/*
** inserts a new key into a hash table; first, check whether key's main
** position is free. If not, check whether colliding node is in its main
** position or not: if it is not, move colliding node to an empty place and
** put new key in its main position; otherwise (colliding node is in its main
** position), new key goes to an empty position.
*/
static TableNode*
table_newkey(Table *t, uint32_t key) {
TableNode *mp = mainposition(t, key);
if(!tisnil(mp)) {
TableNode *n = getfreenode(t);
if(n == NULL) {
table_expand(t);
return table_newkey(t, key);
}
TableNode *othern = mainposition(t, mp->key);
if (othern != mp) {
int mindex = tindex(t, mp);
while(othern->next != mindex) {
othern = tnode(t, othern->next);
}
othern->next = tindex(t, n);
*n = *mp;
initnode(mp);
} else {
n->next = mp->next;
mp->next = tindex(t, n);
mp = n;
}
}
mp->key = key;
mp->flag = 'n';
return mp;
}
/*
* load index for one file
*/
static libmaus::autoarray::AutoArray< IndexEntry > loadIndex(std::string const & filename)
{
uint64_t const indexpos = getIndexPos(filename);
std::ifstream indexistr(filename.c_str(),std::ios::binary);
if ( ! indexistr.is_open() )
{
::libmaus::exception::LibMausException se;
se.getStream() << "RLDecoder::loadIndex(): Failed to open file " << filename << std::endl;
se.finish();
throw se;
}
// seek to index position
indexistr.seekg(indexpos,std::ios::beg);
if ( static_cast<int64_t>(indexistr.tellg()) != static_cast<int64_t>(indexpos) )
{
::libmaus::exception::LibMausException se;
se.getStream() << "Failed to seek to index position " << indexpos << " in file " << filename << " of size "
<< ::libmaus::util::GetFileSize::getFileSize(filename) << std::endl;
se.finish();
throw se;
}
::libmaus::bitio::StreamBitInputStream SBIS(indexistr);
// read size of index
uint64_t const numentries = ::libmaus::bitio::readElias2(SBIS);
// pos bits
unsigned int const posbits = ::libmaus::bitio::readElias2(SBIS);
// k bits
unsigned int const kbits = ::libmaus::bitio::readElias2(SBIS);
// k acc
/* uint64_t const symacc = */ ::libmaus::bitio::readElias2(SBIS);
// v bits
unsigned int const vbits = ::libmaus::bitio::readElias2(SBIS);
// v acc
/* uint64_t const symacc = */ ::libmaus::bitio::readElias2(SBIS);
// align
SBIS.flush();
SBIS.getBitsRead();
// std::cerr << "numentries " << numentries << std::endl;
// read index
libmaus::autoarray::AutoArray< IndexEntry > index(numentries,false);
// #define INDEXLOADERDEBUG
#if defined(INDEXLOADERDEBUG)
libmaus::autoarray::AutoArray< IndexEntry > tindex(numentries+1);
#endif
for ( uint64_t i = 0; i < numentries; ++i )
{
uint64_t const pos = SBIS.read(posbits);
uint64_t const kcnt = SBIS.read(kbits);
uint64_t const vcnt = SBIS.read(vbits);
index[i] = IndexEntry(pos,kcnt,vcnt);
#if defined(INDEXLOADERDEBUG)
tindex[i] = index[i];
#endif
}
if ( numentries )
{
assert ( index[0].kcnt == 0 );
assert ( index[0].vcnt == 0 );
for ( uint64_t i = 1; i < numentries; ++i )
{
index[i-1].kcnt = index[i].kcnt;
index[i-1].vcnt = index[i].vcnt;
}
/* uint64_t const pos = */ SBIS.read(posbits);
index[numentries-1].kcnt = SBIS.read(kbits);
index[numentries-1].vcnt = SBIS.read(vbits);
#if defined(INDEXLOADERDEBUG)
tindex[numentries].kcnt = index[numentries-1].kcnt;
tindex[numentries].vcnt = index[numentries-1].vcnt;
#endif
}
for ( uint64_t i = numentries-1; i >= 1; --i )
{
index[i].kcnt -= index[i-1].kcnt;
index[i].vcnt -= index[i-1].vcnt;
}
#if defined(INDEXLOADERDEBUG)
for ( uint64_t i = 0; i < numentries; ++i )
{
assert ( index[i].kcnt == tindex[i+1].kcnt-tindex[i].kcnt );
assert ( index[i].vcnt == tindex[i+1].vcnt-tindex[i].vcnt );
}
#endif
#if defined(INDEXLOADERDEBUG)
IndexDecoderData IDD(filename);
assert ( IDD.numentries == numentries );
assert ( IDD.posbits == posbits );
assert ( IDD.kbits == kbits );
assert ( IDD.vbits == vbits );
// assert ( IDD.symacc == symacc );
std::cerr << "((**++CHECKING " << numentries << "...";
uint64_t tkacc = 0;
uint64_t tvacc = 0;
for ( uint64_t i = 0; i < numentries; ++i )
{
IndexEntry const P = IDD.readEntry(i);
assert ( P.pos == index[i].pos );
assert ( P.kcnt == tkacc );
assert ( P.vcnt == tvacc );
tkacc += index[i].kcnt;
tvacc += index[i].vcnt;
}
assert ( tkacc == IDD.readEntry(numentries).kcnt );
assert ( tvacc == IDD.readEntry(numentries).vcnt );
std::cerr << "**++))" << std::endl;
#endif
// std::cerr << "loaded index of size " << numentries << std::endl;
return index;
}
