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Change the tgStore constructor to take a 'type' instead of three bool…
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… flags to

decide how to open the store.  Fix issues with the nul terminating byte in the
bases/quals strings.  Finish the tgStoreLoad.
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@brianwalenz
brianwalenz committed Aug 12, 2015
1 parent 10473e6 commit 405faa6
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Showing 7 changed files with 254 additions and 253 deletions.
1 change: 1 addition & 0 deletions src/main.mk
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Original file line number Diff line number Diff line change
Expand Up @@ -159,6 +159,7 @@ SUBMAKEFILES := stores/gatekeeperCreate.mk \
stores/ovStoreIndexer.mk \
stores/ovStoreDump.mk \
stores/tgStoreDump.mk \
stores/tgStoreLoad.mk \
stores/tgTigDisplay.mk \
\
meryl/libleaff.mk \
Expand Down
180 changes: 102 additions & 78 deletions src/stores/tgStore.C
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Original file line number Diff line number Diff line change
Expand Up @@ -28,16 +28,30 @@ static const char *rcsid = "$Id$";
uint32 MASRmagic = 0x5253414d; // 'MASR', as a big endian integer
uint32 MASRversion = 1;

#define MAX_VERS 1024
#define MAX_VERS 1024 // Linked to 10 bits in the header file.

void
tgStore::init(const char *path_, uint32 version_, bool writable_, bool inplace_, bool append_) {

strcpy(_path, path_);
tgStore::tgStore(const char *path_,
uint32 version_,
tgStoreType type_) {

_writable = writable_;
_inplace = inplace_;
_append = append_;
// Handle goofy default parameters. These let us retain the previous behavior (before tgStoreType):
// new tgStore("path") - to create a new store
// new tgStore("path", v) - to open an existing store
//
// And still allow
// new tgStore("path", v, tgStoreCreate) - create new store, make v the current version

if (version_ == 0) {
version_ = 1;
type_ = tgStoreCreate;
}

// Initialize the object.

_type = type_;

strcpy(_path, path_);

_newTigs = false;

Expand All @@ -55,64 +69,31 @@ tgStore::init(const char *path_, uint32 version_, bool writable_, bool inplace_,
_dataFile[i].FP = NULL;
_dataFile[i].atEOF = false;
}
}

// Create a new one?

tgStore::tgStore(const char *path_) {
init(path_, 1, true, false, false);
AS_UTL_mkdir(_path); // Create the directory, if needed.
purgeCurrentVersion(); // Purge any data there currently.
}
if (type_ == tgStoreCreate) {
AS_UTL_mkdir(_path); // Create the directory, if needed.
purgeCurrentVersion(); // Purge any data there currently.

for (int32 vv=1; vv<version_; vv++) // Move to the requested version.
nextVersion();

tgStore::tgStore(const char *path_,
uint32 version_,
bool writable_,
bool inplace_,
bool append_) {

if (writable_ == false)
inplace_ = append_ = false;
_type = tgStoreWrite; // Created, ready for action!

init(path_, version_, writable_, inplace_, append_);

if ((_inplace == true) && (_append == true))
fprintf(stderr, "tgStore::tgStore()-- ERROR, cannot both append and be inplace.\n"), exit(1);
return; // No tigs to load, se we can't do the rest.
}

// Load the tgStoreEntrys for the current version.

loadMASR(_tigEntry, _tigLen, _tigMax, _currentVersion, false);

// Check that there are tigs.

if ((_tigLen == 0) && (_append == false)) {
fprintf(stderr, "tgStore::tgStore()-- ERROR, didn't find any tigs in the store.\n");
fprintf(stderr, "tgStore::tgStore()-- asked for store '%s', correct?\n", _path);
fprintf(stderr, "tgStore::tgStore()-- asked for version '%d', correct?\n", _originalVersion);
fprintf(stderr, "tgStore::tgStore()-- asked for writable=%d inplace=%d append=%d, correct?\n", _writable, _inplace, _append);
exit(1);
}
loadMASR(_tigEntry, _tigLen, _tigMax, _currentVersion);

// Allocate the cache to the proper size

_tigCache = new tgTig * [_tigMax];

for (uint32 xx=0; xx<_tigMax; xx++)
_tigCache[xx] = NULL;
//memset(_tigCache, 0xff, sizeof(tgTig *) * _tigMax);

// Open the next version for writing, and remove what is currently there.

if ((_writable == true) && (_inplace == false) && (_append == false)) {
_currentVersion++;

purgeCurrentVersion();
}

// Open the next version for writing, and keep the data that is currently there.

if (_append == true)
_currentVersion++;

// Check that nothing is marked for flushing, if so, clear the flag. This shouldn't ever trigger.

