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kmeres.c
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/***********************************************************************\
* *
* PROJECT Kmere *
* *
*---------------------------------------------------------------------*
* *
* Kmere - Identification of Centromere and Telomere *
* using Kmer Profiles *
* *
* By *
* *
* Zemin Ning *
* *
* Copyright (C) 2024-2025 by Genome Research Limited *
* All rights reserved *
* *
*---------------------------------------------------------------------*
#######################################################################
# This software has been created by Genome Research Limited (GRL). #
# GRL hereby grants permission to use, copy, modify and distribute #
# this software and its documentation for non-commercial purposes #
# without fee at the user's own risk on the basis set out below. #
# GRL neither undertakes nor accepts any duty whether contractual or #
# otherwise in connection with the software, its use or the use of #
# any derivative, and makes no representations or warranties, express #
# or implied, concerning the software, its suitability, fitness for #
# a particular purpose or non-infringement. #
# In no event shall the authors of the software or GRL be responsible #
# or liable for any loss or damage whatsoever arising in any way #
# directly or indirectly out of the use of this software or its #
# derivatives, even if advised of the possibility of such damage. #
# Our software can be freely distributed under the conditions set out #
# above, and must contain this copyright notice. #
#######################################################################
*---------------------------------------------------------------------*/
/****************************************************************************/
#include <math.h>
#include <values.h>
#include <stdio.h>
#include <netinet/in.h>
#include <stdlib.h>
#include <dirent.h>
#include <string.h>
#include <ctype.h>
#include "fasta.h"
#include "ssaha.h"
static int *list,*readlength;
static B64_long *hist;
static signed char *head;
static B64_long n_Entry;
static char sample[30];
static char Cov_Name[50];
static char Pix_Name[50];
static char Out_Name[50];
static char Plot_Name[50];
static char *SCGname=NULL;//SingleCopyGenome
static B64_long baseSize;
static double set_rate = 10.0;
static double set_rate2 = 3.0;
static int n_step = 0;
static int n_pixel = 32768;
static int n_pixlen = 94000;
static int n_denoise = 0;
static int num_reads=40000000;
static void hpsortl(B64_long n, unsigned B64_long *ra)
{
B64_long l,j,ir,i;
unsigned B64_long rra;
if(n < 2)
return;
l=(n >> 1)+1;
ir=n;
for (;;) {
if (l > 1) {
rra=ra[--l];
} else {
rra=ra[ir];
ra[ir]=ra[1];
if (--ir == 1) {
ra[1]=rra;
return;
}
}
i=l;
j=l << 1;
while (j <= ir) {
