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Haplex.c
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Haplex.c
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/*********************************************************************************************\
*
* Code for produce all potential haplotype k-mers with a single SNP in the center of
* the k-mers
*
* Author: Gene Myers
* Date : October, 2020
*
*********************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <dirent.h>
#include <math.h>
#undef DEBUG_PARTITION
#include "libfastk.h"
static char *Usage = " -H [-g<int>:<int>] <source>[.ktab]";
/****************************************************************************************
*
* Print & compare utilities
*
*****************************************************************************************/
#define COUNT_OF(p) (*((uint16 *) (p+kbyte)))
#define ID_PTR(p) ((uint32 *) (p+kbyte))
static char dna[4] = { 'a', 'c', 'g', 't' };
static char *fmer[256], _fmer[1280];
static void setup_fmer_table()
{ char *t;
int i, l3, l2, l1, l0;
i = 0;
t = _fmer;
for (l3 = 0; l3 < 4; l3++)
for (l2 = 0; l2 < 4; l2++)
for (l1 = 0; l1 < 4; l1++)
for (l0 = 0; l0 < 4; l0++)
{ fmer[i] = t;
*t++ = dna[l3];
*t++ = dna[l2];
*t++ = dna[l1];
*t++ = dna[l0];
*t++ = 0;
i += 1;
}
}
#ifdef DEBUG
static void print_seq(uint8 *seq, int len)
{ int i, b, k;
b = len >> 2;
for (i = 0; i < b; i++)
printf("%s",fmer[seq[i]]);
k = 6;
for (i = b << 2; i < len; i++)
{ printf("%c",(dna[seq[b] >> k) & 0x3]);
k -= 2;
}
}
#endif
static void print_hap(uint8 *seq, int len, int half)
{ int i, b, h, k;
h = half >> 2;
b = len >> 2;
for (i = 0; i < h; i++)
printf("%s",fmer[seq[i]]);
k = 6;
for (i = h << 2; k >= 0; i++)
{ if (i == half)
printf("%c",dna[(seq[h] >> k) & 0x3]-32);
else
printf("%c",dna[(seq[h] >> k) & 0x3]);
k -= 2;
}
for (i = h+1; i < b; i++)
printf("%s",fmer[seq[i]]);
k = 6;
for (i = b << 2; i < len; i++)
{ printf("%c",dna[(seq[b] >> k) & 0x3]);
k -= 2;
}
}
static inline int mycmp(uint8 *a, uint8 *b, int n)
{ while (n-- > 0)
{ if (*a++ != *b++)
return (a[-1] < b[-1] ? -1 : 1);
}
return (0);
}
/****************************************************************************************
*
* Find Haplotype Pairs
*
*****************************************************************************************/
static int HAPLO_LOW, HAPLO_HGH;
static inline int mypref(uint8 *a, uint8 *b, int n)
{ int i;
uint8 x, y;
for (i = 0; i <= n; i += 4)
{ if (*a != *b)
{ x = *a;
y = *b;
if ((x & 0xf0) != (y & 0xf0))
if ((x & 0xc0) != (y & 0xc0))
return (i);
else
return (i + 1);
else
if ((x & 0xfc) != (y & 0xfc))
return (i + 2);
else
return (i + 3);
}
a += 1;
b += 1;
}
return (n+1);
}
void Find_Haplo_Pairs(Kmer_Stream *T)
{ int kmer = T->kmer;
int tbyte = T->tbyte;
int kbyte = T->kbyte;
int khalf;
uint8 prefs[] = { 0x3f, 0x0f, 0x03, 0x00 };
int mask, offs, rem;
uint8 *nptr;
uint8 *cache, *cptr, *ctop;
int f, i;
int index[4];
uint8 *finger[4];
uint8 *flimit[4];
int a, advn[4];
int c, good[4];
int mc, hc;
uint8 *mr, *hr;
setup_fmer_table();
khalf = kmer/2;
mask = prefs[khalf&0x3];
offs = (khalf >> 2) + 1;
rem = ((kmer+3) >> 2) - offs;
#ifdef DEBUG_PARTITION