Expand All @@ -122,12 +103,45 @@ tgStore::tgStore(const char *path_,
_tigEntry[xx].flushNeeded = 0;
}

// Fail (again?) if there are no tigs loaded.
// Set the version for writing.

if (_tigLen == 0) {
fprintf(stderr, "tgStore::tgStore()-- ERROR, didn't find any tigs in the store. Correct version?\n");
exit(1);
switch (type_) {
case tgStoreCreate:
break;

case tgStoreReadOnly:
if (_tigLen == 0) {
fprintf(stderr, "tgStore::tgStore()-- ERROR, didn't find any tigs in the store.\n");
fprintf(stderr, "tgStore::tgStore()-- asked for store '%s', correct?\n", _path);
fprintf(stderr, "tgStore::tgStore()-- asked for version '%d', correct?\n", _originalVersion);
exit(1);
}
break;

case tgStoreWrite:
_currentVersion++; // Writes go to the next version.
purgeCurrentVersion(); // And clear it.
break;

case tgStoreAppend:
_currentVersion++; // Writes go to the next version.
break;

case tgStoreModify:
break;

default:
assert(0);
break;
}


// Fail (again?) if there are no tigs loaded.

//if (_tigLen == 0) {
// fprintf(stderr, "tgStore::tgStore()-- ERROR, didn't find any tigs in the store. Correct version?\n");
// exit(1);
//}
}


Expand All @@ -137,7 +151,9 @@ tgStore::~tgStore() {

// If writable, write the data.

if (_writable)
if ((_type == tgStoreWrite) ||
(_type == tgStoreAppend) ||
(_type == tgStoreModify))
dumpMASR(_tigEntry, _tigLen, _tigMax, _currentVersion);

// Now just trash ourself.
Expand Down Expand Up @@ -173,9 +189,6 @@ tgStore::purgeCurrentVersion(void) {
void
tgStore::nextVersion(void) {

assert(_writable == true);
assert(_inplace == false);

// Write out any tigs that are cached

flushDisk();
Expand Down Expand Up @@ -203,6 +216,11 @@ tgStore::nextVersion(void) {

_currentVersion++;

if (_currentVersion == MAX_VERS) {
fprintf(stderr, "Too many version, I can't proceed.\n");
exit(1);
}

// Remove any existing files at that version level.

purgeCurrentVersion();
Expand All @@ -213,6 +231,8 @@ tgStore::nextVersion(void) {
void
tgStore::writeTigToDisk(tgTig *tig, tgStoreEntry *te) {

assert(_type != tgStoreReadOnly);

FILE *FP = openDB(te->svID);

// The atEOF flag allows us to skip a seek when we're already (supposed) to be at the EOF. This
Expand Down Expand Up @@ -244,7 +264,7 @@ tgStore::insertTig(tgTig *tig, bool keepInCache) {

// Check that the components do not exceed the bound.
//
if (tig->_gappedBases > 0) {
if (tig->_gappedLen > 0) {
uint32 len = tig->_gappedLen;
uint32 swp = 0;
uint32 neg = 0;
Expand All @@ -254,42 +274,39 @@ tgStore::insertTig(tgTig *tig, bool keepInCache) {
tgPosition *read = tig->_children + i;

if ((read->_max < read->_min))
fprintf(stderr, "tgStore::insertTig()-- ERROR: tig %d read %d at (%d,%d) has swapped min/max coordinates\n",
fprintf(stderr, "tgStore::insertTig()-- ERROR: tig %d read %d at (%d,%d) has swapped min/max coordinates\n",
tig->_tigID, read->_objID, read->_min, read->_max), swp++;
// Could fix, but we currently just fail
// Could fix, but we currently just fail. This is an algorithmic problem that should be fixed.

