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ssaha.c
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/***********************************************************************\
* *
* PROJECT SSAHA *
* *
*---------------------------------------------------------------------*
* *
* Sequence Search and Alignment by Hashing Algorithm *
* *
* By *
* *
* Zemin Ning & James C. Mullikin *
* *
* Copyright (C) 1999-2000 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;
static B64_long *hist;
static signed char *head;
static B64_long n_Entry;
static int K_LEN=17;
static int mhist=10;
static int outmod=0;
static int NEDGE=500;
static int nmatch=30;
static int N_SET=6000;
static void hpsortil(B64_long n, int *ra, B64_long *rb)
{
B64_long l,j,ir,i;
B64_long rra;
B64_long rrb;
if(n < 2)
return;
l=(n >> 1)+1;
ir=n;
for (;;) {
if (l > 1) {
rra=ra[--l];
rrb=rb[l];
} else {
rra=ra[ir];
rrb=rb[ir];
ra[ir]=ra[1];
rb[ir]=rb[1];
if (--ir == 1) {
ra[1]=rra;
rb[1]=rrb;
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];
rb[i]=rb[j];
j += (i=j);
}
else j=ir+1;
}
ra[i]=rra;
rb[i]=rrb;
}
}
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 i_Fasta, int SEG_LEN)
/* ============================================= */
{
B64_long i,j,k,n_Sbase=SEG_LEN;
B64_long ps=0,ns=0,IntSeg=0,IntBase=0,lii;
char *b,*ch,*b0;
fasta *seqp,*expp[500];
fasta *seq,*seqr;
int nSeq;
B64_long totalBases;
B64_long mhistc = 0;
B64_long mhistcc = 0;
unsigned B64_long *sarr, *sarrp;
int qthresh=23;
B64_long CG = 6;
int CGneg=0;
// int tb = 0;
int args,ac;
int nseq = 0,seqc;
unsigned B64_long seqcharc = 0;
char **names,**mates;
int sshift,rshift=6;
unsigned B64_long nmask;
int **r_matrix,*n_list,*rd_used,*rd_rept,*rd_name;
int id_read[64],num_sect,n_contig,n_reads,max_edge; //id_read will never exceed mhist
int *num_front,*ind_front,*out_list,*ctg_list;
int *num_pair,*mat_pair,*ins_pair,*dev_pair;
int n_patch,n_outreads,new_patch,n_ctg;
int n_grouped,rd_st,rd_ed,n_input;
int **imatrix(B64_long nrl,B64_long nrh,B64_long ncl,B64_long nch);
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];
/* sort all the names of genes or name entries */
printf("Input data starts ...\n");
fflush(stdout);
system("date");
n_input=0;
args=1;
for(i=1;i<argc;i++)
{
if(!strcmp(argv[i],"-kmer"))
{
sscanf(argv[++i],"%d",&K_LEN);
args=args+2;
printf("kmer size: %d\n",K_LEN);
}
else if(!strcmp(argv[i],"-depth"))
{
sscanf(argv[++i],"%d",&mhist);
args=args+2;
printf("cutoff number: %d\n",mhist);
}
else if(!strcmp(argv[i],"-match"))
{