if (j < ir && ra[j] < ra[j+1]) ++j;
if (rra < ra[j]) {
ra[i]=ra[j];
j += (i=j);
}
else j=ir+1;
}
ra[i]=rra;
}
}
/* Subroutine to sort the DNA sequences into a matrix table */
/* ============================================= */
void fastaSort(char **argv, int argc, int SEG_LEN)
/* ============================================= */
{
B64_long i,j,k,n_Sbase=SEG_LEN;
B64_long ps=0,ns=0,IntSeg=0,IntBase=0,lii;
fasta *seq;
int nSeq;
B64_long totalBases;
B64_long mhistc = 0;
B64_long mhistcc = 0;
int nsorts = 1024;
int nshift = (n_Sbase<<1)-10;//2^10=nsorts
int qthresh=23;
// int tb = 0;
int args,ac;
int m_st,m_ed,step_len = 2,pmod;
int nseq = 0,seqc,n_patch;
int sshift;
unsigned B64_long nmask;
int id_read[64],num_sect,n_reads; //id_read will never exceed mhist
int rd_st,rd_ed,n_input;
char line[500] = {0},outName[60]={0},outFast[60]={0},syscmd[200]={0};
char *ptr,base[20],zero[20]={0},line2[500]={0};
FILE *fpMate,*fpOutname,*fpOutfast;
int rd,read_pair[200];
B64_long kmask = (1L<<(n_Sbase<<1))-1;
double Qerr[100];
B64_long gtBases=0,nclip=0;
Qerr[0] = 1.0;
void Hash_Process(int brr,int len, char **argv, int argc, int args);
for(i=1;i<100;i++) Qerr[i] = pow((double)10.,(double)-.1*i);
/* sort all the names of genes or name entries */
printf("Input data starts ...\n");
args=2;
memset(sample,'\0',30);
strcpy(sample,"Seq-sample");
for(i=1;i<argc;i++)
{
if(!strcmp(argv[i],"-kmer"))
{
i++;
args=args+2;
}
else if(!strcmp(argv[i],"-sample"))
{
memset(sample,'\0',30);
sscanf(argv[++i],"%s",sample);
args=args+2;
}
else if(!strcmp(argv[i],"-denoise"))
{
sscanf(argv[++i],"%d",&n_denoise);
args=args+2;
}
else if(!strcmp(argv[i],"-step"))
{
sscanf(argv[++i],"%d",&n_step);
args=args+2;
}
else if(!strcmp(argv[i],"-pixel"))
{
sscanf(argv[++i],"%d",&n_pixel);
args=args+2;
}
else if(!strcmp(argv[i],"-rate"))
{
sscanf(argv[++i],"%lf",&set_rate);
args=args+2;
}
else if(!strcmp(argv[i],"-SCG"))
{
SCGname = argv[++i];
args=args+2;
}
}
for(ac=0;ac<argc;ac++)
printf("%s ",argv[ac]);
printf("\n");
printf("kmer size: %ld\n",n_Sbase);
if((hist = (B64_long *)calloc(400,sizeof(B64_long))) == NULL)
{
printf("ERROR ssaha_init: calloc - hist\n");
exit(1);
}
pmod=1;
nseq = 0;
if(strcmp(argv[1],"hash")==0)
Hash_Process(nseq,SEG_LEN,argv,argc,args);
else
{
printf("Invalid input command!\n");
exit(1);
}
printf("All jobs finished\n");
fflush(stdout);
system("ps aux |date");
return;
}
int ssaha_init( char **argv, int argc, int SEG_LEN)
{
fastaSort(argv,argc,SEG_LEN);
return(1);
}
/* Subroutine to sort the DNA sequences into a matrix table */
/* ============================================= */
void Hash_Process(int nRead,int SEG_LEN, char **argv, int argc, int args)
/* ============================================= */
{
B64_long i,j,k,w,iseq,n_Sbase=SEG_LEN;
B64_long ps=0,ns=0,IntSeg=0,IntBase=0,lii;
FILE *namef,*namef2,*namef3;
char *b;
