File* FileStreamWrapper::open(const String& filename, const String& mode,
int options, const Variant& context) {
String fname =
!strncmp(filename.data(), "file://", sizeof("file://") - 1)
? filename.substr(sizeof("file://") - 1) : filename;
if (MemFile *file = openFromCache(fname, mode)) {
return file;
}
if (options & File::USE_INCLUDE_PATH) {
struct stat s;
String resolved_fname = Eval::resolveVmInclude(fname.get(), "", &s);
if (!resolved_fname.isNull()) {
fname = resolved_fname;
}
}
std::unique_ptr<PlainFile> file(NEWOBJ(PlainFile)());
bool ret = file->open(File::TranslatePath(fname), mode);
if (!ret) {
raise_warning("%s", file->getLastError().c_str());
return nullptr;
}
return file.release();
}
void readCachedSeqPart(char *seqName, int start, int size, boolean getMasked,
struct hash *hash, struct dlList *fileCache,
struct dnaSeq **retSeq, int *retOffset, boolean *retIsNib)
/* Read sequence hopefully using file cashe. If sequence is in a nib
* file just read part of it. */
{
struct seqFilePos *sfp = hashMustFindVal(hash, seqName);
FILE *f = openFromCache(fileCache, sfp);
if (sfp->isTwoBit)
{
*retSeq = twoBitReadSeqFrag((struct twoBitFile *)f, seqName, start, start + size);
*retOffset = start;
*retIsNib = TRUE;
}
else if (sfp->isNib)
{
*retSeq = nibLdPartMasked((getMasked ? NIB_MASK_MIXED : 0), sfp->file, f, sfp->pos, start, size);
*retOffset = start;
*retIsNib = TRUE;
}
else
{
if (getMasked)
errAbort("masked sequences not supported with fasta files");
*retSeq = readSeqFromFaPos(sfp, f);
*retOffset = 0;
*retIsNib = FALSE;
}
}
void readCachedSeqPart(char *seqName, int start, int size,
struct hash *hash, struct dlList *fileCache,
struct dnaSeq **retSeq, int *retOffset, boolean *retIsPartial)
/* Read sequence hopefully using file cashe. If sequence is in a nib
* file just read part of it. */
{
struct seqFilePos *sfp = hashMustFindVal(hash, seqName);
FILE *f = openFromCache(fileCache, sfp->file);
if (sfp->isNib)
{
*retSeq = nibLdPartMasked(NIB_MASK_MIXED, sfp->file, f, sfp->pos, start, size);
*retOffset = start;
*retIsPartial = TRUE;
}
else if (sfp->isTwoBit)
{
*retSeq = twoBitReadSeqFrag(sfp->tbf, seqName, start, start+size);
*retOffset = start;
*retIsPartial = TRUE;
}
else
{
*retSeq = readSeqFromFaPos(sfp, f);
*retOffset = 0;
*retIsPartial = FALSE;
}
}
SmartPtr<File>
FileStreamWrapper::open(const String& filename, const String& mode,
int options, const SmartPtr<StreamContext>& context) {
String fname;
if (StringUtil::IsFileUrl(filename)) {
fname = StringUtil::DecodeFileUrl(filename);
if (fname.empty()) {
raise_warning("invalid file:// URL");
return nullptr;
}
} else {
fname = filename;
}
if (auto file = openFromCache(fname, mode)) {
return file;
}
if (options & File::USE_INCLUDE_PATH) {
struct stat s;
String resolved_fname = resolveVmInclude(fname.get(), "", &s);
if (!resolved_fname.isNull()) {
fname = resolved_fname;
}
}
auto file = makeSmartPtr<PlainFile>();
bool ret = file->open(File::TranslatePath(fname), mode);
if (!ret) {
raise_warning("%s", file->getLastError().c_str());
return nullptr;
}
return file;
}
File* FileStreamWrapper::open(CStrRef filename, CStrRef mode,
int options, CVarRef context) {
String fname =
!strncmp(filename.data(), "file://", sizeof("file://") - 1)
? filename.substr(sizeof("file://") - 1) : filename;
if (MemFile *file = openFromCache(fname, mode)) {
return file;
}
std::unique_ptr<PlainFile> file(NEWOBJ(PlainFile)());
bool ret = file->open(File::TranslatePath(fname), mode);
if (!ret) {
raise_warning("%s", file->getLastError().c_str());
return NULL;
}
return file.release();
}
struct dnaSeq *readFromCache(struct dlList *cache, char *dirName, char *seqName,
int start, int size, int seqSize, boolean isTwoBit)
/* Return dnaSeq read from the appropriate nib file.
* You need to dnaSeqFree this when done (it is the nib
* file that is cached, not the sequence). */
{
struct cachedSeqFile *cn = openFromCache(cache, dirName, seqName, isTwoBit);
if (isTwoBit)
{
return twoBitReadSeqFrag(cn->tbf, seqName, start, start+size);
}
else
{
if (seqSize != cn->size)
errAbort("%s/%s is %d bases in .lav file and %d in .nib file\n",
dirName, seqName, seqSize, cn->size);
if ((start+size) > cn->size )
printf("%s/%s is %d bases in .lav file and %d in .nib file start %d size %d end %d\n",
dirName, seqName, seqSize, cn->size, start, size, start+size);
return nibLdPartMasked(NIB_MASK_MIXED, cn->fileName, cn->f, cn->size, start, size);
}
}