sscanf(argv[++i],"%d",&nmatch);
args=args+2;
printf("match number: %d\n",nmatch);
}
else if(!strcmp(argv[i],"-output"))
{
sscanf(argv[++i],"%d",&outmod);
args=args+2;
printf("output mode: %d\n",outmod);
}
else if(!strcmp(argv[i],"-matrix"))
{
sscanf(argv[++i],"%d",&NEDGE);
args=args+2;
printf("matrix size: %d\n",NEDGE);
}
else if(!strcmp(argv[i],"-set"))
{
sscanf(argv[++i],"%d",&N_SET);
args=args+2;
printf("outreads size: %d\n",N_SET);
}
}
max_edge=NEDGE;
n_Sbase=K_LEN;
sshift = (64-(n_Sbase<<1));
nmask = (1<<sshift)-1;
for(ac=(args+1);ac<argc;ac++)
{
seq = decodeFastq ( argv[ac], &nSeq, &totalBases, qthresh);
if(seq == NULL)
{
printf("ERROR pileup: no data found\n");
exit(1);
}
fastaUC(seq,nSeq);
nseq += nSeq;
seqp = seq;
b0= (char*)seq->name;
for(i=0;i<nSeq;i++,seqp++)
{
b = (char*)seqp->data;
ns=(seqp->length)-n_Sbase;
seqcharc += strlen(seqp->name);
for(j=0;j<ns;j++)
{
B64_long IntSegRC=0;
IntSeg=0;
ch=b;
for(k=n_Sbase;k>0;k--)
{
B64_long IntBaseRC;
if (*ch == 'A') IntBase=0;
else if(*ch == 'C') IntBase=1;
else if(*ch == 'G') IntBase=2;
else if(*ch == 'T') IntBase=3;
else
{
break;
}
IntBaseRC=(IntBase^3)<<((n_Sbase-k)<<1);
IntBase=IntBase<<((k-1)<<1);
IntSeg=IntSeg+IntBase;
IntSegRC=IntSegRC+IntBaseRC;
ch++;
}
if(0)
{
B64_long mask=3;
B64_long jj;
char *base = "ACGT";
for(jj=n_Sbase;--jj>=0;)
printf("%c",base[(IntSeg>>(jj<<1))&mask]);
printf(" ");
for(jj=n_Sbase;--jj>=0;)
printf("%c",base[(IntSegRC>>(jj<<1))&mask]);
printf("\n");
}
b++;
if(IntSeg > IntSegRC) IntSeg = IntSegRC;
if(k != 0) continue;
if(CGneg)
{
B64_long is=IntSeg;
for(k=SEG_LEN-1;--k>=0;)
{
if((is&15)==CG) break;
is >>= 2;
}
if(k!=-1)
{
if(head[IntSeg] != -127) head[IntSeg]--;
continue;
}
}
if(head[IntSeg] != 127) head[IntSeg]++;
}
}
// printf("ssaha: %ld %ld\n",seq->name,seq);
free(seq->name);
if(seq) free(seq);
n_input++;
}
printf("Input data finished one set\n");
fflush(stdout);
system("date");
for(i=n_Entry;--i>=0;)
{
B64_long mask=3;
B64_long is=i;
char *base = "ACGT";
// for(j=n_Sbase;--j>=0;)
// printf("%c",base[(i>>(j<<1))&mask]);
// printf(" %8d\n",head[i]);
if(CGneg)
{
for(k=SEG_LEN-1;--k>=0;)
{
if((is&15)==CG) break;
is >>= 2;
}
if(k!=-1)
{
head[i]--;
}
}
if(head[i] < 128 && head[i] >= -128)
hist[head[i]+128]++;
if(head[i] < 0) head[i] = -(head[i]+1);
if(head[i] > mhist || head[i] <= 1 )continue;
mhistc += head[i];
}
for(i=0;i<256;i++)
printf("%5d %12ld\n",i-128,hist[i]);
fflush(stdout);
if(0) return;
sarrp = sarr = (unsigned B64_long *) malloc(mhistc*sizeof(unsigned B64_long));
names = (char **) malloc(nseq*sizeof(char *));