fasta *seqp;
fasta *seq;
char nameout_hash[100],nameout_idex[100],nameout_loci[100],nameout_size[100],nameout_list[100];
int nSeq;
B64_long totalBases,nsize[10],n_pix,n_pbase,max_cover;
B64_long mhistc = 0;
B64_long mhistcc = 0;
int de_noise[202],de_index[202];
int nsorts = 1024;
int nshift;
int cover_avechr;
int n_meres,*chr_index,*chr_idpix,*chr_locus,*chr_drate;
int n_meres2,*chr_index2,*chr_idpix2,*chr_locus2;
void Plot_Process(char **argv, int argc, int args);
void Out_Meres(fasta *seq,int nSeq,int n_meres,int n_meres2,int *chr_index,int *chr_idpix,int *chr_locus,int *chr_index2,int *chr_idpix2,int *chr_locus2,char **argv,int argc,int args);
void ArraySort_Int2(int n, int *arr, int *brr);
B64_long offset,sizesm,dsize_4;
int stopflag,num_copy,m,n;
int n_ungroup,split_flag;
int ac,max_nhit,*ctg_list,*ctg_cover;
int seqc,num_refseq;
unsigned B64_long seqcharc = 0;
int step_flag,NLINK,max_contig,sshift;
unsigned B64_long nmask;
B64_long *patch_s_array,*patch_head,*ctg_head,*ray;
int *patch_index,*patch_list,*patch_ofset,*patch_cdex,*patch_iddex,*dex;
int *n_list,*rd_used,*rd_rept,*rd_name,*rd_link;
int id_read[64],num_sect,n_reads; //id_read will never exceed mhist
int *cover_ind,*cover_max,*list_pix,*head_pix;
int rd_st,rd_ed,n_input,n2_contig;
int **imatrix(B64_long nrl,B64_long nrh,B64_long ncl,B64_long nch);
unsigned int **uimatrix(B64_long nrl,B64_long nrh,B64_long ncl,B64_long nch);
B64_long **limatrix(B64_long nrl,B64_long nrh,B64_long ncl,B64_long nch);
void ArraySort_Mix(int n, B64_long *arr, int *brr);
char syscmd[200]={0};
B64_long kmask = (1L<<(n_Sbase<<1))-1;
double Qerr[100],*cover_pix,*cover_chr;
B64_long gtBases=0,nclip=0;
Qerr[0] = 1.0;
FILE *fp,*fpHASH,*fpIDEX,*fpLOCI,*fpLIST,*fpSIZE;
fasta *segg;
B64_long Size_q_pdata;
int num_seqque;
char *pdata;
if((fp=fopen(argv[args],"rb"))==NULL) printf("Cannot open file\n");
fseek(fp, 0, SEEK_END);
Size_q_pdata = ftell(fp) + 1;
fclose(fp);
if((pdata=(char*)calloc(Size_q_pdata,sizeof(char)))==NULL)
printf("calloc pdata\n");
num_seqque = extractFastq(argv[args],pdata,Size_q_pdata);
if((segg=(fasta*)calloc((num_seqque+1),sizeof(fasta)))==NULL)
printf("calloc segg\n");
if((seq=decodeFastq(argv[args],&num_seqque,&totalBases,pdata,Size_q_pdata,segg))==NULL)
printf("no query data found.\n");
nRead = num_seqque;
nSeq = num_seqque;
fastaUC(seq,nRead);
printf("Number of Chromosomes: %d \n",nSeq);
printf("Number of Bases: %ld \n",totalBases);
if((ctg_head = (B64_long *)calloc(nSeq+100,sizeof(int))) == NULL)
{
printf("fmate: calloc - ctg_head\n");
exit(1);
}
if((ctg_list = (int *)calloc(nSeq+100,sizeof(int))) == NULL)
{
printf("fmate: calloc - ctg_list\n");
exit(1);
}
if((ctg_cover = (int *)calloc(totalBases+100,sizeof(int))) == NULL)
{
printf("fmate: calloc - ctg_list\n");
exit(1);
}
mhistc = 0;
gtBases = 0;
nsorts = num_reads;
for(i=0;nsorts > 10;i++)
