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QV.c
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QV.c
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/*******************************************************************************************
*
* Compressor/decompressor for .quiv files: customized Huffman codes for each stream based on
* the histogram of values occuring in a given file. The two low complexity streams
* (deletionQV and substitutionQV) use a Huffman coding of the run length of the prevelant
* character.
*
* Author: Gene Myers
* Date: Jan 18, 2014
* Modified: July 25, 2014
*
********************************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <unistd.h>
#include "DB.h"
#undef DEBUG
#define MIN_BUFFER 1000
#define HUFF_CUTOFF 16 // This cannot be larger than 16 !
/*******************************************************************************************
*
* Endian flipping routines
*
********************************************************************************************/
static int LittleEndian; // Little-endian machine ?
// Referred by: Decode & Decode_Run
static int Flip; // Flip endian of all coded shorts and ints
// Referred by: Decode & Decode_Run & Read_Scheme
static void Set_Endian(int flip)
{ uint32 x = 3;
uint8 *b = (uint8 *) (&x);
Flip = flip;
LittleEndian = (b[0] == 3);
}
static void Flip_Long(void *w)
{ uint8 *v = (uint8 *) w;
uint8 x;
x = v[0];
v[0] = v[3];
v[3] = x;
x = v[1];
v[1] = v[2];
v[2] = x;
}
static void Flip_Short(void *w)
{ uint8 *v = (uint8 *) w;
uint8 x;
x = v[0];
v[0] = v[1];
v[1] = x;
}
/*******************************************************************************************
*
* Routines for computing a Huffman Encoding Scheme
*
********************************************************************************************/
typedef struct
{ int type; // 0 => normal, 1 => normal but has long codes, 2 => truncated
uint32 codebits[256]; // If type = 2, then code 255 is the special code for
int codelens[256]; // non-Huffman exceptions
int lookup[0x10000]; // Lookup table (just for decoding)
} HScheme;
typedef struct _HTree
{ struct _HTree *lft, *rgt;
uint64 count;
} HTree;
// Establish heap property from node s down (1 is root, siblings of n are 2n and 2n+1)
// assuming s is the only perturbation in the tree.
static void Reheap(int s, HTree **heap, int hsize)
{ int c, l, r;
HTree *hs, *hr, *hl;
c = s;
hs = heap[s];
while ((l = 2*c) <= hsize)
{ r = l+1;
hl = heap[l];
hr = heap[r];
if (r > hsize || hr->count > hl->count)
{ if (hs->count > hl->count)
{ heap[c] = hl;
c = l;
}
else
break;
}
else
{ if (hs->count > hr->count)
{ heap[c] = hr;
c = r;
}
else
break;
}
}
if (c != s)
heap[c] = hs;
}
// Given Huffman tree build a table of codes from it, the low-order codelens[s] bits
// of codebits[s] contain the code for symbol s.
static void Build_Table(HTree *node, int code, int len, uint32 *codebits, int *codelens)
{ if (node->rgt == NULL)
{ uint64 symbol = (uint64) (node->lft);
codebits[symbol] = code;
codelens[symbol] = len;
}
else
{ code <<= 1;
len += 1;
Build_Table(node->lft,code,len,codebits,codelens);
Build_Table(node->rgt,code+1,len,codebits,codelens);
}
}
// For the non-zero symbols in hist, compute a huffman tree over them, and then
// build a table of the codes. If inscheme is not NULL, then place all symbols
// with code 255 or with more than HUFF_CUTOFF bits in the encoding by inscheme
// as a single united entity, whose code signals that the value of these symbols
// occur explicitly in 8 (values) or 16 (run lengths) bits following the code.
// All the symbols in this class will have the same entry in the code table and
// 255 is always in this class.