printf("Extension = K[%d]&%02x . K[%d..%d)\n",offs-1,mask,offs,offs+rem);
#endif
cache = Malloc(4097*tbyte,"Allocating entry buffer");
cptr = cache;
ctop = cache + 4096*tbyte;
First_Kmer_Entry(T);
while (T->csuf != NULL)
{ f = 0;
cptr = cache;
index[f++] = 0;
Current_Entry(T,cptr);
nptr = cptr+tbyte;
for (Next_Kmer_Entry(T); T->csuf != NULL; Next_Kmer_Entry(T))
{ int x = mypref(cptr,Current_Entry(T,nptr),khalf);
if (x < khalf)
break;
if (x == khalf)
index[f++] = nptr-cache;
if (nptr >= ctop)
{ int64 cidx = ctop-cache;
int64 cmax = ((cidx*14)/(10*tbyte) + 2048)*tbyte;
cache = Realloc(cache,cmax+tbyte,"Reallocting entry buffer");
ctop = cache + cmax;
nptr = cache + cidx;
}
cptr = nptr;
nptr = cptr+tbyte;
}
#ifdef DEBUG_PARTITION
printf("part %d",f);
for (i = 0; i < f; i++)
printf(" %d",index[i]/tbyte);
printf(" %ld\n",(nptr-cache)/tbyte);
#endif
if (f <= 1)
continue;
for (i = 0; i < f; i++)
finger[i] = cache + index[i];
for (i = 1; i < f; i++)
flimit[i-1] = finger[i];
flimit[f-1] = nptr;
#define ADD(i) \
{ int cn = COUNT_OF(finger[i]); \
advn[a++] = i; \
if (HAPLO_LOW <= cn && cn <= HAPLO_HGH) \
good[c++] = i; \
}
#define SET(i) \
{ mc = hc; \
mr = hr; \
a = c = 0; \
ADD(i); \
}
while (1)
{ for (i = 0; i < f; i++)
if (finger[i] < flimit[i])
break;
if (i >= f)
break;
hr = finger[i]+offs;
hc = hr[-1] & mask;
SET(i);
for (i++; i < f; i++)
if (finger[i] < flimit[i])
{ hr = finger[i]+offs;
hc = hr[-1] & mask;
if (hc == mc)
{ int v = mycmp(hr,mr,rem);
if (v == 0)
ADD(i)
else if (v < 0)
SET(i)
}
else if (hc < mc)
SET(i)
}
#ifdef DEBUG_PARTITION
{ int j;
j = 0;
for (i = 0; i < a; i++)
{ printf(" %d",advn[i]);
if (j < c && advn[i] == good[j])
{ printf("+");
j += 1;
}
}
printf("\n");
}
#endif
if (c > 1)
{ for (i = 0; i < c; i++)
{ uint8 *fp = finger[good[i]];
print_hap(fp,kmer,khalf);
printf(" %d\n",COUNT_OF(fp));
}
printf("\n");
}
for (i = 0; i < a; i++)
finger[advn[i]] += tbyte;
#ifdef DEBUG_PARTITION
for (i = 0; i < f; i++)
printf(" %ld",(finger[i]-cache)/tbyte);
printf("\n");
#endif
}
}
}
void Find_Haplo_Pairs2(Kmer_Stream *T)
{ int kmer = T->kmer;
int tbyte = T->tbyte;
int kbyte = T->kbyte;
int ibyte = tbyte + 2;
int khalf;
uint8 prefs[] = { 0x3f, 0x0f, 0x03, 0x00 };
int mask, offs, rem;
uint8 *nptr;
uint8 *cache, *cptr, *ctop;
int f, i;
int index[4];
uint8 *finger[4];
uint8 *flimit[4];
int a, advn[4];
int c, good[4];
int mc, hc;
uint8 *mr, *hr;
int ictr;
setup_fmer_table();
khalf = kmer/2;
mask = prefs[khalf&0x3];
offs = (khalf >> 2) + 1;
rem = ((kmer+3) >> 2) - offs;
#ifdef DEBUG_PARTITION
printf("Extension = K[%d]&%02x . K[%d..%d)\n",offs-1,mask,offs,offs+rem);
#endif
cache = Malloc(4097*ibyte,"Allocating entry buffer");
cptr = cache;
ctop = cache + 4096*ibyte;
ictr = 0;
First_Kmer_Entry(T);
while (T->csuf != NULL)
{ f = 0;
cptr = cache;
index[f++] = 0;
Current_Entry(T,cptr);
nptr = cptr+ibyte;
for (Next_Kmer_Entry(T); T->csuf != NULL; Next_Kmer_Entry(T))
{ int x = mypref(cptr,Current_Entry(T,nptr),khalf);
if (x < khalf)
break;
if (x == khalf)
index[f++] = nptr-cache;
if (nptr >= ctop)
{ int64 cidx = ctop-cache;
int64 cmax = ((cidx*14)/(10*ibyte) + 2048)*ibyte;
cache = Realloc(cache,cmax+ibyte,"Reallocting entry buffer");
ctop = cache + cmax;
nptr = cache + cidx;
}
cptr = nptr;