names[0] = (char *) calloc(seqcharc+nseq,1);
// tb = 0;
seqc = 0;
for(ac=(args+1);ac<argc;ac++)
{
seq = decodeFastq ( argv[ac], &nSeq, &totalBases, qthresh);
if(seq == NULL)
{
printf("ERROR pileup: no data found\n");
exit(1);
}
fastaUC(seq,nSeq);
seqp = seq;
for(i=0;i<nSeq;i++,seqp++,seqc++)
{
// B64_long apr=0;
strcpy(names[seqc],(char*)seqp->name);
names[seqc+1] = names[seqc]+strlen((char*)seqp->name)+1;
b = (char*)seqp->data;
ns=(seqp->length)-n_Sbase;
for(j=0;j<ns;j++)
{
B64_long IntSegRC=0;
IntSeg=0;
ch=b;
for(k=n_Sbase;k>0;k--)
{
B64_long IntBaseRC;
if (*ch == 'A') IntBase=0;
else if(*ch == 'C') IntBase=1;
else if(*ch == 'G') IntBase=2;
else if(*ch == 'T') IntBase=3;
else
{
break;
}
IntBaseRC=(IntBase^3)<<((n_Sbase-k)<<1);
IntBase=IntBase<<((k-1)<<1);
IntSeg=IntSeg+IntBase;
IntSegRC=IntSegRC+IntBaseRC;
ch++;
}
b++;
if(IntSeg > IntSegRC) IntSeg = IntSegRC;
if(k != 0) continue;
if(head[IntSeg] > mhist || head[IntSeg] <= 1 ) continue;
// apr++;
// tb++;
mhistcc++;
*sarrp++ = (IntSeg<<sshift) + seqc;
}
// printf(" %-30s %4d\n",names[seqc],apr);
}
// printf("ssaha: %ld %ld\n",seq->name,seq);
free(seq->name);
if(seq) free(seq);
// freeRead(&seq);
}
free(head);
printf("Sorting starts ...\n");
fflush(stdout);
system("date");
hpsortl(mhistcc,sarr-1);
printf("Sorting finished\n");
printf("Start read groups %ld %ld",mhistc,mhistcc);
fflush(stdout);
system("date");
lii = -1;
/* allocate memery for arrays to calculate the link number */
if((n_list= (int *)calloc(nseq,sizeof(int))) == NULL)
{
printf("ssaha: calloc - n_list\n");
exit(1);
}
r_matrix=imatrix(0,nseq,0,max_edge);
num_sect=0;
for(i=0;i<mhistcc;i++)
{
int j = (int)(sarr[i]&nmask);
B64_long ii=(B64_long)sarr[i]>>sshift;
int match,idk,idi,kk,ki,km,a_index,a_links;
if(ii != lii)
{
for(kk=0;kk<num_sect;kk++)
{
for(ki=0;ki<num_sect;ki++)
{
if(ki!=kk)
{
idk=id_read[kk];
idi=id_read[ki];
if(n_list[idk]<max_edge)
{
match=0;
for(km=0;km<n_list[idk];km++)
{
a_index=r_matrix[idk][km]>>rshift;
a_links=r_matrix[idk][km]&077;
// a_links=r_matrix[idk][km]-(a_index<<rshift);
if(a_index==idi)
{
if(a_links<60)
r_matrix[idk][km]++;
match=1;
break;
}
}
if(match==0)
{
r_matrix[idk][n_list[idk]]=(idi<<rshift)+1;
n_list[idk]++;
}
}
}
}
}
num_sect=0;
// putchar ('\n');
}
else
{
// putchar(' ');
}
lii = ii;
// printf("%s",names[j]);
id_read[num_sect]=j;
num_sect++;
}
putchar('\n');
// free(sarrp);dont free this this is a temporary pointer to index sarr
free(sarr);
if((ind_front= (int *)calloc(nseq,sizeof(int))) == NULL)//worst case all reads are linked together
