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#include "pilercr.h"
const int DP_PAD = 50; // padding to stop alignments
static bool g_TruncateLabels = false;
#define APPEND_CHAR(c) \
{ \
if (Pos >= BufferSize) \
Quit("ReadMFA: buffer too small"); \
Buffer[Pos++] = (c); \
}
#define APPEND_LABEL(c) \
{ \
if (LabelLength >= LabelBufferLength-1) \
{ \
LabelBufferLength += 128; \
char *NewLabel = all(char, LabelBufferLength); \
memcpy(NewLabel, Label, LabelLength); \
freemem(Label); \
Label = NewLabel; \
} \
Label[LabelLength] = c; \
++LabelLength; \
}
#define INIT_CONTIGS() \
{ \
ContigBufferCount = 128; \
Contigs = all(ContigData, ContigBufferCount); \
ContigCount = 0; \
}
#define APPEND_CONTIG() \
{ \
if (ContigCount >= ContigBufferCount) \
{ \
ContigBufferCount += 128; \
ContigData *NewContigs = all(ContigData, ContigBufferCount); \
memcpy(NewContigs, Contigs, ContigCount*sizeof(ContigData)); \
freemem(Contigs); \
Contigs = NewContigs; \
} \
++ContigCount; \
}
void LogContigs(const ContigData *Contigs, int ContigCount)
{
Log(" Index Label From Length End\n");
Log("------ -------------------------------- ----------- ----------- -----------\n");
for (int i = 0; i < ContigCount; ++i)
{
const ContigData *ptrContig = Contigs + i;
Log("%6d %32.32s %11d %11d %11d",
ptrContig->Index,
ptrContig->Label,
ptrContig->From,
ptrContig->Length,
ptrContig->From + ptrContig->Length - 1);
if (ptrContig->From%CONTIG_MAP_BIN_SIZE)
Log(" Bin %d Remainder %d",
ptrContig->From/CONTIG_MAP_BIN_SIZE,
ptrContig->From%CONTIG_MAP_BIN_SIZE);
Log("\n");
}
}
char *ReadMFA(FILE *f, int *ptrLength, ContigData **ptrContigs, int *ptrContigCount)
{
rewind(f);
int FileSize = GetFileSize(f);
int BufferSize = FileSize + MAX_CONTIGS*CONTIG_MAP_BIN_SIZE;
char *Buffer = all(char, BufferSize);
char prev_c = '\n';
bool InLabel = false;
int ContigFrom = 0;
char *Label = 0;
int LabelLength = 0;
int LabelBufferLength = 0;
int Pos = 0;
int PrevContigTo = -1;
int ContigBufferCount = 0;
int ContigCount = 0;
ContigData *Contigs;
INIT_CONTIGS()
for (;;)
{
int c = fgetc(f);
if (EOF == c)
{
if (feof(f))
break;
Quit("Stream error");
}
if (InLabel)
{
if (c == '\r')
continue;
if ('\n' == c)
{
APPEND_CONTIG()
ContigData *ptrContig = Contigs + ContigCount - 1;
ptrContig->From = ContigFrom;
ptrContig->Index = ContigCount - 1;
InLabel = false;
}
else
{
APPEND_LABEL(c)
}
}
else
{
if ('>' == c && '\n' == prev_c)
{
InLabel = true;
if (ContigCount > 0)
{
PrevContigTo = Pos - 1;
ContigData *ptrPrevContig = Contigs + ContigCount - 1;
ptrPrevContig->Length = PrevContigTo - ptrPrevContig->From + 1;
Label[LabelLength] = 0;
if (g_TruncateLabels)
{
char *ptrSpace = strchr(Label, ' ');
if (0 != ptrSpace)
*ptrSpace = 0;
}
ptrPrevContig->Label = strsave(Label);
LabelLength = 0;
int BinRemaining = CONTIG_MAP_BIN_SIZE - (PrevContigTo + 1)%CONTIG_MAP_BIN_SIZE;
int PadLength = BinRemaining;
if (PadLength < DP_PAD)
PadLength += CONTIG_MAP_BIN_SIZE;
for (int i = 0; i < PadLength; ++i)
{
APPEND_CHAR('!')
}
}
ContigFrom = Pos;
if (ContigFrom%CONTIG_MAP_BIN_SIZE != 0)
Quit("ReadMFA logic error");
}
else if (!isspace(c))
{
APPEND_CHAR(c)
}
}
prev_c = c;
}
if (ContigCount > 0)
{
ContigData *ptrPrevContig = Contigs + ContigCount - 1;
ptrPrevContig->Length = Pos - ptrPrevContig->From;
Label[LabelLength] = 0;
if (g_TruncateLabels)
{
char *ptrSpace = strchr(Label, ' ');
if (0 != ptrSpace)
*ptrSpace = 0;
}
ptrPrevContig->Label = strsave(Label);
}
*ptrContigs = Contigs;
*ptrContigCount = ContigCount;
*ptrLength = Pos;
return Buffer;
}
char *ReadMFA(const char FileName[], int *ptrSeqLength, ContigData **ptrContigs,
int *ptrContigCount, int **ptrContigMap)
{
FILE *f = OpenStdioFile(FileName);
char *Seq = ReadMFA(f, ptrSeqLength, ptrContigs, ptrContigCount);
MakeContigMap(*ptrContigs, *ptrContigCount, ptrContigMap);
fclose(f);
return Seq;
}
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