int Encryptor::update() {
if (pCaesarSettings->adType == CAESAR_TYPE_COUNTER) { increaseArray(m_ad, pCaesarSettings->adLength); }
if (pCaesarSettings->keyType == CAESAR_TYPE_COUNTER) { increaseArray(m_key, pCaesarSettings->keyLength); }
if (pCaesarSettings->smnType == CAESAR_TYPE_COUNTER) { increaseArray(m_smn, pCaesarSettings->smnLength); }
if (pCaesarSettings->pmnType == CAESAR_TYPE_COUNTER) { increaseArray(m_pmn, pCaesarSettings->pmnLength); }
if (pCaesarSettings->plaintextType == CAESAR_TYPE_COUNTER) { increaseArray(m_plaintext, pCaesarSettings->adLength); }
return STAT_OK;
}
uint16
abColumn::extendRead(abColumn *column, uint16 beadLink) {
increaseArray(_beads, _beadsLen, _beadsMax, 1);
uint32 link = _beadsLen++;
_beads[link]._unused = column->_beads[beadLink]._unused;
_beads[link]._isRead = column->_beads[beadLink]._isRead;
_beads[link]._isUnitig = column->_beads[beadLink]._isUnitig;
_beads[link]._base = '-';
_beads[link]._qual = 0;
if (column->_beads[beadLink]._prevOffset == UINT16_MAX) {
assert(column->_beads[beadLink]._nextOffset != UINT16_MAX);
assert(_nextColumn == column);
_beads[link]._prevOffset = UINT16_MAX;
_beads[link]._nextOffset = beadLink;
column->_beads[beadLink]._prevOffset = link;
} else {
assert(column->_beads[beadLink]._prevOffset != UINT16_MAX);
assert(_prevColumn == column);
_beads[link]._prevOffset = beadLink;
_beads[link]._nextOffset = UINT16_MAX;
column->_beads[beadLink]._nextOffset = link;
}
return(link);
}
gkRead *
gkStore::gkStore_addEmptyRead(gkLibrary *lib) {
assert(_readsMMap == NULL);
assert(_info.numReads <= _readsAlloc);
assert(_mode != gkStore_readOnly);
// We reserve the zeroth read for "null". This is easy to accomplish
// here, just pre-increment the number of reads. However, we need to be sure
// to iterate up to and including _info.numReads.
_info.numReads++;
if (_info.numReads == _readsAlloc)
increaseArray(_reads, _info.numReads, _readsAlloc, _info.numReads/2);
_reads[_info.numReads] = gkRead();
_reads[_info.numReads]._readID = _info.numReads;
_reads[_info.numReads]._libraryID = lib->gkLibrary_libraryID();
//fprintf(stderr, "ADD READ %u = %u alloc = %u\n", _info.numReads, _reads[_info.numReads]._readID, _readsAlloc);
return(_reads + _info.numReads);
}
abSeqID
abAbacus::addRead(gkStore *gkpStore,
uint32 readID,
uint32 askip, uint32 bskip,
bool complemented) {
// Grab the read
gkRead *read = gkpStore->gkStore_getRead(readID);
gkReadData *readData = new gkReadData;
//fprintf(stderr, "abAbacus::addRead()-- want readID=%u, store returned read %u\n",
// readID, read->gkRead_readID());
gkpStore->gkStore_loadReadData(read, readData);
uint32 seqLen = read->gkRead_sequenceLength() - askip - bskip;
// Tell abacus about it.