static HScheme *Huffman(uint64 *hist, HScheme *inscheme)
{ HScheme *scheme;
HTree *heap[259];
HTree node[512];
int hsize;
HTree *lft, *rgt;
int value, range;
int i;
scheme = (HScheme *) Malloc(sizeof(HScheme),"Allocating Huffman scheme record");
if (scheme == NULL)
return (NULL);
hsize = 0; // Load heap
value = 0;
if (inscheme != NULL)
{ node[0].count = 0;
node[0].lft = (HTree *) (uint64) 255;
node[0].rgt = NULL;
heap[++hsize] = node+(value++);
}
for (i = 0; i < 256; i++)
if (hist[i] > 0)
{ if (inscheme != NULL && (inscheme->codelens[i] > HUFF_CUTOFF || i == 255))
node[0].count += hist[i];
else
{ node[value].count = hist[i];
node[value].lft = (HTree *) (uint64) i;
node[value].rgt = NULL;
heap[++hsize] = node+(value++);
}
}
for (i = hsize/2; i >= 1; i--) // Establish heap property
Reheap(i,heap,hsize);
range = value; // Merge pairs with smallest count until have a tree
for (i = 1; i < value; i++)
{ lft = heap[1];
heap[1] = heap[hsize--];
Reheap(1,heap,hsize);
rgt = heap[1];
node[range].lft = lft;
node[range].rgt = rgt;
node[range].count = lft->count + rgt->count;
heap[1] = node+(range++);
Reheap(1,heap,hsize);
}
for (i = 0; i < 256; i++) // Build the code table
{ scheme->codebits[i] = 0;
scheme->codelens[i] = 0;
}
Build_Table(node+(range-1),0,0,scheme->codebits,scheme->codelens);
if (inscheme != NULL) // Set scheme type and if truncated (2), map truncated codes
{ scheme->type = 2; // to code and length for 255
for (i = 0; i < 255; i++)
if (inscheme->codelens[i] > HUFF_CUTOFF || scheme->codelens[i] > HUFF_CUTOFF)
{ scheme->codelens[i] = scheme->codelens[255];
scheme->codebits[i] = scheme->codebits[255];
}
}
else
{ scheme->type = 0;
for (i = 0; i < 256; i++)
{ if (scheme->codelens[i] > HUFF_CUTOFF)
scheme->type = 1;
}
}
return (scheme);
}
#ifdef DEBUG
// For debug, show the coding table
static void Print_Table(HScheme *scheme, uint64 *hist, int infosize)
{ uint64 total_bits;
uint32 specval, mask, code, *bits;
int speclen, clen, *lens;
int i, k;
total_bits = 0;
bits = scheme->codebits;
lens = scheme->codelens;
if (scheme->type == 2)
{ specval = bits[255];
speclen = lens[255];
}
else
specval = speclen = 0x7fffffff;
printf("\nCode Table:\n");
for (i = 0; i < 256; i++)
if (lens[i] > 0)
{ clen = lens[i];
mask = (1 << clen);
code = bits[i];
printf(" %3d: %2d ",i,clen);
for (k = 0; k < clen; k++)
{ mask >>= 1;
if (code & mask)
printf("1");
else
printf("0");
}
if (code == specval && clen == speclen)
{ printf(" ***");
if (hist != NULL)
total_bits += (clen+infosize)*hist[i];
}
else if (hist != NULL)
total_bits += clen*hist[i];
printf("\n");
}
if (hist != NULL)
printf("\nTotal Bytes = %lld\n",(total_bits-1)/8+1);
}
// For debug, show the histogram
static void Print_Histogram(uint64 *hist)
{ int i, low, hgh;
uint64 count;
for (hgh = 255; hgh >= 0; hgh--)
if (hist[hgh] != 0)
break;
for (low = 0; low < 256; low++)
if (hist[low] != 0)
break;
count = 0;
for (i = low; i <= hgh; i++)
count += hist[i];
for (i = hgh; i >= low; i--)
printf(" %3d: %8llu %5.1f%%\n",i,hist[i],(hist[i]*100.)/count);
}
#endif
/*******************************************************************************************
*
* Read and Write Huffman Schemes
*
********************************************************************************************/
// Write the code table to out.
static void Write_Scheme(HScheme *scheme, FILE *out)
{ int i;
uint8 x;
uint32 *bits;
int *lens;
lens = scheme->codelens;
bits = scheme->codebits;
x = (uint8) (scheme->type);
fwrite(&x,1,1,out);
for (i = 0; i < 256; i++)
{ x = (uint8) (lens[i]);
fwrite(&x,1,1,out);
if (x > 0)
fwrite(bits+i,sizeof(uint32),1,out);
}
}
// Allocate and read a code table from in, and return a pointer to it.
