static lk_TimerState *lkT_newstate (lk_State *S) {
lk_TimerState *ts = (lk_TimerState*)
lk_malloc(S, sizeof(lk_TimerState));
memset(ts, 0, sizeof(*ts));
if (!lk_initlock(&ts->lock))
lk_discard(S);
ts->S = S;
lk_initmempool(S, &ts->timers, sizeof(lk_Timer), 0);
return ts;
}
static int read_ranges_file(char *fname,struct contig **contig_ptr,struct lk_compress *lkc)
{
int i,err;
u_int32_t x1,x1a,x2,x3,x;
struct contig *ctg,*c;
struct range_blk *r,*r1;
char *estr;
FILE *fptr;
string *s;
tokens *tok;
void *tbuf;
s=0;
tok=0;
tbuf=0;
err=0;
fptr=open_readfile_and_check(fname,&i,lkc);
printf("Reading ranges file '%s'\n",fname);
ctg=0;
while(!err) {
s=fget_string(fptr,s,&tbuf);
if(!s->len) break;
tok=tokenize(get_cstring(s),'\t',tok);
if(tok->n_tok>=3) {
HASH_FIND_STR(ctg,tok->toks[0],c);
if(!c) {
c=lk_malloc(sizeof(struct contig));
c->name=strdup(tok->toks[0]);
c->size=0;
c->ranges=lk_malloc(sizeof(struct range_blk));
c->ranges->idx=0;
c->ranges->next=0;
c->tranges=0;
c->counts=0;
c->tcounts=0;
c->tot_count=0;
c->tot_tcount=0;
c->tot_bases=0;
c->tot_tbases=0;
HASH_ADD_KEYPTR(hh,ctg,c->name,strlen(c->name),c);
}
r=c->ranges;
if(r->idx==RANGE_BLK_SIZE) {
r=lk_malloc(sizeof(struct range_blk));
r->idx=0;
r->next=c->ranges;
c->ranges=r;
}
x1=(u_int32_t)getlnumcolumn(tok,1,0,&estr);
if(!estr) x2=(u_int32_t)getlnumcolumn(tok,2,0,&estr);
if(estr || x1<1 || x2<x1) {
err=1;
fprintf(stderr,"Error in coordinate format: %s\n",estr);
} else {
r->name[r->idx]=getstrcolumn(tok,3,0,0);
r->x1[r->idx]=x1;
r->x2[r->idx++]=x2;
}
}
}
fclose(fptr);
if(s) free_string(s);
if(tok) free_tokens(tok);
if(tbuf) free_fget_buffer(&tbuf);
signal(SIGCHLD,SIG_DFL);
x2=x3=0;
for(c=ctg; c && !err; c=c->hh.next) {
x1=0;
r=c->ranges;
c->ranges=0;
while(r) {
for(i=0; i<r->idx; i++) {
if(r->x2[i]>x1) x1=r->x2[i];
}
r1=r->next;
r->next=c->ranges;
c->ranges=r;
r=r1;
}
c->size=x1;
x1a=0;
if(!x1) err=2;
else {
x2+=x1;
c->counts=lk_malloc(sizeof(count)*c->size);
for(i=0; i<(int)c->size; i++) c->counts[i]=NO_COUNT;
for(r=c->ranges; r; r=r->next) {
for(i=0; i<r->idx; i++) {
for(x=r->x1[i]-1; x<r->x2[i]; x++) c->counts[x]=0;
}
}
for(i=0; i<(int)c->size; i++) if(!c->counts[i]) x1a++;
}
c->tot_bases=x1a;
x3+=x1a;
}
printf("total=%u, in ranges=%u\n",x2,x3);
while(waitpid(-1,&i,WNOHANG)>0);
*contig_ptr=err?0:ctg;
return err;
}
int main(int argc,char *argv[])
{
int i,j,k,c,err,nthr;
int block_size,extend,detail,combine,out_cnt,format;
struct lk_compress *lkc;
struct contig *contigs,*ctg;
struct range_blk *r;
struct tdc_par tp;
char *ranges_file,*target_file,*output_file,*compare_ref;
