////////////////////////////////////
// (0) Check the inputs.
///////////////////////////////////////////////////////////////////////////
assert(flowerName != NULL);
assert(referenceEventString != NULL);
assert(cactusDiskDatabaseString != NULL);
assert(outputFile != NULL);
//////////////////////////////////////////////
//Set up logging
//////////////////////////////////////////////
st_setLogLevelFromString(logLevelString);
//////////////////////////////////////////////
//Log (some of) the inputs
//////////////////////////////////////////////
st_logInfo("Flower name : %s\n", flowerName);
st_logInfo("Sequence name : %s\n", referenceEventString);
st_logInfo("Output file : %s\n", outputFile);
//////////////////////////////////////////////
//Load the database
//////////////////////////////////////////////
stKVDatabaseConf *kvDatabaseConf = stKVDatabaseConf_constructFromString(
cactusDiskDatabaseString);
CactusDisk *cactusDisk = cactusDisk_construct(kvDatabaseConf, false, true);
st_logInfo("Set up the flower disk\n");
///////////////////////////////////////////////////////////////////////////
// Parse the basic reconstruction problem
///////////////////////////////////////////////////////////////////////////
Flower *flower = cactusDisk_getFlower(cactusDisk, cactusMisc_stringToName(
flowerName));
st_logInfo("Parsed the top level flower of the cactus tree to check\n");
///////////////////////////////////////////////////////////////////////////
// Recursive check the flowers.
///////////////////////////////////////////////////////////////////////////
//int64_t startTime = time(NULL);
//flower = flower_addReferenceSequence(flower, cactusDisk, name);
//st_logInfo("Added the reference sequence in %" PRIi64 " seconds/\n", time(NULL) - startTime);
int64_t numSequences = flower_getSequenceNumber(flower);
//Make sure that referenceSequence has already been added:
if(getSequenceMatchesEvent(flower, referenceEventString) == NULL &&
numSequences > 0){
fprintf(stderr, "No reference sequence found in cactusDisk\n");
exit(EXIT_FAILURE);
}
FILE *fileHandle = fopen(outputFile, "w");
if (numSequences > 0) {
getReferenceSequences(fileHandle, flower, referenceEventString);
}
else {
st_logCritical("cactus_getReferenceSeq found no reference sequence in empty cactus disk %s",
cactusDiskDatabaseString);
}
fclose(fileHandle);
///////////////////////////////////////////////////////////////////////////
// Clean up.
///////////////////////////////////////////////////////////////////////////
cactusDisk_destruct(cactusDisk);
return 0; //Exit without clean up is quicker, enable cleanup when doing memory leak detection.
stKVDatabaseConf_destruct(kvDatabaseConf);
return 0;
}
int main(int argc, char *argv[]) {
/*
* Arguments/options
*/
char * logLevelString = NULL;
char * mAFFile1 = NULL;
char * mAFFile2 = NULL;
char * outputFile = NULL;
int32_t sampleNumber = 1000000; // by default do a million samples per pair.
char * trioFile = NULL;
///////////////////////////////////////////////////////////////////////////
// (0) Parse the inputs handed by genomeCactus.py / setup stuff.
///////////////////////////////////////////////////////////////////////////
while(1) {
static struct option long_options[] = {
{ "logLevel", required_argument, 0, 'a' },
{ "mAFFile1", required_argument, 0, 'b' },
{ "mAFFile2", required_argument, 0, 'c' },
{ "outputFile", required_argument, 0, 'd' },
{ "sampleNumber", required_argument, 0, 'e' },
{ "trioFile", required_argument, 0, 'f' },
{ "help", no_argument, 0, 'h' },
{ 0, 0, 0, 0 }
};
int option_index = 0;
int key = getopt_long(argc, argv, "a:b:c:d:e:f:h", long_options, &option_index);
if(key == -1) {
break;
}
switch(key) {
case 'a':
logLevelString = stString_copy(optarg);
break;
case 'b':
mAFFile1 = stString_copy(optarg);
break;
case 'c':
mAFFile2 = stString_copy(optarg);
break;
case 'd':
outputFile = stString_copy(optarg);
break;
case 'e':
assert(sscanf(optarg, "%i", &sampleNumber) == 1);
break;
case 'f':
trioFile = stString_copy(optarg);
break;
case 'h':
usage();
return 0;
default:
usage();
return 1;
}
}
///////////////////////////////////////////////////////////////////////////
// (0) Check the inputs.