if ((read->_min < 0) || (read->_max < 0))
fprintf(stderr, "tgStore::insertTig()-- ERROR: tig %d read %d at (%d,%d) has negative position\n",
fprintf(stderr, "tgStore::insertTig()-- WARNING: tig %d read %d at (%d,%d) has negative position\n",
tig->_tigID, read->_objID, read->_min, read->_max), neg++;
if (read->_min < 0) read->_min = 0;
if (read->_max < 0) read->_max = 0;

if ((read->_min > len) || (read->_max > len))
fprintf(stderr, "tgStore::insertTig()-- ERROR: tig %d read %d at (%d,%d) exceeded multialign length %d\n",
fprintf(stderr, "tgStore::insertTig()-- WARNING: tig %d read %d at (%d,%d) exceeded multialign length %d\n",
tig->_tigID, read->_objID, read->_min, read->_max, len), pos++;
if (read->_min > len) read->_min = len;
if (read->_max > len) read->_max = len;
}

if (neg + pos + swp > 0) {
#if 0
if (swp + neg + pos > 0) {
tig->dumpLayout(stderr);
fprintf(stderr, "tgStore::insertTig()-- ERROR: tig %d has invalid layout, exceeds bounds of consensus sequence (length %d) -- neg=%d pos=%d -- swp=%d.\n",
tig->_tigID, len, neg, pos, swp);
}

assert(neg == 0);
assert(pos == 0);
#endif
assert(swp == 0);
//assert(neg == 0);
//assert(pos == 0);
}

if (tig->_tigID == UINT32_MAX) {
tig->_tigID = _tigLen;
_newTigs = true;

// Make sure that the UTG line (if present) agrees with our new tigID
//if (GetNumIntUnitigPoss(tig->u_list) == 1)
// GetIntUnitigPos(tig->u_list, 0)->_id = tig->_tigID;

fprintf(stderr, "tgStore::insertTig()-- Added new tig %d\n", tig->_tigID);
}

Expand Down Expand Up @@ -333,7 +350,7 @@ tgStore::insertTig(tgTig *tig, bool keepInCache) {
// Write to disk RIGHT NOW unless we're keeping it in cache. If it is written, the flushNeeded
// flag is cleared.
//
if (keepInCache == false)
if ((keepInCache == false) && (_type != tgStoreReadOnly))
writeTigToDisk(tig, _tigEntry + tig->_tigID);

// If the cache is different from this tig, delete the cache. Not sure why this happens --
Expand Down Expand Up @@ -390,12 +407,11 @@ tgStore::loadTig(uint32 tigID) {
if (_tigEntry[tigID].isDeleted == true)
return(NULL);

// This _is_ an error. Every tig should be in a non-zero version!
// This _is_ an error. If a tig is in version zero, it isn't in the store at all.
// Someone did something stupid when adding tigs.

if (_tigEntry[tigID].svID == 0) {
fprintf(stderr, "WARNING: tried to load tig %u, but it isn't in a non-zero version!\n", tigID);
if (_tigEntry[tigID].svID == 0)
return(NULL);
}

// Otherwise, we can load something.

Expand Down Expand Up @@ -586,7 +602,7 @@ tgStore::dumpMASR(tgStoreEntry* &R, uint32& L, uint32& M, uint32 V) {


void
tgStore::loadMASR(tgStoreEntry* &R, uint32& L, uint32& M, uint32 V, bool onlyThisV) {
tgStore::loadMASR(tgStoreEntry* &R, uint32& L, uint32& M, uint32 V) {

// Allocate space for the data. Search for the latest version, ask it how many tigs are in the
// store.
Expand All @@ -608,6 +624,14 @@ tgStore::loadMASR(tgStoreEntry* &R, uint32& L, uint32& M, uint32 V, bool onlyThi

sprintf(_name, "%s/seqDB.v%03d.tig", _path, V);

while ((AS_UTL_fileExists(_name) == false) && (V > 0)) {
V--;
sprintf(_name, "%s/seqDB.v%03d.tig", _path, V);
}

if (V == 0)
fprintf(stderr, "tgStore::loadMASR()-- Failed to find any tigs in store '%s'.\n", _path), exit(1);

errno = 0;
FILE *F = fopen(_name, "r");
if (errno)
Expand Down Expand Up @@ -667,7 +691,7 @@ tgStore::openDB(uint32 version) {

errno = 0;

if ((_writable) && (version == _currentVersion)) {
if ((_type != tgStoreReadOnly) && (version == _currentVersion)) {
_dataFile[version].FP = fopen(_name, "a+");
_dataFile[version].atEOF = false;
} else {
Expand Down
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