char *filter,*suffix,*tn,*prefix,*pp;
count *ct,cc,cbuf[OUT_WIDTH];
u_int64_t *hist,*thist,nn,kk,tnn,tkk,number;
u_int32_t x;
pthread_t *read_threads;
FILE *ofptr,*ctg_fptr;
static struct option longopts[]= {
{"ranges_file",required_argument,0,'r'},
{"target_file",required_argument,0,'t'},
{"block_size",required_argument,0,'b'},
{"number",required_argument,0,'n'},
{"output",required_argument,0,'o'},
{"extend_regions",required_argument,0,'x'},
{"detailed_output",no_argument,0,'d'},
{"combine",no_argument,0,'c'},
{"compare",required_argument,0,'C'},
{"eland",no_argument,0,'E'},
{"gem",no_argument,0,'G'},
{"prefix",no_argument,0,'p'},
{0,0,0,0}
};
err=0;
detail=combine=0;
ranges_file=target_file=output_file=compare_ref=prefix=0;
block_size=1;
extend=0;
contigs=0;
number=0;
format=GEM_FMT;
while((c=getopt_long(argc,argv,"p:r:t:b:o:n:x:C:dcEG",longopts,0))!=-1) {
switch(c) {
case 'p':
set_opt("prefix",&prefix,optarg);
break;
case 'r':
set_opt("ranges_file",&ranges_file,optarg);
break;
case 't':
set_opt("target_file",&target_file,optarg);
break;
case 'C':
set_opt("compare",&compare_ref,optarg);
break;
case 'o':
set_opt("output",&output_file,optarg);
break;
case 'b':
block_size=atoi(optarg);
break;
case 'E':
format=ELAND_FMT;
break;
case 'G':
format=GEM_FMT;
break;
case 'x':
extend=atoi(optarg);
break;
case 'n':
number=strtoul(optarg,&pp,10);
break;
case 'd':
detail=1;
break;
case 'c':
combine=1;
break;
}
}
if(!ranges_file) {
fprintf(stderr,"No ranges file specified. Use -r or --ranges_file option\n");
exit(-1);
}
if(!output_file) output_file=strdup("coverage_hist.txt");
if(block_size<1) {
fprintf(stderr,"Invalid block size specified - must be >0\n");
exit(-1);
}
printf("Block size = %d, extend range = %d\n",block_size,extend);
hist=lk_malloc(sizeof(u_int64_t)*(MAX_COUNT+1));
if(target_file) thist=lk_malloc(sizeof(u_int64_t)*(MAX_COUNT+1));
else thist=0;
lkc=init_compress();
err=read_ranges_file(ranges_file,&contigs,lkc);
if(!err && target_file) err=read_target_file(target_file,contigs,extend,lkc);
nthr=(int)sysconf(_SC_NPROCESSORS_ONLN);
input_files=argv;
input_idx=optind;
n_input_files=argc;
if(!nthr) nthr=1;
read_threads=malloc(sizeof(pthread_t)*nthr);
if(combine) {
tp.ctg=contigs;
tp.lkc=lkc;
for(i=0; i<nthr; i++) {
if((j=pthread_create(read_threads+i,NULL,read_det_cov,&tp))) abt(__FILE__,__LINE__,"Thread creation %d failed: %d\n",i+1,j);
}
for(i=0; i<nthr; i++) pthread_join(read_threads[i],NULL);
} else {
for(i=optind; !err && i<argc; i++) {
err=process_file(argv[i],contigs,block_size,format,&number,lkc);