///////////////////////////////////////////////////////////////////////////
if (argc == 1) {
usage();
return 1;
}
assert(mAFFile1 != NULL);
assert(mAFFile2 != NULL);
assert(outputFile != NULL);
assert(trioFile != NULL);
FILE *fileHandle = fopen(mAFFile1, "r");
if (fileHandle == NULL) {
fprintf(stderr, "ERROR, unable to open `%s', is path correct?\n", mAFFile1);
exit(1);
}
fclose(fileHandle);
fileHandle = fopen(mAFFile2, "r");
if (fileHandle == NULL) {
fprintf(stderr, "ERROR, unable to open `%s', is path correct?\n", mAFFile2);
exit(1);
}
fclose(fileHandle);
fileHandle = fopen(trioFile, "r");
if (fileHandle == NULL) {
fprintf(stderr, "ERROR, unable to open `%s', is path correct?\n", trioFile);
exit(1);
}
fclose(fileHandle);
//////////////////////////////////////////////
//Set up logging
//////////////////////////////////////////////
st_setLogLevelFromString(logLevelString);
//////////////////////////////////////////////
//Log (some of) the inputs
//////////////////////////////////////////////
st_logInfo("MAF file 1 name : %s\n", mAFFile1);
st_logInfo("MAF file 2 name : %s\n", mAFFile2);
st_logInfo("Trio species name : %s\n", trioFile);
st_logInfo("Output stats file : %s\n", outputFile);
/* Parse the trioFile triples into a list */
struct List *speciesList = parseTrioFile(trioFile);
//////////////////////////////////////////////
// Create hashtable for the first MAF file.
//////////////////////////////////////////////
struct hashtable *seqNameHash;
seqNameHash = create_hashtable(256, hashtable_stringHashKey, hashtable_stringEqualKey, free, free);
populateNameHash(mAFFile1, seqNameHash);
// TODO: Check if query species are in maf file
//////////////////////////////////////////////
//Do comparisons.
//////////////////////////////////////////////
struct avl_table *results_12 = compareMAFs_AB_Trio(mAFFile1, mAFFile2, sampleNumber, seqNameHash, speciesList);
struct avl_table *results_21 = compareMAFs_AB_Trio(mAFFile2, mAFFile1, sampleNumber, seqNameHash, speciesList);
fileHandle = fopen(outputFile, "w");
if (fileHandle == NULL) {
fprintf(stderr, "ERROR, unable to open `%s' for writing.\n", outputFile);
exit(1);
}
fprintf(fileHandle, "<trio_comparisons sampleNumber=\"%i\">\n", sampleNumber);
reportResultsTrio(results_12, mAFFile1, mAFFile2, fileHandle);
reportResultsTrio(results_21, mAFFile2, mAFFile1, fileHandle);
fprintf(fileHandle, "</trio_comparisons>\n");
fclose(fileHandle);
///////////////////////////////////////////////////////////////////////////
// Clean up.
///////////////////////////////////////////////////////////////////////////
free(mAFFile1);
free(mAFFile2);
free(outputFile);
free(trioFile);
free(logLevelString);
hashtable_destroy(seqNameHash, 1, 1);
avl_destroy(results_12, (void (*)(void *, void *))aTrio_destruct);
avl_destroy(results_21, (void (*)(void *, void *))aTrio_destruct);
destructList(speciesList);
return 0;
}
stKVDatabaseConf *stKVDatabaseConf_constructTokyoCabinet(const char *databaseDir) {
stKVDatabaseConf *conf = stSafeCCalloc(sizeof(stKVDatabaseConf));
conf->type = stKVDatabaseTypeTokyoCabinet;
conf->databaseDir = stString_copy(databaseDir);
return conf;
}