static HScheme *Read_Scheme(FILE *in)
{ HScheme *scheme;
int *look, *lens;
uint32 *bits, base;
int i, j, powr;
uint8 x;
scheme = (HScheme *) Malloc(sizeof(HScheme),"Allocating Huffman scheme record");
if (scheme == NULL)
return (NULL);
lens = scheme->codelens;
bits = scheme->codebits;
look = scheme->lookup;
if (fread(&x,1,1,in) != 1)
{ EPRINTF(EPLACE,"Could not read scheme type byte (Read_Scheme)\n");
free(scheme);
return (NULL);
}
scheme->type = x;
for (i = 0; i < 256; i++)
{ if (fread(&x,1,1,in) != 1)
{ EPRINTF(EPLACE,"Could not read length of %d'th code (Read_Scheme)\n",i);
return (NULL);
}
lens[i] = x;
if (x > 0)
{ if (fread(bits+i,sizeof(uint32),1,in) != 1)
{ EPRINTF(EPLACE,"Could not read bit encoding of %d'th code (Read_Scheme)\n",i);
free(scheme);
return (NULL);
}
}
else
bits[i] = 0;
}
if (Flip)
{ for (i = 0; i < 256; i++)
Flip_Long(bits+i);
}
for (i = 0; i < 256; i++)
{ if (lens[i] > 0)
{ base = (bits[i] << (16-lens[i]));
powr = (1 << (16-lens[i]));
for (j = 0; j < powr; j++)
look[base+j] = i;
}
}
return (scheme);
}
/*******************************************************************************************
*
* Encoders and Decoders
*
********************************************************************************************/
// Encode read[0..rlen-1] according to scheme and write to out
static void Encode(HScheme *scheme, FILE *out, uint8 *read, int rlen)
{ uint32 x, c, ocode;
int n, k, olen, llen;
int *nlens;
uint32 *nbits;
uint32 nspec;
int nslen;
nlens = scheme->codelens;
nbits = scheme->codebits;
if (scheme->type == 2)
{ nspec = nbits[255];
nslen = nlens[255];
}
else
nspec = nslen = 0x7fffffff;
#define OCODE(L,C) \
{ int len = olen + (L); \
uint32 code = (C); \
\
llen = olen; \
if (len >= 32) \
{ olen = len-32; \
ocode |= (code >> olen); \
fwrite(&ocode,sizeof(uint32),1,out); \
if (olen > 0) \
ocode = (code << (32-olen)); \
else \
ocode = 0; \
} \
else \
{ olen = len; \
ocode |= (code << (32-olen));; \
} \
}
llen = 0;
olen = 0;
ocode = 0;
for (k = 0; k < rlen; k++)
{ x = read[k];
n = nlens[x];
c = nbits[x];
OCODE(n,c);
if (c == nspec && n == nslen)
OCODE(8,x);
}
if (olen > 0) // Tricky: must pad so decoder does not read past
{ fwrite(&ocode,sizeof(uint32),1,out); // last integer int the coded output.
if (llen > 16 && olen > llen)
fwrite(&ocode,sizeof(uint32),1,out);
}
else if (llen > 16)
fwrite(&ocode,sizeof(uint32),1,out);
}
// Encode read[0..rlen-1] according to non-rchar table neme, and run-length table reme for
// runs of rchar characters. Write to out.
static void Encode_Run(HScheme *neme, HScheme *reme, FILE *out, uint8 *read, int rlen, int rchar)
{ uint32 x, c, ocode;
int n, h, k, olen, llen;
int *nlens, *rlens;
uint32 *nbits, *rbits;
uint32 nspec, rspec;
int nslen, rslen;
nlens = neme->codelens;
nbits = neme->codebits;
rlens = reme->codelens;
rbits = reme->codebits;
if (neme->type == 2)
{ nspec = nbits[255];
nslen = nlens[255];
}
else
nspec = nslen = 0x7fffffff;
rspec = rbits[255];
rslen = rlens[255];
llen = 0;
olen = 0;
ocode = 0;
k = 0;
while (k < rlen)
{ h = k;
while (k < rlen && read[k] == rchar)
k += 1;
if (k-h >= 255)
x = 255;
else
x = k-h;
n = rlens[x];
c = rbits[x];
OCODE(n,c);
if (c == rspec && n == rslen)
OCODE(16,k-h);
if (k < rlen)
{ x = read[k];
n = nlens[x];
c = nbits[x];
OCODE(n,c);
if (c == nspec && n == nslen)
OCODE(8,x);
k += 1;