}
}
printf("Generating histogram\n");
filter=suffix=0;
if(lkc->default_compress<COMPRESS_NONE) {
i=lkc->default_compress;
filter=lkc->comp_path[i][i==COMPRESS_ZIP?1:0];
suffix=lkc->compress_suffix[i];
}
tn=0;
if(prefix) {
asprintf(&tn,"%s_contig_summ.txt",prefix);
assert(tn);
ctg_fptr=fopen(tn,"w");
free(tn);
} else ctg_fptr=fopen("contig_summ.txt","w");
if(target_file) {
for(i=0; i<=MAX_COUNT; i++) hist[i]=thist[i]=0;
for(ctg=contigs; ctg; ctg=ctg->hh.next) {
ct=ctg->counts;
for(i=0; i<(int)ctg->size; i+=block_size) {
cc=ct[i];
if(cc<=MAX_COUNT) {
hist[cc]++;
ctg->tot_count+=cc;
}
}
ct=ctg->tcounts;
for(i=0; i<(int)ctg->tsize; i+=block_size) {
cc=ct[i];
if(cc<=MAX_COUNT) {
thist[cc]++;
ctg->tot_tcount+=cc;
}
}
if(ctg_fptr) {
fprintf(ctg_fptr,"%s\t%u\t%"PRIu64"\t%g",ctg->name,ctg->tot_bases,ctg->tot_count,(double)ctg->tot_count/(double)ctg->tot_bases);
fprintf(ctg_fptr,"\t%u\t%"PRIu64"\t%g\n",ctg->tot_tbases,ctg->tot_tcount,ctg->tot_tbases?(double)ctg->tot_tcount/(double)ctg->tot_tbases:0.0);
}
}
if(ctg_fptr) fclose(ctg_fptr);
nn=tnn=0;
for(i=0; i<=MAX_COUNT; i++) {
nn+=hist[i];
tnn+=thist[i];
}
kk=tkk=0;
ofptr=fopen(output_file,"w");
if(!ofptr) ofptr=stdout;
for(i=0; i<=MAX_COUNT; i++) {
kk+=hist[i];
tkk+=thist[i];
fprintf(ofptr,"%d\t%"PRIu64"\t%g\t%g\t",i,hist[i],(double)hist[i]/(double)nn,(double)kk/(double)nn);
fprintf(ofptr,"%"PRIu64"\t%g\t%g\n",thist[i],(double)thist[i]/(double)tnn,(double)tkk/(double)tnn);
}
if(ofptr!=stdout) fclose(ofptr);
} else {
for(i=0; i<=MAX_COUNT; i++) hist[i]=0;
for(ctg=contigs; ctg; ctg=ctg->hh.next) {
ct=ctg->counts;
for(i=0; i<(int)ctg->size; i+=block_size) {
cc=ct[i];
if(cc<=MAX_COUNT) {
hist[cc]++;
ctg->tot_count+=cc;
}
}
if(ctg_fptr) {
fprintf(ctg_fptr,"%s\t%u\t%"PRIu64"\t%g\n",ctg->name,ctg->tot_bases,ctg->tot_count,(double)ctg->tot_count/(double)ctg->tot_bases);
}
}
if(ctg_fptr) fclose(ctg_fptr);
nn=0;
for(i=0; i<=MAX_COUNT; i++) nn+=hist[i];
kk=0;
ofptr=fopen(output_file,"w");
if(!ofptr) ofptr=stdout;
for(i=0; i<=MAX_COUNT; i++) {
kk+=hist[i];
fprintf(ofptr,"%d\t%"PRIu64"\t%g\t%g\n",i,hist[i],(double)hist[i]/(double)nn,(double)kk/(double)nn);
}
if(ofptr!=stdout) fclose(ofptr);
}
if(detail) {
tn=0;
ofptr=0;
if(filter && suffix) {
asprintf(&tn,"detailed_coverage.txt.%s",suffix);
if(tn) {
i=child_open(WRITE,tn,filter);
ofptr=fdopen(i,"w");
}
}
if(!ofptr) ofptr=fopen("detailed_coverage.txt","w");
if(!ofptr) ofptr=stdout;
printf("Writing detailed coverage information\n");
for(ctg=contigs; ctg; ctg=ctg->hh.next) {
k=0;
ct=ctg->counts;