{
nsorts = nsorts>>1;
}
nsorts = 1L<<i;
if(n_Sbase <= 31)
nshift = (n_Sbase<<1)-i;
else
nshift = (31<<1)-i;
nshift = 40;
if((patch_list= (int *)calloc(nsorts,sizeof(int))) == NULL)
{
printf("phusion: calloc - patch_list\n");
exit(1);
}
if((patch_head= (B64_long *)calloc(nsorts,sizeof(B64_long))) == NULL)
{
printf("phusion: calloc - patch_head\n");
exit(1);
}
num_refseq = 0;
for(iseq=0;iseq<nSeq;iseq++)
{
double e=0.0,eh[32];
B64_long IntBaseRC;
B64_long IntSegRC=0;
int pos=0;
char *q;
IntSeg=0;
seqp=seq+iseq;
b = (char*)seqp->data;
if(seqp->finished) {
q = NULL;
} else {
q = NULL; //(char*)seqp->qual;
}
ns=seqp->length;
ctg_list[iseq] = ns;
printf("chrlen: %ld %ld %d\n",iseq+1,ns,nshift);
seqcharc += strlen(seqp->name);
k=n_Sbase;
if(k > ns) k=ns;
for(;k>0;k--,b++,pos++)
{
if (*b == 'A') IntBase=0;
else if(*b == 'C') IntBase=1;
else if(*b == 'G') IntBase=2;
else if(*b == 'T') IntBase=3;
else
{
e += eh[pos] = 1.;
continue;
}
e += eh[pos] = (q != NULL) ? Qerr[q[pos]] : 0;
IntBaseRC=(IntBase^3)<<((n_Sbase-k)<<1);
IntBase=IntBase<<((k-1)<<1);
IntSeg+=IntBase;
IntSegRC+=IntBaseRC;
}
for(j=ns-n_Sbase;--j>=0;b++,pos++)
{
int p=pos%n_Sbase;
if(e < .99)
{
if(IntSeg > IntSegRC)
{
int itt = IntSegRC>>nshift;
patch_list[itt]++;
}
else
{
int itt = IntSeg>>nshift;
patch_list[itt]++;
}
gtBases++;
}
e -= eh[p];
IntSeg = (IntSeg<<2)&kmask;
IntSegRC = (IntSegRC>>2)&kmask;
if (*b == 'A') IntBase=0;
else if(*b == 'C') IntBase=1;
else if(*b == 'G') IntBase=2;
else if(*b == 'T') IntBase=3;
else
{
e += eh[p] = 1.;
continue;
}
e += eh[p] = (q != NULL) ? Qerr[q[pos]] : 0;
IntBaseRC=(IntBase^3)<<((n_Sbase-1)<<1);
IntSeg+=IntBase;
IntSegRC+=IntBaseRC;
}
if(e < .99)
{
if(IntSeg > IntSegRC)
{
int itt = IntSegRC>>nshift;
patch_list[itt]++;
}
else
{
int itt = IntSeg>>nshift;
patch_list[itt]++;
}
gtBases++;
}
}
printf("data reading finished ...\n");
fflush(stdout);
system("ps aux | date");
ctg_head[0] = 0;
for(i=1;i<nSeq;i++)
ctg_head[i] = ctg_head[i-1]+ctg_list[i-1];
printf("Input data finished one set, nsorts=%d, totalgoodBP=%ld\n",nsorts,gtBases);
fflush(stdout);
system("ps aux | grep HASH; date");
max_nhit=0;
patch_head[0]=0;
for(i=0;i<nsorts;i++)
{
if(patch_list[i]>max_nhit)
max_nhit = patch_list[i];
if(i>0)
patch_head[i] = patch_head[i-1] + patch_list[i-1];
// patch_list[i] = 0;
}
memset(patch_list,0,4*nsorts);
mhistcc=patch_head[nsorts-1]+patch_list[nsorts-1]+20000;
printf("setting array memory: %ld\n",mhistcc);
fflush(stdout);
system("ps aux | grep HASH; date");
if((patch_index= (int *)calloc(mhistcc,sizeof(int))) == NULL)
{
printf("ssaha: calloc - patch_index\n");
exit(1);
}
if((patch_ofset= (int *)calloc(mhistcc,sizeof(int))) == NULL)
{
printf("ssaha: calloc - patch_index\n");
exit(1);
}
if((patch_s_array= (B64_long *)calloc(mhistcc+50000,sizeof(B64_long))) == NULL)
{
printf("ssaha: calloc - patch_s_array\n");
