int main(int argc, char **argv) {
options_t *options = options_construct();
stHash *sequenceHash = NULL; // keyed on fasta headers, valued with mtfseq_t pointers
stHash *alignmentHash = stHash_construct3(stHash_stringKey, stHash_stringEqualKey, free, destroyRow); // keyed on species names, valued with row_t pointers
stList *rowOrder = stList_construct3(0, free); // when adding keys to alignmentHash, append to this list
parseOptions(argc, argv, options);
// read fastas, populate sequenceHash
de_verbose("Creating sequence hash.\n");
sequenceHash = createSequenceHash(options->seqs);
mafFileApi_t *mfapi = maf_newMfa(options->maf, "r");
de_verbose("Creating alignment hash.\n");
buildAlignmentHash(mfapi, alignmentHash, sequenceHash, rowOrder, options);
if (options->outMfa != NULL) {
// fasta output
de_verbose("Writing fasta output.\n");
writeFastaOut(alignmentHash, rowOrder, options);
}
if (options->outMaf != NULL) {
// maf output
de_verbose("Writing maf output.\n");
writeMafOut(alignmentHash, rowOrder, options);
}
// cleanup
maf_destroyMfa(mfapi);
stHash_destruct(alignmentHash);
stHash_destruct(sequenceHash);
stList_destruct(rowOrder);
destroyOptions(options);
return(EXIT_SUCCESS);
}
int main(int argc, char **argv) {
char filename[kMaxStringLength];
parseOptions(argc, argv, filename);
mafFileApi_t *mfa = maf_newMfa(filename, "r");
processBody(mfa);
maf_destroyMfa(mfa);
return EXIT_SUCCESS;
}
int main(int argc, char **argv) {
char filename[kMaxStringLength];
char targetName[kMaxStringLength];
uint64_t targetPos;
parseOptions(argc, argv, filename, targetName, &targetPos);
mafFileApi_t *mfa = maf_newMfa(filename, "r");
searchInput(mfa, targetName, targetPos);
maf_destroyMfa(mfa);
return EXIT_SUCCESS;
}
int main(int argc, char **argv) {
extern const int kMaxStringLength;
char seq[kMaxSeqName];
char filename[kMaxStringLength];
uint32_t start, stop;
parseOptions(argc, argv, filename, seq, &start, &stop);
mafFileApi_t *mfa = maf_newMfa(filename, "r");
processBody(mfa, seq, start, stop);
maf_destroyMfa(mfa);
return EXIT_SUCCESS;
}
