void Uri::Private::parsePathAbempty()
{
m_parserAux.clear();
m_pathStack.clear();
while (expectChar('/')) {
m_pathStack.push(String('/'));
parseSegment();
constructPath();
}
constructPath();
m_path.clear();
const size_t stackSize = m_pathStack.size();
for (size_t i = 0; i < stackSize; ++i) {
m_path.prepend(m_pathStack.pop());
}
}
bool Uri::Private::parsePathRootless()
{
m_parserAux.clear();
if (!parseSegmentNz()) {
return false;
}
m_pathStack.clear();
m_pathStack.push(m_parserAux);
m_parserAux.clear();
while (expectChar('/')) {
m_pathStack.push(String('/'));
parseSegment();
constructPath();
}
constructPath();
m_path.clear();
const size_t stackSize = m_pathStack.size();
for (size_t i = 0; i < stackSize; ++i) {
m_path.prepend(m_pathStack.pop());
}
return true;
}
void gsBig(char *faName, char *gtfName,
char *suboptName,
char *transName,
char *exeName,
char *parName,
char *tmpDirName)
/* gsBig - Run Genscan on big input and produce GTF files. */
{
struct dnaSeq seq;
struct lineFile *lf = lineFileOpen(faName, TRUE);
FILE *gtfFile = mustOpen(gtfName, "w");
FILE *subFile = NULL;
FILE *transFile = NULL;
ZeroVar(&seq);
if (suboptName != NULL)
subFile = mustOpen(suboptName, "w");
if (transName != NULL)
transFile = mustOpen(transName, "w");
if (exeName != NULL)
exePath = cloneString(exeName);
if (parName != NULL)
parPath = cloneString(parName);
if (tmpDirName != NULL)
tmpDir = cloneString(tmpDirName);
if (optionExists("prerun"))
{
char *preFileName = optionVal("prerun", NULL);
char seqName[128];
struct segment *seg = parseSegment(preFileName, 0, 100000000, seqName);
writeSeg(seqName, seg, gtfFile, subFile, transFile);
}
else
{
struct dyString *dy = newDyString(1024);
char tempFa[512], tempGs[512];
char dir1[256], root1[128], ext1[64];
int myPid = (int)getpid();
splitPath(faName, dir1, root1, ext1);
while (faSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
{
int offset, sizeOne;
struct segment *segList = NULL, *seg;
char *seqName = cloneString(seq.name);
int chunkNum = 0;
for (offset = 0; offset < seq.size; offset += stepSize)
{
boolean allN = TRUE;
int i;
safef(tempFa, sizeof(tempFa), "%s/temp_gsBig_%d_%s_%d.fa",
tmpDir, myPid, seqName, chunkNum);
safef(tempGs, sizeof(tempGs), "%s/temp_gsBig_%d_%s_%d.genscan",
tmpDir, myPid, seqName, chunkNum);
sizeOne = seq.size - offset;
if (sizeOne > winSize) sizeOne = winSize;
/* Genscan hangs forever if a chunk is all-N's... if so,
* then skip this chunk. */
for (i=offset; i < (offset+sizeOne); i++)
{
if (seq.dna[i] != 'N' && seq.dna[i] != 'n')
{
allN = FALSE;
break;
}
}
if (allN)
{
printf("\ngsBig: skipping %s[%d:%d] -- it's all N's.\n\n",
seqName, offset, (offset+sizeOne-1));
}
else
{
faWrite(tempFa, "split", seq.dna + offset, sizeOne);
dyStringClear(dy);
dyStringPrintf(dy, "%s %s %s", exePath, parPath, tempFa);
if (suboptName != NULL)
dyStringPrintf(dy, " -subopt");
dyStringPrintf(dy, " > %s", tempGs);
verbose(3, "%s\n", dy->string);
mustSystem(dy->string);
seg = parseSegment(tempGs, offset, offset+sizeOne, NULL);
slAddHead(&segList, seg);
}
chunkNum++;
}
slReverse(&segList);
seg = mergeSegs(segList);
writeSeg(seqName, seg, gtfFile, subFile, transFile);
freez(&seqName);
}
if (! optionExists("noRemove"))
{
remove(tempFa);
remove(tempGs);
}
}
}