exit(1);
}
if((patch_cdex= (int *)calloc(mhistcc+50000,sizeof(int))) == NULL)
{
printf("ssaha: calloc - patch_index\n");
exit(1);
}
fflush(stdout);
system("ps aux | grep HASH; date");
seqc = 0;
printf("Here: %ld\n",mhistcc);
mhistcc=0;
for(iseq=0;iseq<nSeq;iseq++,seqc++)
{
char *q;
double e=0,eh[32];
B64_long IntBaseRC;
B64_long IntSegRC=0;
B64_long IntSeg=0;
int ic,pos=0;
seqp=seq+iseq;
b = (char*)seqp->data;
if(seqp->finished) {
q = NULL;
} else {
q = NULL; //(char*)seqp->qual;
}
ns=(seqp->length);
for(k=n_Sbase;k>0;k--,b++,pos++)
{
if (*b == 'A') IntBase=0;
else if(*b == 'C') IntBase=1;
else if(*b == 'G') IntBase=2;
else if(*b == 'T') IntBase=3;
else
{
e += eh[pos] = 1.;
continue;
}
e += eh[pos] = (q != NULL) ? Qerr[q[pos]] : 0;
IntBaseRC=(IntBase^3)<<((n_Sbase-k)<<1);
IntBase=IntBase<<((k-1)<<1);
IntSeg+=IntBase;
IntSegRC+=IntBaseRC;
}
for(j=ns-n_Sbase;--j>=0;b++,pos++)
{
int p=pos%n_Sbase;
if(e < .99)
{
B64_long patch_pos;
if(IntSeg > IntSegRC)
{
int itt = IntSegRC>>nshift;
patch_pos = patch_head[itt]+patch_list[itt];
patch_index[patch_pos]=seqc;
patch_ofset[patch_pos]=pos-n_Sbase+1;
patch_s_array[patch_pos] = IntSegRC;
patch_list[itt]++;
mhistcc++;
}
else
{
int itt = IntSeg>>nshift;
patch_pos = patch_head[itt]+patch_list[itt];
patch_index[patch_pos]=seqc;
patch_ofset[patch_pos]=pos-n_Sbase+1;
patch_s_array[patch_pos] = IntSeg;
patch_list[itt]++;
mhistcc++;
}
// printf("Herenn: %ld %ld\n",j,mhistcc);
gtBases++;
}
e -= eh[p];
IntSeg = (IntSeg<<2)&kmask;
IntSegRC = (IntSegRC>>2)&kmask;
if (*b == 'A') IntBase=0;
else if(*b == 'C') IntBase=1;
else if(*b == 'G') IntBase=2;
else if(*b == 'T') IntBase=3;
else
{
e += eh[p] = 1.;
continue;
}
e += eh[p] = 0;
IntBaseRC=(IntBase^3)<<((n_Sbase-1)<<1);
IntSeg+=IntBase;
IntSegRC+=IntBaseRC;
}
if(e < .99)
{
B64_long patch_pos;
if(IntSeg > IntSegRC)
{
int itt = IntSegRC>>nshift;
patch_pos = patch_head[itt]+patch_list[itt];
patch_index[patch_pos]=seqc;
patch_ofset[patch_pos]=pos-n_Sbase+1;
patch_s_array[patch_pos] = IntSegRC;
patch_list[itt]++;
mhistcc++;
}
else
{
int itt = IntSeg>>nshift;
patch_pos = patch_head[itt]+patch_list[itt];
patch_index[patch_pos]=seqc;
patch_ofset[patch_pos]=pos-n_Sbase+1;
patch_s_array[patch_pos] = IntSeg;
patch_list[itt]++;
mhistcc++;
}
gtBases++;
}
}
printf("Here: %ld\n",mhistcc);
ray = patch_s_array;
for(i=0;i<nsorts;i++)
{
if(patch_list[i] > 1)
{
B64_long patch_offpos;
if(i > 0)
patch_offpos = patch_head[i]-patch_head[0];
else
patch_offpos = 0;
for(k=0;k<patch_list[i];k++)
patch_cdex[k] = k;
ArraySort_Mix(patch_list[i],ray+patch_offpos,patch_cdex);
for(k=0;k<patch_list[i];k++)
{
B64_long patch_pos = patch_head[i]-patch_head[0];
stopflag = 0;
j=k+1;
while((j<patch_list[i])&&(stopflag==0))
{
if(patch_s_array[patch_pos+j] == patch_s_array[patch_pos+k])
{
j++;
}
else
stopflag=1;
}
num_copy = j-k;
for(m=0;m<num_copy;m++)
