MersenneTwister::MersenneTwister(const bool use_seed, size_t seed){
if (!use_seed) seed = generateRandomSeed();
this->construct_common(seed);
}
void readNextQuery(AlignmentArgs_t * AAs, QueryState_t * QS)
{
// Lock the input file.
flockfile(qFile);
// Continue until we find a valid read or hit end of file.
QS->queryLen = 0;
while (TRUE)
{
// First read in the ">" or "@" line for the query ID.
int charCount = 0;
while (TRUE)
{
int curChar = fgetchar(qFile);
// Check if we are done.
if (curChar == '\n' || curChar == EOF) break;
// Input the next char into the query ID buf (if it will fit),
// Also convert spaces to underscores to aid further pipeline commands.
if (charCount < MAX_QUERY_ID_LEN)
{
QS->queryID[charCount] = (curChar == ' ' ? '_' : curChar);
}
charCount += 1;
}
if (charCount > MAX_QUERY_ID_LEN)
{
fprintf(stderr, "Warning, Query Id length of %d exceeds maximum length %d. Id will be truncated.\n",
charCount, MAX_QUERY_ID_LEN);
QS->queryIDLen = MAX_QUERY_ID_LEN;
}
else
{
QS->queryIDLen = charCount;
}
// Now read in the query string.
int reverseOff = AAs->maxQueryLength;
char breakChar = AAs->fastq ? '+' : '>';
int qbaseCount = 0;
BOOL Fail = FALSE;
while (TRUE)
{
int curChar = fgetchar(qFile);
if (curChar == breakChar || curChar == EOF) break;
if (curChar == '\n') continue;
// Check to see that we are within bounds of maximum query length.
if (qbaseCount >= AAs->maxQueryLength)
{
fprintf(stderr, "Warning. Query sequence exceeds maximum length of %d. Query will be skipped.\n",
AAs->maxQueryLength);
// Throw away rest of query.
readToChar(qFile, breakChar, FALSE);
Fail = TRUE;
break;
}
// process the next char of the query.
// We fill both the forward and reverse query buffers as we go along.
// In each case, store both the char for the base for output.
// And also the 4-bit code for comparison to compressed reference.
char forCode = map8to4(curChar);
QS->forwardBuf[qbaseCount] = curChar;
QS->forwardCodeBuf[qbaseCount] = forCode;
reverseOff -= 1;
char revCode = complement4to4(forCode);
QS->reverseBufBase[reverseOff] = unmap4to8(revCode);
QS->reverseCodeBufBase[reverseOff] = revCode;
qbaseCount += 1;
}
// For a fastq file, we need to also find the quality string.
int qualCount = 0;
if (AAs->fastq)
{
// The '+' line can contain extra information.
// First dump that.
readToChar(qFile, '\n', FALSE);
// Reading in the quality informtion is harder, as the @ needs to be preceded by a newline.
// Given that '@' and newlines can appear in the quality string,
// is even that good enough to ensure we are at the start of a new query?
char prevChar = 0;
while (TRUE)
{
int curChar = fgetchar(qFile);
if ((curChar == '@' && prevChar == '\n') || curChar == EOF) break;
prevChar = curChar;
if (curChar == '\n') continue;
if (qualCount >= AAs->maxQueryLength)
{
fprintf(stderr, "Warning. Quality score sequence exceeds maximum length of %d. Query will be skipped.\n",
AAs->maxQueryLength);
// Throw away rest of quality string
readToChar(qFile, '@', TRUE);
Fail = TRUE;
break;
}
QS->qualBuf[qualCount] = curChar;
qualCount += 1;
}
// Make sure the fastq file is well formed.
if (qbaseCount != qualCount)
{
fprintf(stderr, "Warning. Query sequence (%d) and quality score sequence (%d) have different lengths in fastq file."
" Query will be skipped.\n", qbaseCount, qualCount);
Fail = TRUE;
}
}
if (qbaseCount > 0 && qbaseCount < AAs->wordLen)
{
fprintf(stderr, "Query length must be at least wordlen bases long. Query will be skipped.\n");
Fail = TRUE;
}
// If anything has gone wrong, try again.
if (Fail) continue;
funlockfile(qFile);
// Fill in the QS fields of interest.
// Since reverse buf is filled in from back to front, now set the starting ptrs.
QS->reverseCodeBuf = &QS->reverseCodeBufBase[reverseOff];
QS->reverseBuf = &QS->reverseBufBase[reverseOff];
QS->queryLen = qbaseCount;
// Use the query sequence to generate a random seed for stocastically choosing amonst equal alignments.
// By using the query sequence for the seed, the same one is chosen among equals regardless of file context of the query.
generateRandomSeed(QS);
return;
}
// This will never be executed, as EOF will result in qbaseCount of zero in while(TRUE) loop.
// It is here just to avoid the compiler warning.
return;
}
MersenneTwister::MersenneTwister() {
this->construct_common(generateRandomSeed());
}
