static void writeFastaSequence(FILE * outfile, const char * str)
{
size_t length = strlen(str);
size_t start;
for (start = 0; start < length; start += 60)
velvetFprintf(outfile, "%.60s\n", &str[start]);
}
static void writeSeqName(char*seq_name, SequencesWriter *seqWriteInfo, Category cat, IDnum *sequenceIndex)
{
char name[5001];
if (isCreateBinary()) {
cnySeqInsertStart(seqWriteInfo);
sprintf(name, ">%s", seq_name);
cnySeqInsertSequenceName(name, (long) ((*sequenceIndex)++), seqWriteInfo, cat);
} else {
velvetFprintf(seqWriteInfo->m_pFile,">%s\t%ld\t%d\n", seq_name, (long) ((*sequenceIndex)++), (int) cat);
}
}
static void writeSequence(char*seq, SequencesWriter *seqWriteInfo)
{
char str[100];
velvetifySequence(seq, seqWriteInfo);
if (isCreateBinary()) {
cnySeqInsertNucleotideString(seq, seqWriteInfo);
cnySeqInsertEnd(seqWriteInfo);
} else {
Coordinate start = 0;
while (start <= strlen(seq)) {
strncpy(str, seq + start, 60);
str[60] = '\0';
velvetFprintf(seqWriteInfo->m_pFile, "%s\n", str);
start += 60;
}
}
}
static void writeBuffers(FILE *outFile, int nbThreads)
{
int i;
for (i = 0; i < nbThreads; i++)
{
StringBuffer *b;
char *s;
b = annotationBufferW[i];
#pragma omp flush(b)
s = b->str;
#pragma omp flush(s)
if (*s)
{
velvetFprintf(outFile, "%s", annotationBufferW[i]->str);
resetStringBuffer(annotationBufferW[i]);
}
}
}