}
}
if (olen > 0)
{ fwrite(&ocode,sizeof(uint32),1,out);
if (llen > 16 && olen > llen)
fwrite(&ocode,sizeof(uint32),1,out);
}
else if (llen > 16)
fwrite(&ocode,sizeof(uint32),1,out);
}
// Read and decode from in, the next rlen symbols into read according to scheme
static int Decode(HScheme *scheme, FILE *in, char *read, int rlen)
{ int *look, *lens;
int signal, ilen;
uint64 icode;
uint32 *ipart;
uint16 *xpart;
uint8 *cpart;
int j, n, c;
if (LittleEndian)
{ ipart = ((uint32 *) (&icode));
xpart = ((uint16 *) (&icode)) + 2;
cpart = ((uint8 *) (&icode)) + 5;
}
else
{ ipart = ((uint32 *) (&icode)) + 1;
xpart = ((uint16 *) (&icode)) + 1;
cpart = ((uint8 *) (&icode)) + 2;
}
if (scheme->type == 2)
signal = 255;
else
signal = 256;
lens = scheme->codelens;
look = scheme->lookup;
#define GET \
if (n > ilen) \
{ icode <<= ilen; \
if (fread(ipart,sizeof(uint32),1,in) != 1) \
{ EPRINTF(EPLACE,"Could not read more bits (Decode)\n"); \
return (1); \
} \
ilen = n-ilen; \
icode <<= ilen; \
ilen = 32-ilen; \
} \
else \
{ icode <<= n; \
ilen -= n; \
}
#define GETFLIP \
if (n > ilen) \
{ icode <<= ilen; \
if (fread(ipart,sizeof(uint32),1,in) != 1) \
{ EPRINTF(EPLACE,"Could not read more bits (Decode)\n"); \
return (1); \
} \
Flip_Long(ipart); \
ilen = n-ilen; \
icode <<= ilen; \
ilen = 32-ilen; \
} \
else \
{ icode <<= n; \
ilen -= n; \
}
n = 16;
ilen = 0;
icode = 0;
if (Flip)
for (j = 0; j < rlen; j++)
{ GETFLIP
c = look[*xpart];
n = lens[c];
if (c == signal)
{ GETFLIP
c = *cpart;
n = 8;
}
read[j] = (char) c;
}
else
for (j = 0; j < rlen; j++)
{ GET
c = look[*xpart];
n = lens[c];
if (c == signal)
{ GET
c = *cpart;
n = 8;
}
read[j] = (char) c;
}
return (0);
}
// Read and decode from in, the next rlen symbols into read according to non-rchar scheme
// neme, and the rchar runlength shceme reme
static int Decode_Run(HScheme *neme, HScheme *reme, FILE *in, char *read,
int rlen, int rchar)
{ int *nlook, *nlens;
int *rlook, *rlens;
int nsignal, ilen;
uint64 icode;
uint32 *ipart;
uint16 *xpart;
uint8 *cpart;
int j, n, c, k;
if (LittleEndian)
{ ipart = ((uint32 *) (&icode));
xpart = ((uint16 *) (&icode)) + 2;
cpart = ((uint8 *) (&icode)) + 5;
}
else
{ ipart = ((uint32 *) (&icode)) + 1;
xpart = ((uint16 *) (&icode)) + 1;
cpart = ((uint8 *) (&icode)) + 2;
}
if (neme->type == 2)
nsignal = 255;
else
nsignal = 256;
nlens = neme->codelens;
nlook = neme->lookup;
rlens = reme->codelens;
rlook = reme->lookup;
n = 16;
ilen = 0;
icode = 0;
if (Flip)
for (j = 0; j < rlen; j++)
{ GETFLIP
c = rlook[*xpart];
n = rlens[c];
if (c == 255)
{ GETFLIP
c = *xpart;
n = 16;
}
for (k = 0; k < c; k++)
read[j++] = (char) rchar;
if (j < rlen)
{ GETFLIP
c = nlook[*xpart];
n = nlens[c];
if (c == nsignal)
{ GETFLIP
c = *cpart;
n = 8;
}
read[j] = (char) c;
}
}
else
for (j = 0; j < rlen; j++)
{ GET
c = rlook[*xpart];
n = rlens[c];
if (c == 255)
{ GET
c = *xpart;
n = 16;
}
for (k = 0; k < c; k++)
read[j++] = (char) rchar;
if (j < rlen)
{ GET
c = nlook[*xpart];
n = nlens[c];
if (c == nsignal)
{ GET
c = *cpart;
n = 8;
}
read[j] = (char) c;
}
}
return (0);
}
/*******************************************************************************************
*
* Histogrammers
*
********************************************************************************************/
// Histogram runlengths of symbol runChar in stream[0..rlen-1] into run.