{
B64_long idd = patch_pos+patch_cdex[k+m];
int ictg = patch_index[idd];
B64_long idt = ctg_head[ictg]+patch_ofset[idd];
ctg_cover[idt]=num_copy;
// if(patch_list[i] >= 9)
// printf("kmer: %ld %d %d %ld %d %d || %ld %d %d %ld %ld\n",k,patch_list[i],ictg,patch_s_array[patch_pos+k+m],patch_ofset[idd],patch_index[idd],idt,ctg_cover[idt],num_copy,idt,ctg_head[ictg]);
}
k = j-1;
}
}
else if(patch_list[i] == 1)
{
B64_long patch_pos = patch_head[i]-patch_head[0];
B64_long idd = patch_pos;
int ictg = patch_index[idd];
B64_long idt = ctg_head[ictg]+patch_ofset[idd];
ctg_cover[idt]=1;
// printf("kmer: %ld %d %d %ld %d %d || %ld %d %d %ld %ld\n",i,patch_list[i],patch_s_array[patch_pos+k+m],patch_ofset[idd],patch_index[idd],idt,ctg_cover[idt],num_copy,idt,ctg_head[ictg]);
}
}
memset(Plot_Name,'\0',50);
sprintf(Plot_Name,"plot-%s.sh",sample);
memset(Out_Name,'\0',50);
sprintf(Out_Name,"chr2meres-%s.dat",sample);
memset(Pix_Name,'\0',50);
sprintf(Pix_Name,"chr2pix-%s.dat",sample);
memset(Cov_Name,'\0',50);
sprintf(Cov_Name,"cover-pix-%s.dat",sample);
if((namef = fopen(Pix_Name,"w")) == NULL)
{
printf("ERROR main:: args \n");
exit(1);
}
if((cover_chr= (double *)calloc(nSeq,sizeof(double))) == NULL)
{
printf("phusion: calloc - patch_head\n");
exit(1);
}
if((cover_pix= (double *)calloc(n_pixel,sizeof(double))) == NULL)
{
printf("phusion: calloc - patch_head\n");
exit(1);
}
if((cover_ind = (int *)calloc(n_pixel,sizeof(int))) == NULL)
{
printf("phusion: calloc - chr_index\n");
exit(1);
}
if((cover_max = (int *)calloc(nSeq,sizeof(int))) == NULL)
{
printf("phusion: calloc - chr_index\n");
exit(1);
}
if((list_pix = (int *)calloc(n_pixel,sizeof(int))) == NULL)
{
printf("phusion: calloc - chr_index\n");
exit(1);
}
if((head_pix = (int *)calloc(n_pixel,sizeof(int))) == NULL)
{
printf("phusion: calloc - chr_index\n");
exit(1);
}
if((chr_index = (int *)calloc(n_pixel,sizeof(int))) == NULL)
{
printf("phusion: calloc - chr_index\n");
exit(1);
}
if((chr_idpix = (int *)calloc(n_pixel,sizeof(int))) == NULL)
{
printf("phusion: calloc - chr_index\n");
exit(1);
}
if((chr_locus = (int *)calloc(n_pixel,sizeof(int))) == NULL)
{
printf("phusion: calloc - chr_index\n");
exit(1);
}
if((chr_index2 = (int *)calloc(n_pixel,sizeof(int))) == NULL)
{
printf("phusion: calloc - chr_index\n");
exit(1);
}
if((chr_idpix2 = (int *)calloc(n_pixel,sizeof(int))) == NULL)
{
printf("phusion: calloc - chr_index\n");
exit(1);
}
if((chr_locus2 = (int *)calloc(n_pixel,sizeof(int))) == NULL)
{
printf("phusion: calloc - chr_index\n");
exit(1);
}
if((chr_drate = (int *)calloc(n_pixel,sizeof(int))) == NULL)
{
printf("phusion: calloc - chr_index\n");
exit(1);
}
for(j=0;j<nSeq;j++)
{
double ave_cover;
int idd = ctg_list[j];
long int sum_cover;
sum_cover = 0;
for(i=0;i<idd;i++)
{
sum_cover = sum_cover+ctg_cover[ctg_head[j]+i];
}
ave_cover = sum_cover;