/* ct1=ctg->tcounts;*/
for(r=ctg->ranges; r; r=r->next) {
for(i=0; i<r->idx; i++) {
if(!k++) fprintf(ofptr,"*%s\t%x\n",ctg->name,r->x1[i]);
else fprintf(ofptr,"*\t%x\n",r->x1[i]);
out_cnt=0;
for(x=r->x1[i]; x<=r->x2[i]; x++) {
cbuf[out_cnt++]=ct[x-1];
if(out_cnt==OUT_WIDTH) {
out_cnt=write_cbuf(cbuf,out_cnt,ofptr);
}
}
while(out_cnt) out_cnt=write_cbuf(cbuf,out_cnt,ofptr);
}
}
}
if(ofptr!=stdout) {
fclose(ofptr);
if(tn) {
free(tn);
while(waitpid(-1,&i,WNOHANG)>0);
}
}
}
return err;
}
static int read_target_file(char *fname,struct contig *ctg,int extend,struct lk_compress *lkc)
{
int i,err;
u_int32_t x1,x2,x3,x,cs,x1a;
struct contig *c;
struct range_blk *r;
char *estr;
FILE *fptr;
string *s;
tokens *tok;
void *tbuf;
s=0;
tok=0;
tbuf=0;
err=0;
fptr=open_readfile_and_check(fname,&i,lkc);
printf("Reading target file '%s'\n",fname);
while(!err) {
s=fget_string(fptr,s,&tbuf);
if(!s->len) break;
tok=tokenize(get_cstring(s),'\t',tok);
if(tok->n_tok>=3) {
HASH_FIND_STR(ctg,tok->toks[0],c);
if(c) {
r=c->tranges;
if(!r) {
r=c->tranges=lk_malloc(sizeof(struct range_blk));
r->idx=0;
} else {
if(r->idx==RANGE_BLK_SIZE) {
r=lk_malloc(sizeof(struct range_blk));
r->idx=0;
r->next=c->tranges;
c->tranges=r;
}
}
x1=(u_int32_t)getlnumcolumn(tok,1,0,&estr);
if(!estr) x2=(u_int32_t)getlnumcolumn(tok,2,0,&estr);
if(estr || x1<1 || x2<x1) {
err=1;
fprintf(stderr,"Error in coordinate format: %s\n",estr);
} else {
if(x1<=(unsigned int)extend) x1=1;
else x1-=extend;
x2+=extend;
if(x1<1) x1=1;
r->name[r->idx]=getstrcolumn(tok,3,0,0);
r->x1[r->idx]=x1;
r->x2[r->idx++]=x2;
}
} else {
printf("Not found %s\n",tok->toks[0]);
}
}
}
fclose(fptr);
if(s) free_string(s);
if(tok) free_tokens(tok);
if(tbuf) free_fget_buffer(&tbuf);
signal(SIGCHLD,SIG_DFL);
x2=x3=0;
for(c=ctg; c && !err; c=c->hh.next) {
if(!c->tranges) continue;
x1=0;
for(r=c->tranges; r; r=r->next) {
for(i=0; i<r->idx; i++) {
if(r->x2[i]>x1) x1=r->x2[i];
}
}
if(x1>c->size) x1=c->size;
c->tsize=x1;
x1a=0;
if(!x1) {
fprintf(stderr,"Illegal target range for %s\n",c->name);
err=2;
continue;
} else {
x2+=x1;
/* printf("%s\t%d\n",c->name,c->tsize);*/
c->tcounts=lk_malloc(sizeof(count)*c->tsize);
cs=c->tsize;
for(i=0; i<(int)cs; i++) c->tcounts[i]=NO_COUNT;
for(r=c->tranges; r; r=r->next) {
for(i=0; i<r->idx; i++) {
for(x=r->x1[i]-1; x<r->x2[i]; x++) {
if(x>=cs) break;
if(!c->counts[x]) c->tcounts[x]=0;
}
}
}
for(i=0; i<(int)cs; i++) if(!c->tcounts[i]) x1a++;
}
c->tot_tbases=x1a;
x3+=x1a;
}
printf("total=%u, on target=%u\n",x2,x3);
while(waitpid(-1,&i,WNOHANG)>0);
return err;
}