{
printf("ssaha: calloc - ind_front\n");
exit(1);
}
if((num_front= (int *)calloc(nseq,sizeof(int))) == NULL)//worst case all reads are linked together
{
printf("ssaha: calloc - num_front\n");
exit(1);
}
if((out_list= (int *)calloc(nseq,sizeof(int))) == NULL)
{
printf("ssaha: calloc - out_list\n");
exit(1);
}
if((ctg_list= (int *)calloc(nseq,sizeof(int))) == NULL)
{
printf("ssaha: calloc - ctg_list\n");
exit(1);
}
if((rd_name= (int *)calloc(nseq,sizeof(int))) == NULL)
{
printf("ssaha: calloc - rd_name\n");
exit(1);
}
if((rd_used= (int *)calloc(nseq,sizeof(int))) == NULL)
{
printf("ssaha: calloc - rd_used\n");
exit(1);
}
if((rd_rept= (int *)calloc(nseq,sizeof(int))) == NULL)
{
printf("ssaha: calloc - rd_rept\n");
exit(1);
}
/* get the readnames for each contigs */
n_contig=0;
n_reads=0;
n_grouped=0;
for(i=0;i<nseq;i++)
{
int id_pt,n_front,n_midd,n_end,n_over,NLINK=nmatch;
int a_index,a_links;
n_reads=0;
n_over=0;
n_front=n_list[i];
if((rd_used[i]==0)&&(n_front>0))
{
for(j=0;j<n_front;j++)
{
a_index=r_matrix[i][j]>>rshift;
a_links=r_matrix[i][j]&077;
ind_front[j]=a_index;
num_front[j]=a_links;
if(a_links>=NLINK)
{
n_over++;
}
}
if(n_over==0)
n_front=0;
else
{
rd_used[i]=1;
rd_name[n_reads]=i;
n_reads++;
rd_rept[i]=1;
for(j=0;j<n_front;j++)
{
a_index=r_matrix[i][j]>>rshift;
a_links=r_matrix[i][j]&077;
if((a_links>=NLINK)&&(rd_used[a_index]==0))
{
rd_name[n_reads]=a_index;
rd_rept[a_index]=1;
n_reads++;
}
}
}
while(n_front>0)
{
n_midd=0;
for(j=0;j<n_front;j++)
{
id_pt=ind_front[j];
if((num_front[j]>=NLINK)&&(rd_used[id_pt]==0))
{
rd_used[id_pt]=1;
for(k=0;k<n_list[id_pt];k++)
{
a_index=r_matrix[id_pt][k]>>rshift;
a_links=r_matrix[id_pt][k]&077;
if((a_links>=NLINK)&&(rd_rept[a_index]==0)&&(rd_used[a_index]==0))
{
rd_name[n_reads]=a_index;
n_reads++;
rd_rept[a_index]=1;
num_front[n_front+n_midd]=a_links;
ind_front[n_front+n_midd]=a_index;
n_midd++;
}
}
}
}
n_end=0;
for(j=0;j<(n_front+n_midd);j++)
{
if((rd_used[ind_front[j]]==0)&&(num_front[j]>=NLINK))
{
num_front[n_end]=num_front[j];
ind_front[n_end]=ind_front[j];
n_end++;
}
}
n_front=n_end;
}
if(n_reads>=2)
{
if(outmod==0)
printf("readnames for contig %d %s %d \n",n_contig,names[i],n_reads);
for(j=0;j<n_reads;j++)
{
if(outmod==0)
printf("%s\n",names[rd_name[j]]);
// printf("%s %d %d\n",names[rd_name[j]],rd_name[j],num_pair[rd_name[j]]);
out_list[n_grouped]=rd_name[j];
n_grouped++;
}
n_contig++;
ctg_list[n_contig]=n_reads;
}
// printf("\n");
}
}
if(outmod==0)
{
printf("All jobs finished\n");
fflush(stdout);
system("date");