cover_chr[j] = ave_cover/idd;
}
n_pix = n_pixel-10;
n_pbase = totalBases;
n_pbase = n_pbase/n_pix;
n_pixlen = n_pbase;
n_pix = 0;
max_cover = 0;
printf("Genome2pix: %ld %d\n",n_pix,1);
fprintf(namef,"%ld %d\n",n_pix,1);
if(n_denoise == 10)
{
for(j=0;j<nSeq;j++)
{
int winsize = 200;
int idd = ctg_list[j];
long int sum_locs;
for(i=0;i<(ctg_list[j]-201);i++)
{
double cover_ave = 0.0;
double rate = 0.0;
int n_lows,n_high,n_max;
memset(de_noise,'\0',808);
memset(de_index,'\0',808);
sum_locs = 0;
n_max = 0;
for(m=0;m<200;m++)
{
de_noise[m] = ctg_cover[ctg_head[j]+i+m];
sum_locs = de_noise[m]+sum_locs;
de_index[m] = m;
if(de_noise[m] > n_max)
n_max = de_noise[m];
}
ArraySort_Int2(200,de_noise,de_index);
cover_ave = sum_locs;
cover_ave = cover_ave/200;
rate = n_max;
rate = n_max/cover_chr[j];
if((j==0)&&(i>691500)&&(i<691700))
printf("hit: %ld %ld %d || %ld %lf %lf || %d %lf\n",j,i,n_max,sum_locs,rate,cover_ave,ctg_cover[ctg_head[j]+i],cover_chr[j]);
if(rate >= 10.0)
{
n_lows = 0;
n_high = 0;
for(m=0;m<100;m++)
{
if(de_index[m] > 100)
n_lows++;
if(de_index[m] < 100)
n_high++;
}
printf("www: %ld %ld %d || %ld %lf %lf || %d %d\n",j,i,n_max,sum_locs,rate,cover_ave,n_lows,n_high);
if((n_lows > 20)&&(n_high > 20))
{
for(m=0;m<200;m++)
ctg_cover[ctg_head[j]+i+m] = 1;
i = i+200;
}
}
// printf("yyy: %ld %ld %d\n",j,i,ctg_cover[ctg_head[j]+i]);
}
}
}
for(j=0;j<nSeq;j++)
{
long int ave_cover;
int idd = ctg_list[j];
long int sum_cover;
idd = idd/n_pbase;
list_pix[j] = idd;
cover_max[j] = 0;
for(i=1;i<idd;i++)
{
int idt = i*n_pbase;
int idi = (i-1)*n_pbase;
sum_cover = 0;
for(k=idi;k<idt;k++)
{
sum_cover = sum_cover+ctg_cover[ctg_head[j]+k];
}
ave_cover = sum_cover;
ave_cover = ave_cover/n_pbase;
cover_pix[n_pix+i] = ave_cover;
cover_ind[n_pix+i] = j+1;
if(ave_cover > cover_max[j])
cover_max[j] = ave_cover;
if(ave_cover > max_cover)
max_cover = ave_cover;
printf("Chr: %ld %ld %d %ld %ld %ld || %lf %d\n",j+1,i,idt,n_pix+i,ave_cover,ctg_head[j]+idi,cover_chr[j],cover_max[j]);
}
printf("Genome2pix: %ld %d\n",n_pix+idd,1);
fprintf(namef,"%ld %d\n",n_pix+idd,1);
n_pix = n_pix + idd;
}
fclose(namef);
cover_avechr = 0;
for(j=0;j<nSeq;j++)
cover_avechr = cover_avechr+cover_max[j];
cover_avechr = cover_avechr/nSeq;
for(j=0;j<nSeq;j++)
{
if(cover_max[j] < 1000)
cover_max[j] = cover_avechr;
}
head_pix[0] = 0;
for(j=1;j<nSeq;j++)
head_pix[j] = head_pix[j-1]+list_pix[j-1];
if(n_denoise > 0)
{
for(j=0;j<nSeq;j++)
{
for(i=0;i<(list_pix[j]-10);i++)
{
int n_max = 0;
int idt = head_pix[j]+i;
for(m=0;m<20;m++)
{
if(cover_pix[idt+m] > 2.0*cover_chr[j])
n_max++;
}
if(n_max < 12)
cover_pix[idt] = cover_chr[j]/10;
else if(cover_pix[idt] < cover_chr[j])
cover_pix[idt] = 5.0*cover_chr[j];
}
}
}
if((namef2 = fopen(Cov_Name,"w")) == NULL)
{
printf("ERROR main:: args \n");
exit(1);
}
if((namef3 = fopen(Out_Name,"w")) == NULL)
{
