/* Read all parameters from the files */
void read_param(char *file_name)
{
FILE *fp;
char buf[MAXLEN],*c,*word;
TextLine *line;
double number;
int i,n,rinput[NINPUT];
for(i=0;i<NINPUT;i++)
rinput[i] = FALSE;
error = 0;
line = NULL;
fp = fopen(file_name,"r");
if(fp == NULL){
error_dialog_open(file_name);
return;
}
while(fgets(buf,MAXLEN,fp)!=NULL){
i = 0;
while(i<NINPUT && (c=strstr(buf,inlines[i]))==NULL)
i++;
if(i<NINPUT){
c += strlen(inlines[i]);
c = trim_space(c);
}
switch(i){
case I_TYPE:
if(c != NULL && strcmp(c, "")){
word = get_word(c,&n); /* we should free word-memory also! */
if(strcmp(word,"ERD") == 0)
sim_type = SIM_ERD;
else if(strcmp(word,"RBS") == 0)
sim_type = SIM_RBS;
else{
sim_type = SIM_ERD;
error = 1;
}
free(word);
}
else{
sim_type = SIM_ERD;
error = 1;
}
break;
case I_ION:
if(c != NULL){
if(strcmp(c, "")){
c = get_string(c);
beam_ion = c;
}
else
beam_ion = "";
}
else{
beam_ion = "";
error = 1;
}
break;
case I_ENERGY:
if(c != NULL && strcmp(c, "")){
c = get_number(c,&number);
beam_energy = number;
}
else{
beam_energy = 0;
error = 1;
}
break;
case I_RECOIL:
if(c != NULL){
if(strcmp(c, "")){
c = get_string(c);
recoil_atom = c;
}
else
recoil_atom = "";
}
else{
recoil_atom = "";
error = 1;
}
break;
case I_TANGLE:
if(c != NULL && strcmp(c, "")){
c = get_number(c,&number);
target_angle = number;
}
else{
target_angle = 0;
error = 1;
}
break;
case I_SPOTSIZE:
if(c != NULL && strcmp(c, "")){
c = get_number(c,&number);
beam_size_x = number;
}
else{
beam_size_x = 0;
error = 1;
}
if(c != NULL && strcmp(c, "")){
c = get_number(c,&number);
beam_size_y = number;
}
else{
beam_size_y = 0;
error = 1;
}
break;
case I_MINANGLE:
if(c != NULL && strcmp(c, "")){
c = get_number(c,&number);
min_angle = number;
}
else{
min_angle = 0;
error = 1;
}
break;
case I_MINENERGY:
if(c != NULL && strcmp(c, "")){
c = get_number(c,&number);
min_energy = number;
}
else{
min_energy = 0;
error = 1;
}
break;
case I_NIONS:
if(c != NULL && strcmp(c, "")){
c = get_number(c,&number);
nions = number;
}
else{
nions = 0;
error = 1;
}
break;
case I_NPREIONS:
if(c != NULL && strcmp(c, "")){
c = get_number(c,&number);
nions_presim = number;
}
else{
nions_presim = 0;
error = 1;
}
break;
case I_RECAVE:
if(c != NULL && strcmp(c, "")){
c = get_number(c,&number);
aver_nions = number;
}
else{
aver_nions = 0;
error = 1;
}
break;
case I_SEED:
if(c != NULL && strcmp(c, "")){
c = get_number(c,&number);
nseed = number;
}
else{
nseed = 0;
error = 1;
}
break;
case I_RECWIDTH:
if(c != NULL && strcmp(c, "")){
word = get_word(c,&n);
if(strcmp(word,"wide") == 0 || strcmp(word,"WIDE") == 0)
angle_width = REC_WIDE;
else if(strcmp(word,"narrow") == 0 || strcmp(word,"NARROW") == 0)
angle_width = REC_NARROW;
else{
angle_width = REC_NARROW;
error = 1;
}
free(word);
}
else{
angle_width = REC_NARROW;
error = 1;
}
break;
default:
break;
}
}
read_target_file(file_name, TYPE_TARGET);
read_target_file(file_name, TYPE_FOIL);
read_detector_file(file_name);
read_rdist_file(file_name);
read_presimu_file(file_name);
read_espe_params_file(file_name);
/* If error occurs somewhere */
if(error)
error_dialog("Problems with reading the data");
fclose(fp);
/* Clean "memory" */
format_layers(nlayers);
format_foils(nfoils);
saved = 1;
}
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;
}