return;
}
free(*r_matrix);
free(r_matrix);
printf("Relation matrix finished\n");
fflush(stdout);
system("date");
if((num_pair= (int *)calloc(nseq,sizeof(int))) == NULL)
{
printf("ssaha: calloc - num_pair\n");
exit(1);
}
if((mat_pair= (int *)calloc(nseq,sizeof(int))) == NULL)
{
printf("ssaha: calloc - mat_pair\n");
exit(1);
}
if((ins_pair= (int *)calloc(nseq,sizeof(int))) == NULL)
{
printf("ssaha: calloc - ins_pair\n");
exit(1);
}
if((dev_pair= (int *)calloc(nseq,sizeof(int))) == NULL)
{
printf("ssaha: calloc - dev_pair\n");
exit(1);
}
/* input mates information */
if((fpMate = fopen(argv[args],"r")) == NULL)
{
printf("Error ssaha: mate input\n");
exit(1);
}
seqcharc=0;
while(!feof(fpMate))
{
fgets(line,500,fpMate);
seqcharc += strlen(line);
}
fclose(fpMate);
mates = (char **) malloc(nseq*sizeof(char *));
mates[0] = (char *) calloc(seqcharc+nseq,1);
if((fpMate = fopen(argv[args],"r")) == NULL)
{
printf("Error ssaha: mate input\n");
exit(1);
}
seqc = 0;
while(!feof(fpMate))
{
int id_pt,nPair;
fgets(line,500,fpMate);
strcpy(mates[seqc],line);
mates[seqc+1] = mates[seqc]+strlen(line)+1;
nPair=0;
strcpy(line2,line);
for(ptr=strtok(line," ");ptr!=NULL;ptr=strtok((char *)NULL," "),nPair++)
{
}
i=0;
for(ptr=strtok(line2," ");ptr!=NULL;ptr=strtok((char *)NULL," "),i++)
{
if(i==0)
{
strcpy(base,zero);
strcat(base,ptr);
id_pt = atoi(base);
}
else if(i==1)
{
strcpy(base,zero);
strcat(base,ptr);
num_pair[id_pt] = atoi(base);
}
else if(i==2)
{
strcpy(base,zero);
strcat(base,ptr);
mat_pair[id_pt] = atoi(base);
}
else if((nPair>2)&&(i==(nPair-2)))
{
strcpy(base,zero);
strcat(base,ptr);
ins_pair[id_pt] = atoi(base);
}
else if((nPair>2)&&(i==(nPair-1)))
{
strcpy(base,zero);
strcat(base,ptr);
dev_pair[id_pt] = atoi(base);
}
}
seqc++;
}
fclose(fpMate);
// for(i=0;i<nseq;i++)
// printf("%d %d %d %d %d\n",i,num_pair[i],mat_pair[i],ins_pair[i],dev_pair[i]);
// for(i=0;i<nseq;i++)
// printf("len: %d %s\n",i,mates[i]);
/* output read names, fasta and fastq dat in every contig */
nseq=0;
n_input=0;
for(ac=(args+1);ac<argc;ac++)
{
seq = decodeFastq ( argv[ac], &nSeq, &totalBases, qthresh);
if(seq == NULL)
{
printf("ERROR ssaha: no data found\n");
exit(1);
}
fastaUC(seq,nSeq);
expp[n_input]=seq;
/* rd_used and rd_rept are used again to store the read index */
for(i=0;i<nSeq;i++)
{
rd_used[i+nseq]=n_input;
rd_rept[i+nseq]=i;
}
nseq=nseq+nSeq;
n_input++;
}
ctg_list[0]=0;
for(i=1;i<=n_contig;i++)
ctg_list[i]=ctg_list[i]+ctg_list[i-1];
n_patch=0;
n_outreads=0;
new_patch=0;
rd_st=0;
rd_ed=0;
n_ctg=0;
