int main(int argc, char *argv[]) {
FILE *fileHandle;
struct List *seqs;
struct List *seqLengths;
struct List *seqNames;
int32_t i;
assert(argc == 3);
seqs = constructEmptyList(0, free);
seqLengths = constructEmptyList(0, (void (*)(void *))destructInt);
seqNames = constructEmptyList(0, free);
fileHandle = fopen(argv[1], "r");
fastaRead(fileHandle, seqs, seqLengths, seqNames);
fclose(fileHandle);
fileHandle = fopen(argv[2], "w");
for(i=0; i < seqs->length; i++) {
assert(strlen(seqs->list[i]) == *((int32_t *)seqLengths->list[i]));
fastaWrite(seqs->list[i], seqNames->list[i], fileHandle);
}
fclose(fileHandle);
return 0;
}
static void getReferenceSequences(FILE *fileHandle, Flower *flower, char *referenceEventString){
//get names of all the sequences in 'flower' for event with name 'referenceEventString'
Sequence *sequence;
Flower_SequenceIterator * seqIterator = flower_getSequenceIterator(flower);
while((sequence = flower_getNextSequence(seqIterator)) != NULL)
{
Event* event = sequence_getEvent(sequence);
const char* eventName = event_getHeader(event);
if (strcmp(eventName, referenceEventString) == 0 &&
sequence_getLength(sequence) > 0 &&
!metaSequence_isTrivialSequence(sequence_getMetaSequence(sequence))) {
const char *sequenceHeader = formatSequenceHeader(sequence);
st_logInfo("Sequence %s\n", sequenceHeader);
char *string = sequence_getString(sequence, sequence_getStart(sequence), sequence_getLength(sequence), 1);
fastaWrite(string, (char *)sequenceHeader, fileHandle);
free(string);
}
}
flower_destructSequenceIterator(seqIterator);
return;
}