nptr = cptr+ibyte;
}
#ifdef DEBUG_PARTITION
printf("part %d",f);
for (i = 0; i < f; i++)
printf(" %d",index[i]/ibyte);
printf(" %ld\n",(nptr-cache)/ibyte);
#endif
if (f <= 1)
continue;
for (i = 0; i < f; i++)
finger[i] = cache + index[i];
for (i = 1; i < f; i++)
flimit[i-1] = finger[i];
flimit[f-1] = nptr;
#define ADD(i) \
{ int cn = COUNT_OF(finger[i]); \
advn[a++] = i; \
if (HAPLO_LOW <= cn && cn <= HAPLO_HGH) \
good[c++] = i; \
}
#define SET(i) \
{ mc = hc; \
mr = hr; \
a = c = 0; \
ADD(i); \
}
while (1)
{ for (i = 0; i < f; i++)
if (finger[i] < flimit[i])
break;
if (i >= f)
break;
hr = finger[i]+offs;
hc = hr[-1] & mask;
SET(i);
for (i++; i < f; i++)
if (finger[i] < flimit[i])
{ hr = finger[i]+offs;
hc = hr[-1] & mask;
if (hc == mc)
{ int v = mycmp(hr,mr,rem);
if (v == 0)
ADD(i)
else if (v < 0)
SET(i)
}
else if (hc < mc)
SET(i)
}
#ifdef DEBUG_PARTITION
{ int j;
j = 0;
for (i = 0; i < a; i++)
{ printf(" %d",advn[i]);
if (j < c && advn[i] == good[j])
{ printf("+");
j += 1;
}
}
printf("\n");
}
#endif
for (i = 0; i < a; i++)
*ID_PTR(finger[advn[i]]) = 0;
if (c > 1)
{ ictr += 4;
for (i = 0; i < c; i++)
{ uint8 *fp = finger[good[i]];
*ID_PTR(fp) = ictr | good[i];
}
}
for (i = 0; i < a; i++)
finger[advn[i]] += ibyte;
#ifdef DEBUG_PARTITION
for (i = 0; i < f; i++)
printf(" %ld",(finger[i]-cache)/ibyte);
printf("\n");
#endif
}
for (cptr = cache; cptr < nptr; cptr += ibyte)
{ f = *ID_PTR(cptr);
if (f > 0)
{ printf(" %6d: %c ",f>>2,dna[f&0x2]);
print_hap(cptr,kmer,khalf);
printf("\n");
}
}
}
printf("A total of %d hetero-sites found\n",ictr>>2);
}
/****************************************************************************************
*
* Main
*
*****************************************************************************************/
int main(int argc, char *argv[])
{ Kmer_Stream *T;
int FOR_HAYNES;
{ int i, j, k;
int flags[128];
char *eptr, *fptr;
(void) flags;
ARG_INIT("Haplex");
HAPLO_LOW = 1;
HAPLO_HGH = 0x7fff;
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("H")
break;
case 'g':
HAPLO_LOW = strtol(argv[i]+2,&eptr,10);
if (eptr > argv[i]+2)
{ if (HAPLO_LOW < 1 || HAPLO_LOW > 0x7fff)
{ fprintf(stderr,"%s: Good minimum count %d is out of range\n",
Prog_Name,HAPLO_LOW);
exit (1);
}
if (*eptr == ':')
{ HAPLO_HGH = strtol(eptr+1,&fptr,10);
if (fptr > eptr+1 && *fptr == '\0')
{ if (HAPLO_HGH < 1 || HAPLO_HGH > 0x7fff)
{ fprintf(stderr,"%s: Good maximum count %d is out of range\n",
Prog_Name,HAPLO_HGH);
exit (1);
}
if (HAPLO_LOW > HAPLO_HGH)
{ fprintf(stderr,"%s: Good count range is invalid\n",Prog_Name);
exit (1);
}
break;
}
}
}
fprintf(stderr,"%s: Syntax of -g option invalid -h<int>:<int>\n",Prog_Name);
exit (1);
}
else
argv[j++] = argv[i];
argc = j;
FOR_HAYNES = flags['H'];
if (argc != 2)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
fprintf(stderr,"\n");
fprintf(stderr," -g: Accept only haplotypes with count in given range (inclusive).\n");
exit (1);
}
}
T = Open_Kmer_Stream(argv[1]);
if (T == NULL)
{ fprintf(stderr,"%s: Cannot open table %s\n",Prog_Name,argv[1]);
exit (1);
}
if (FOR_HAYNES)
Find_Haplo_Pairs2(T);
else
Find_Haplo_Pairs(T);
Free_Kmer_Stream(T);
Catenate(NULL,NULL,NULL,NULL);
Numbered_Suffix(NULL,0,NULL);
free(Prog_Name);
exit (0);
}