for(i=1;i<=n_contig;i++)
{
n_outreads=n_outreads+ctg_list[i]-ctg_list[i-1];
if(n_outreads>N_SET)
{
new_patch=1;
rd_st=rd_ed+1;
rd_ed=i;
n_ctg=0;
n_outreads=0;
}
n_ctg++;
if(new_patch)
{
sprintf(outName,"readname%04d",n_patch);
if((fpOutname = fopen(outName,"w")) == NULL)
{
printf("Unable to open file for name out\n");
exit(1);
}
sprintf(outFast,"%04d.fastq",n_patch);
if((fpOutfast = fopen(outFast,"w")) == NULL)
{
printf("Unable to open file for fastq out\n");
exit(1);
}
for(k=rd_st;k<=rd_ed;k++)
{
int id=out_list[ctg_list[k-1]];
n_reads=ctg_list[k]-ctg_list[k-1];
seqp=expp[rd_used[id]]+rd_rept[id];
fprintf(fpOutname,"readnames for contig %d %s %d \n",k-1,seqp->name,n_reads);
for(j=0;j<n_reads;j++)
{
int rdrc,rd=out_list[ctg_list[k-1]+j],rc,i_pair,np;
int nPair,iPair;
seqp=expp[rd_used[rd]]+rd_rept[rd];
fprintf(fpOutfast,"@%s %s\n",seqp->name,seqp->name2);
for(rc=0;rc<seqp->length;rc++)
fprintf(fpOutfast,"%c",seqp->data[rc]);
fprintf(fpOutfast,"\n");
fprintf(fpOutfast,"+%s %s\n",seqp->name,seqp->name2);
putc(041,fpOutfast);
for(rc=1;rc<seqp->length;rc++)
{
if(seqp->finished)
putc(40+041,fpOutfast);
else
putc(seqp->qual[rc]+041,fpOutfast);
}
fprintf(fpOutfast,"\n");
if(num_pair[rd]==0)
{
fprintf(fpOutname,"%s\n",seqp->name);
}
else if(num_pair[rd]>0)
{
i_pair=0;
if(num_pair[rd]==1)
{
read_pair[i_pair]=mat_pair[rd];
i_pair++;
}
else
{
strcpy(line,mates[rd]);
strcpy(line2,mates[rd]);
nPair=0;
iPair=0;
for(ptr=strtok(line," ");ptr!=NULL;ptr=strtok((char *)NULL," "),nPair++)
{
}
for(ptr=strtok(line," ");ptr!=NULL;ptr=strtok((char *)NULL," "),iPair++)
{
if((iPair>1)&&(iPair<(nPair-2)))
{
strcpy(base,zero);
strcat(base,ptr);
read_pair[i_pair]=atoi(base);
i_pair++;
}
}
}
fprintf(fpOutname,"%s ",seqp->name);
for(np=0;np<i_pair;np++)
{
rdrc=read_pair[np];
seqr=expp[rd_used[rdrc]]+rd_rept[rdrc];
fprintf(fpOutfast,"@%s %s\n",seqr->name,seqr->name2);
for(rc=0;rc<seqr->length;rc++)
fprintf(fpOutfast,"%c",seqr->data[rc]);
fprintf(fpOutfast,"\n");
fprintf(fpOutfast,"+%s %s\n",seqr->name,seqr->name2);
putc(041,fpOutfast);
for(rc=1;rc<seqr->length;rc++)
{
if(seqr->finished)
putc(40+041,fpOutfast);
else
putc(seqr->qual[rc]+041,fpOutfast);
}
fprintf(fpOutfast,"\n");
fprintf(fpOutname,"%s ",seqr->name);
}
fprintf(fpOutname,"%d %d\n",ins_pair[rd],dev_pair[rd]);
}
}
}
n_patch++;
fclose(fpOutname);
fclose(fpOutfast);
sprintf(syscmd,"gzip %s",outName);
system (syscmd);
sprintf(syscmd,"gzip %s",outFast);
system (syscmd);
new_patch=0;
}
}
if(rd_ed<n_contig)
{
sprintf(outName,"readname%04d",n_patch);