printf("ERROR main:: args \n");
exit(1);
}
n_pix = 0;
n_meres = 0;
n_meres2 = 0;
for(j=0;j<nSeq;j++)
{
int idd = ctg_list[j];
idd = idd/n_pbase;
for(i=1;i<idd;i++)
{
int idt = i*n_pbase;
int idi = (i-1)*n_pbase;
double dimpix,dimpix2;
dimpix = cover_pix[n_pix+i];
dimpix = dimpix*100;
dimpix2 = dimpix;
dimpix2 = dimpix2/cover_max[j];
// dimpix = dimpix/cover_max[j];
dimpix = dimpix/max_cover;
printf("Chr-Denoise: %ld %ld %d %lf || %lf %f %lf || %d %lf %ld\n",j+1,n_pix+i,idt,cover_pix[n_pix+i],dimpix,set_rate,cover_chr[j],cover_max[j],dimpix2,max_cover);
fprintf(namef2,"%ld %lf\n",n_pix+i,dimpix);
if((dimpix > set_rate)||(dimpix2 > 90))
{
fprintf(namef3,"M1 %ld %ld %d %ld %lf\n",j+1,i,idt,n_pix+i,dimpix);
printf("M1 %ld %ld %d %ld %lf %d %lf\n",j+1,i,idt,n_pix+i,dimpix,n_meres,dimpix2);
chr_index[n_meres] = j+1;
chr_idpix[n_meres] = i;
chr_locus[n_meres] = idt;
n_meres++;
}
else if((dimpix > set_rate2)&&(dimpix <= set_rate)&&(dimpix2 > 30)&&(dimpix2 <= 90))
{
fprintf(namef3,"M2 %ld %ld %d %ld %lf\n",j+1,i,idt,n_pix+i,dimpix);
printf("M2 %ld %ld %d %ld %lf %d %lf\n",j+1,i,idt,n_pix+i,dimpix,n_meres2,dimpix2);
chr_index2[n_meres2] = j+1;
chr_idpix2[n_meres2] = i;
chr_locus2[n_meres2] = idt;
n_meres2++;
}
}
n_pix = n_pix + idd;
}
fclose(namef2);
fclose(namef3);
if(n_step > 0)
{
for(i=0;i<nSeq;i++)
{
for(k=0;k<ctg_list[i];k++)
{
if(k%n_step==0)
printf("Cover: %ld %ld %ld %d %d %ld\n",i+1,k,ctg_head[i]+k,ctg_cover[ctg_head[i]+k],ctg_list[i],totalBases);
}
}
}
free(patch_list);
free(patch_head);
free(patch_s_array);
free(patch_index);
printf("here1: %d %d %d || %d\n",nSeq,n_meres,n_meres2,n_pixlen);
Out_Meres(seq,nSeq,n_meres,n_meres2,chr_index,chr_idpix,chr_locus,chr_index2,chr_idpix2,chr_locus2,argv,argc,args);
Plot_Process(argv,argc,args);
}
/* Subroutine to output sequences of centromeres and telomeres */
/* ============================================= */
void Out_Meres(fasta *seq,int nSeq,int n_meres,int n_meres2,int *chr_index,int *chr_idpix,int *chr_locus,int *chr_index2,int *chr_idpix2,int *chr_locus2,char **argv, int argc, int args)
/* ============================================= */
{
int i,j,k,m,n,numMeres,numMeres2,num_hits;
int stopflag;
char *st;
FILE *namef;
fasta *seqp;
if((namef = fopen(argv[args+1],"w")) == NULL)
{
printf("ERROR main:: args \n");
exit(1);
}
numMeres = 0;
numMeres2 = 0;
for(i=0;i<n_meres;i++)
{
stopflag=0;
j=i+1;
while((j<n_meres)&&(stopflag==0))
{
if((chr_index[i] == chr_index[j])&&((chr_idpix[j]-chr_idpix[j-1]) <= 8))
{
j++;
}
else
stopflag=1;
}
num_hits = j-i;
printf("Meres: %d %d || %d %d || %d %d || %d %d\n",chr_index[j-1],i,chr_idpix[j-1],chr_idpix[i],numMeres,chr_locus[j-1]-chr_locus[i],chr_locus[i],chr_locus[j-1]);
numMeres++;
if((num_hits >= 2))
{
int i_st,i_ed,nline,seq_len;
int set_len = 100;
seqp = seq+chr_index[i]-1;
if(num_hits == 1)
{
i_st = chr_locus[i]-n_pixlen;