increaseArray(_sequences, _sequencesLen, _sequencesMax, 1);
abSequence *ns = _sequences + _sequencesLen;
ns->initialize(readID, _sequencesLen++, seqLen, complemented, _basesLen, _beadsLen);
// Make a complement table
char inv[256] = {0};
inv['a'] = 't'; inv['A'] = 'T';
inv['c'] = 'g'; inv['C'] = 'G';
inv['g'] = 'c'; inv['G'] = 'C';
inv['t'] = 'a'; inv['T'] = 'A';
inv['n'] = 'n'; inv['N'] = 'N';
inv['-'] = '-';
// Stash the bases/quals
{
char *seq = readData->gkReadData_getSequence() + ((complemented == false) ? askip : bskip);
char *qlt = readData->gkReadData_getQualities() + ((complemented == false) ? askip : bskip);
while (_basesMax <= _basesLen + seqLen + 1)
resizeArrayPair(_bases, _quals, _basesLen, _basesMax, 2 * _basesMax);
for (uint32 ii=0; ii<seqLen; ii++)
assert((seq[ii] == 'A') ||
(seq[ii] == 'C') ||
(seq[ii] == 'G') ||
(seq[ii] == 'T') ||
(seq[ii] == 'N'));
if (complemented == false)
for (uint32 ii=0, pp=_basesLen; ii<seqLen; ii++, pp++, _basesLen++) {
_bases[pp] = seq[ii];
_quals[pp] = qlt[ii];
assert(CNS_MIN_QV + '0' <= _quals[pp]);
assert(_quals[pp] <= CNS_MAX_QV + '0');
}
else
for (uint32 ii=seqLen, pp=_basesLen; ii-->0; pp++, _basesLen++) {
_bases[pp] = inv[ seq[ii] ];
_quals[pp] = qlt[ii];
assert(CNS_MIN_QV + '0' <= _quals[pp]);
assert(_quals[pp] <= CNS_MAX_QV + '0');
}
_bases[_basesLen] = 0; // NUL terminate the strings so we can use them in aligners
_quals[_basesLen] = 0;
_basesLen++;
}
delete readData;
// Make beads for each base, set the pointer to the first bead
{
increaseArray(_beads, _beadsLen, _beadsMax, seqLen);
uint32 firstBead = _beadsLen;
for (uint32 bp=0; bp<ns->length(); bp++, _beadsLen++) {
_beads[_beadsLen].boffset.set(_beadsLen); // Offset into the beads array
_beads[_beadsLen].soffset.set(ns->firstBase().get() + bp); // Offset into the sequence array
_beads[_beadsLen].foffset = bp; // Offset into the read itself
// Check that nothing odd happened with the ident.
assert(_beads[_beadsLen].ident().get() == ns->firstBead().get() + bp);
// Set previous/next bead appropriately.
if (_beads[_beadsLen].foffset == 0)
_beads[_beadsLen].prev = abBeadID();
else
_beads[_beadsLen].prev.set(_beads[_beadsLen].ident().get() - 1);
if (_beads[_beadsLen].foffset == ns->length() - 1)
_beads[_beadsLen].next = abBeadID();
else
_beads[_beadsLen].next.set(_beads[_beadsLen].ident().get() + 1);
_beads[_beadsLen].up = abBeadID(); // No up bead yet.
_beads[_beadsLen].down = abBeadID(); // No down bead yet.
_beads[_beadsLen].frag_index = ns->ident(); // Bead is for this read idx.
_beads[_beadsLen].column_index = abColID(); // Isn't in a column yet.
}
}
assert(_beads[_beadsLen-1].ident() == ns->lastBead());
// Return the (internal) index we saved this read at.
#if 0
fprintf(stderr, "read %d firstBead %d lastBead %d _basesLen %u\n",
ns->ident().get(),
ns->firstBead().get(),
ns->lastBead().get(),
_basesLen);
#endif
return(ns->ident());
}
gkLibrary *
gkStore::gkStore_addEmptyLibrary(char const *name) {
assert(_librariesMMap == NULL);
assert(_info.numLibraries <= _librariesAlloc);
// Library[0] doesn't exist, see comments in addEmptyRead below.
_info.numLibraries++;
if (_info.numLibraries == _librariesAlloc)
increaseArray(_libraries, _info.numLibraries, _librariesAlloc, 128);
// Bullet proof the library name - so we can make files with this prefix.
char libname[LIBRARY_NAME_SIZE];
uint32 libnamepos = 0;
bool modified = false;
bool truncated = false;
for (char const *orig=name; *orig; orig++) {
if (*orig == '/') {
libname[libnamepos++] = '_';
libname[libnamepos++] = '-';
libname[libnamepos++] = '_';
modified = true;
} else if (isspace(*orig) == 0) {
libname[libnamepos++] = *orig;
} else {
libname[libnamepos++] = '_';
modified = true;
}
if (libnamepos >= LIBRARY_NAME_SIZE) {
libname[LIBRARY_NAME_SIZE-1] = 0;
truncated = true;
break;
}
}
libname[libnamepos] = 0;
#if 0
if (modified || truncated)
fprintf(stderr, "gkStore_addEmptyLibrary()-- added library '%s' (original name '%s')\n",
libname, name);
else
fprintf(stderr, "gkStore_addEmptyLibrary()-- added library '%s'\n",
libname);
#endif
_libraries[_info.numLibraries] = gkLibrary();
strcpy(_libraries[_info.numLibraries]._libraryName, libname);
_libraries[_info.numLibraries]._libraryID = _info.numLibraries;
return(_libraries + _info.numLibraries);
}