if((fpOutname = fopen(outName,"w")) == NULL)
{
printf("Unable to open file for name out\n");
exit(1);
}
sprintf(outFast,"%04d.fastq",n_patch);
if((fpOutfast = fopen(outFast,"w")) == NULL)
{
printf("Unable to open file for fastq out\n");
exit(1);
}
for(k=rd_ed+1;k<=n_contig;k++)
{
int id=out_list[ctg_list[k-1]];
n_reads=ctg_list[k]-ctg_list[k-1];
seqp=expp[rd_used[id]]+rd_rept[id];
fprintf(fpOutname,"readnames for contig %d %s %d \n",k-1,seqp->name,n_reads);
for(j=0;j<n_reads;j++)
{
int rdrc,rd=out_list[ctg_list[k-1]+j],rc,i_pair,np;
int nPair,iPair;
seqp=expp[rd_used[rd]]+rd_rept[rd];
fprintf(fpOutfast,"@%s %s\n",seqp->name,seqp->name2);
for(rc=0;rc<seqp->length;rc++)
fprintf(fpOutfast,"%c",seqp->data[rc]);
fprintf(fpOutfast,"\n");
fprintf(fpOutfast,"+%s %s\n",seqp->name,seqp->name2);
putc(041,fpOutfast);
for(rc=1;rc<seqp->length;rc++)
{
if(seqp->finished)
putc(40+041,fpOutfast);
else
putc(seqp->qual[rc]+041,fpOutfast);
}
fprintf(fpOutfast,"\n");
if(num_pair[rd]==0)
{
fprintf(fpOutname,"%s\n",seqp->name);
}
else if(num_pair[rd]>0)
{
i_pair=0;
if(num_pair[rd]==1)
{
read_pair[i_pair]=mat_pair[rd];
i_pair++;
}
else
{
strcpy(line,mates[rd]);
strcpy(line2,mates[rd]);
nPair=0;
iPair=0;
for(ptr=strtok(line," ");ptr!=NULL;ptr=strtok((char *)NULL," "),nPair++)
{
}
for(ptr=strtok(line2," ");ptr!=NULL;ptr=strtok((char *)NULL," "),iPair++)
{
if((iPair>1)&&(iPair<(nPair-2)))
{
strcpy(base,zero);
strcat(base,ptr);
read_pair[i_pair]=atoi(base);
i_pair++;
}
}
}
fprintf(fpOutname,"%s ",seqp->name);
for(np=0;np<i_pair;np++)
{
rdrc=mat_pair[rd];
seqr=expp[rd_used[rdrc]]+rd_rept[rdrc];
fprintf(fpOutfast,"@%s %s\n",seqr->name,seqr->name2);
for(rc=0;rc<seqr->length;rc++)
fprintf(fpOutfast,"%c",seqr->data[rc]);
fprintf(fpOutfast,"\n");
fprintf(fpOutfast,"+%s %s\n",seqr->name,seqr->name2);
putc(041,fpOutfast);
for(rc=1;rc<seqr->length;rc++)
{
if(seqr->finished)
putc(40+041,fpOutfast);
else
putc(seqr->qual[rc]+041,fpOutfast);
}
fprintf(fpOutfast,"\n");
fprintf(fpOutname,"%s ",seqr->name);
}
fprintf(fpOutname,"%d %d\n",ins_pair[rd],dev_pair[rd]);
}
}
}
n_patch++;
fclose(fpOutname);
fclose(fpOutfast);
sprintf(syscmd,"gzip %s",outName);
system (syscmd);
sprintf(syscmd,"gzip %s",outFast);
system (syscmd);
}
printf("All jobs finished\n");
fflush(stdout);
system("date");
return;
{
int j = (int)sarr[i]&nmask;
B64_long ii=(B64_long)sarr[i]>>sshift;
B64_long mask=3;
B64_long jj;
char *base = "ACGT";
for(jj=n_Sbase;--jj>=0;)
printf("%c",base[(ii>>(jj<<1))&mask]);
printf(" %-30s\n",names[j]);
}
seqp = seq;
for(i=0;i<nSeq;i++,seqp++)