static void Histogram_Seqs(uint64 *hist, uint8 *stream, int rlen)
{ int k;
for (k = 0; k < rlen; k++)
hist[stream[k]] += 1;
}
static void Histogram_Runs(uint64 *run, uint8 *stream, int rlen, int runChar)
{ int k, h;
k = 0;
while (k < rlen)
{ h = k;
while (k < rlen && stream[k] == runChar)
k += 1;
if (k-h >= 256)
run[255] += 1;
else
run[k-h] += 1;
if (k < rlen)
k += 1;
}
}
/*******************************************************************************************
*
* Reader
*
********************************************************************************************/
static char *Read = NULL; // Referred by: QVentry, Read_Lines, QVcoding_Scan,
static int Rmax = -1; // Compress_Next_QVentry
static int Nline; // Referred by: QVcoding_Scan
char *QVentry()
{ return (Read); }
void Set_QV_Line(int line)
{ Nline = line; }
int Get_QV_Line()
{ return (Nline); }
// If nlines == 1 trying to read a single header, nlines = 5 trying to read 5 QV/fasta lines
// for a sequence. Place line j at Read+j*Rmax and the length of every line is returned
// unless eof occurs in which case return -1. If any error occurs return -2.
int Read_Lines(FILE *input, int nlines)
{ int i, rlen;
int tmax;
char *tread;
char *other;
if (Read == NULL)
{ tmax = MIN_BUFFER;
tread = (char *) Malloc(5*tmax,"Allocating QV entry read buffer");
if (tread == NULL)
EXIT(-2);
Rmax = tmax;
Read = tread;
}
Nline += 1;
if (fgets(Read,Rmax,input) == NULL)
return (-1);
rlen = strlen(Read);
while (Read[rlen-1] != '\n')
{ tmax = ((int) 1.4*Rmax) + MIN_BUFFER;
tread = (char *) Realloc(Read,5*tmax,"Reallocating QV entry read buffer");
if (tread == NULL)
EXIT(-2);
Rmax = tmax;
Read = tread;
if (fgets(Read+rlen,Rmax-rlen,input) == NULL)
{ EPRINTF(EPLACE,"Line %d: Last line does not end with a newline !\n",Nline);
EXIT(-2);
}
rlen += strlen(Read+rlen);
}
other = Read;
for (i = 1; i < nlines; i++)
{ other += Rmax;
Nline += 1;
if (fgets(other,Rmax,input) == NULL)
{ EPRINTF(EPLACE,"Line %d: incomplete last entry of .quiv file\n",Nline);
EXIT(-2);
}
if (rlen != (int) strlen(other))
{ EPRINTF(EPLACE,"Line %d: Lines for an entry are not the same length\n",Nline);
EXIT(-2);
}
}
return (rlen-1);
}
/*******************************************************************************************
*
* Tag compression and decompression routines
*
********************************************************************************************/
// Keep only the symbols in tags[0..rlen-1] for which qvs[k] != rchar and
// return the # of symbols kept.
static int Pack_Tag(char *tags, char *qvs, int rlen, int rchar)
{ int j, k;
j = 0;
for (k = 0; k < rlen; k++)
if (qvs[k] != rchar)
tags[j++] = tags[k];
tags[j] = '\0';
return (j);
}
// Count the # of non-rchar symbols in qvs[0..rlen-1]
static int Packed_Length(char *qvs, int rlen, int rchar)
{ int k, clen;
clen = 0;
for (k = 0; k < rlen; k++)
if (qvs[k] != rchar)
clen += 1;
return (clen);
}
// Unpack tags by moving its i'th char to position k where qvs[k] is the i'th non-rchar
// symbol in qvs. All other chars are set to rchar. rlen is the length of qvs and
// the unpacked result, clen is the initial length of tags.
static void Unpack_Tag(char *tags, int clen, char *qvs, int rlen, int rchar)
{ int j, k;
j = clen-1;
for (k = rlen-1; k >= 0; k--)
{ if (qvs[k] == rchar)
tags[k] = 'n';
else
tags[k] = tags[j--];
}
}
/*******************************************************************************************
*
* Statistics Scan and Scheme creation and write
*
********************************************************************************************/
// Read up to the next num entries or until eof from the .quiva file on input and record
// frequency statistics. Copy these entries to the temporary file temp if != NULL.
