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#include "piler2.h"
const int INSANE_LENGTH = 500000000;
// Arbitrarily chosen prime number
static ContigData *HashTable[HASH_TABLE_SIZE];
static ContigData **ContigMap;
static int SeqLength;
void SetSeqLength(int Length)
{
SeqLength = Length;
}
static ContigData *HashLookup(const char *Label)
{
unsigned h = Hash(Label);
assert(h < HASH_TABLE_SIZE);
ContigData *p = HashTable[h];
while (p != 0)
{
if (0 == strcmp(Label, p->Label))
return p;
p = p->Next;
}
return 0;
}
void LogContigs()
{
Log(" Label Hash Pos Length\n");
Log("-------------------- ------ ---------- ----------\n");
for (int h = 0; h < HASH_TABLE_SIZE; ++h)
{
for (const ContigData *p = HashTable[h]; p != 0; p = p->Next)
{
const ContigData &Contig = *p;
Log("%20.20s %6d %10d %10d",
Contig.Label,
h,
Contig.From,
Contig.Length);
if (Hash(Contig.Label) != h)
Log(" ** Hash=%d", Hash(Contig.Label));
Log("\n");
}
}
}
static void AppendContig(const char *Label, int Pos)
{
ContigData *Contig = all(ContigData, 1);
Contig->Label = strsave(Label);
char *Space = strchr(Contig->Label, ' ');
if (0 != Space)
*Space = 0;
unsigned h = Hash(Label);
assert(h < HASH_TABLE_SIZE);
ContigData *p = HashTable[h];
Contig->Length = Pos + 1;
Contig->Next = p;
HashTable[h] = Contig;
}
void AddContigPos(const char *Label, int Pos)
{
ContigData *Contig = HashLookup(Label);
if (0 == Contig)
AppendContig(Label, Pos);
else
{
if (Pos > Contig->Length)
Contig->Length = Pos;
}
}
void AddContig(const char *Label, int GlobalPos, int Length)
{
ContigData *Contig = all(ContigData, 1);
Contig->Label = strsave(Label);
char *Space = strchr(Contig->Label, ' ');
if (0 != Space)
*Space = 0;
unsigned h = Hash(Contig->Label);
assert(h < HASH_TABLE_SIZE);
ContigData *p = HashTable[h];
Contig->From = GlobalPos;
Contig->Length = Length;
Contig->Next = p;
HashTable[h] = Contig;
}
int GlobalizeContigs()
{
int GlobalPos = 0;
for (int h = 0; h < HASH_TABLE_SIZE; ++h)
{
for (ContigData *p = HashTable[h]; p != 0; p = p->Next)
{
ContigData &Contig = *p;
const int Length = p->Length;
if (Length < 1 || Length >= INSANE_LENGTH)
Quit("GlobalizeContigs, insane length %d", Length);
p->From = GlobalPos;
GlobalPos += Length;
// Pad up to start of next bin
// (required for contig map)
int BinRemainder = GlobalPos%CONTIG_MAP_BIN_SIZE;
if (BinRemainder > 0)
GlobalPos += CONTIG_MAP_BIN_SIZE - BinRemainder;
if (GlobalPos%CONTIG_MAP_BIN_SIZE)
Quit("Dumb mistake rounding contig");
}
}
SeqLength = GlobalPos;
return SeqLength;
}
void MakeContigMap()
{
if (SeqLength%CONTIG_MAP_BIN_SIZE)
Quit("MakeContigMap: expects rounded size");
const int BinCount = SeqLength/CONTIG_MAP_BIN_SIZE;
ContigMap = all(ContigData *, BinCount);
zero(ContigMap, ContigData *, BinCount);
for (int h = 0; h < HASH_TABLE_SIZE; ++h)
{
for (ContigData *p = HashTable[h]; p != 0; p = p->Next)
{
ContigData &Contig = *p;
int From = p->From;
int To = From + p->Length - 1;
if (From%CONTIG_MAP_BIN_SIZE)
Quit("MakeContigMap: expected rounded contig from");
int BinFrom = From/CONTIG_MAP_BIN_SIZE;
int BinTo = To/CONTIG_MAP_BIN_SIZE;
for (int Bin = BinFrom; Bin <= BinTo; ++Bin)
{
if (ContigMap[Bin] != 0)
Quit("MakeContigMap: overlap error");
ContigMap[Bin] = p;
}
}
}
}
const char *GlobalToContig(int GlobalPos, int *ptrContigPos)
{
if (GlobalPos < 0 || GlobalPos >= SeqLength)
Quit("GlobalToContig: invalid pos");
const int Bin = GlobalPos/CONTIG_MAP_BIN_SIZE;
ContigData *Contig = ContigMap[Bin];
if (0 == Contig)
Quit("GlobalToContig: doesn't map");
int ContigPos = GlobalPos - Contig->From;
if (ContigPos < 0 || ContigPos >= Contig->Length)
Quit("GlobalToContig: out of bounds");
*ptrContigPos = ContigPos;
return Contig->Label;
}
int ContigToGlobal(int ContigPos, const char *Label)
{
const ContigData *Contig = HashLookup(Label);
if (0 == Contig)
Quit("ContigToGlobal: contig not found (%s)", Label);
if (ContigPos < 0 || ContigPos >= Contig->Length)
Quit("ContigToGlobal: out of bounds");
return Contig->From + ContigPos;
}
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