// If there is an error then -1 is returned, otherwise the number of entries read.
static uint64 delHist[256], insHist[256], mrgHist[256], subHist[256], delRun[256], subRun[256];
static uint64 totChar;
static int delChar, subChar;
// Referred by: QVcoding_Scan, Create_QVcoding
void QVcoding_Scan1(int rlen, char *delQV, char *delTag, char *insQV, char *mergeQV, char *subQV)
{
if (rlen == 0) // Initialization call
{ int i;
// Zero histograms
bzero(delHist,sizeof(uint64)*256);
bzero(mrgHist,sizeof(uint64)*256);
bzero(insHist,sizeof(uint64)*256);
bzero(subHist,sizeof(uint64)*256);
for (i = 0; i < 256; i++)
delRun[i] = subRun[i] = 1;
totChar = 0;
delChar = -1;
subChar = -1;
return;
}
// Add streams to accumulating histograms and figure out the run chars
// for the deletion and substition streams
Histogram_Seqs(delHist,(uint8 *) delQV,rlen);
Histogram_Seqs(insHist,(uint8 *) insQV,rlen);
Histogram_Seqs(mrgHist,(uint8 *) mergeQV,rlen);
Histogram_Seqs(subHist,(uint8 *) subQV,rlen);
if (delChar < 0)
{ int k;
for (k = 0; k < rlen; k++)
if (delTag[k] == 'n' || delTag[k] == 'N')
{ delChar = delQV[k];
break;
}
}
if (delChar >= 0)
Histogram_Runs( delRun,(uint8 *) delQV,rlen,delChar);
totChar += rlen;
if (subChar < 0)
{ if (totChar >= 100000)
{ int k;
subChar = 0;
for (k = 1; k < 256; k++)
if (subHist[k] > subHist[subChar])
subChar = k;
}
}
if (subChar >= 0)
Histogram_Runs( subRun,(uint8 *) subQV,rlen,subChar);
return;
}
int QVcoding_Scan(FILE *input, int num, FILE *temp)
{ char *slash;
int rlen;
int i, r;
// Zero histograms
bzero(delHist,sizeof(uint64)*256);
bzero(mrgHist,sizeof(uint64)*256);
bzero(insHist,sizeof(uint64)*256);
bzero(subHist,sizeof(uint64)*256);
for (i = 0; i < 256; i++)
delRun[i] = subRun[i] = 1;
totChar = 0;
delChar = -1;
subChar = -1;
// Make a sweep through the .quiva entries, histogramming the relevant things
// and figuring out the run chars for the deletion and substition streams
r = 0;
for (i = 0; i < num; i++)
{ int well, beg, end, qv;
rlen = Read_Lines(input,1);
if (rlen == -2)
EXIT(-1);
if (rlen < 0)
break;
if (rlen == 0 || Read[0] != '@')
{ EPRINTF(EPLACE,"Line %d: Header in quiva file is missing\n",Nline);
EXIT(-1);
}
slash = index(Read+1,'/');
if (slash == NULL)
{ EPRINTF(EPLACE,"%s: Line %d: Header line incorrectly formatted ?\n",
Prog_Name,Nline);
EXIT(-1);
}
if (sscanf(slash+1,"%d/%d_%d RQ=0.%d\n",&well,&beg,&end,&qv) != 4)
{ EPRINTF(EPLACE,"%s: Line %d: Header line incorrectly formatted ?\n",
Prog_Name,Nline);
EXIT(-1);
}
if (temp != NULL)
fputs(Read,temp);
rlen = Read_Lines(input,5);
if (rlen < 0)
{ if (rlen == -1)
EPRINTF(EPLACE,"Line %d: incomplete last entry of .quiv file\n",Nline);
EXIT(-1);
}
if (temp != NULL)
{ fputs(Read,temp);
fputs(Read+Rmax,temp);
fputs(Read+2*Rmax,temp);
fputs(Read+3*Rmax,temp);
fputs(Read+4*Rmax,temp);
}
Histogram_Seqs(delHist,(uint8 *) (Read),rlen);
Histogram_Seqs(insHist,(uint8 *) (Read+2*Rmax),rlen);
Histogram_Seqs(mrgHist,(uint8 *) (Read+3*Rmax),rlen);
Histogram_Seqs(subHist,(uint8 *) (Read+4*Rmax),rlen);
if (delChar < 0)
{ int k;
char *del = Read+Rmax;
for (k = 0; k < rlen; k++)
if (del[k] == 'n' || del[k] == 'N')
{ delChar = Read[k];
break;