// TODO: optimize this
void copy_read(long offset,FILE *from,FILE* to) {
fseek(from,offset,SEEK_SET);
fputs(READ_LINE(from),to);
fputs(READ_LINE(from),to);
fputs(READ_LINE(from),to);
fputs(READ_LINE(from),to);
}
void index_file(char *filename,hashtable index,long start_offset,long length) {
FILE *fd1=fopen(filename,"r");
if (fd1==NULL) {
fprintf(stderr,"Unable to open %s\n",filename);
exit(1);
}
// move to the right position
if(length>0) {
fprintf(stderr, " Not implemented\n");
exit(1);
}
long cline=1;
// index creation could be done in parallel
while(!feof(fd1)) {
long start_pos=ftell(fd1);
char *hdr=READ_LINE(fd1);
if ( hdr==NULL) break;
if ( hdr[0]!='@' ) {
fprintf(stderr,"line %ul: error in header %s",cline,hdr);
exit(1);
}
// discard @ (one less byte)
hdr=&hdr[1];
int len=strlen(hdr);
len--;
hdr[len-1]='\0'; //
// get seq
//printf("cline=%ld\nLEN=%ld hdr=%s\n",cline,len,hdr);
if ( new_indexentry(index,hdr,len,start_pos)==NULL) {
fprintf(stderr,"line %ul: malloc failed?",cline);
exit(1);
}
char *seq=READ_LINE(fd1);
char *hdr2=READ_LINE(fd1);
char *qual=READ_LINE(fd1);
if (seq==NULL || hdr2==NULL || qual==NULL ) {
fprintf(stderr,"line %ul: file truncated",cline);
exit(1);
}
PRINT_READS_PROCESSED(cline/4);
//
cline+=4;
}
fclose(fd1);
return;
}
// check if the read name format was generated by casava 1.8
int is_casava_1_8(char *f) {
regex_t regex;
int reti;
int is_casava_1_8=0;
reti = regcomp(®ex,"[A-Z0-9:]* [12]:[YN]:[0-9]*:.*",0);
if ( reti ) {
fprintf(stderr, "Internal error: Could not compile regex\n");
exit(2);
}
FILE *fd1=open_fastq(f);
char *hdr=READ_LINE(fd1);
fclose(fd1);
/* Execute regular expression */
//fprintf(stderr,"%s\n",hdr);
reti = regexec(®ex, hdr, 0, NULL, 0);
if ( !reti ) { // match
is_casava_1_8=1;
}
/* else{
char msgbuf[100];
regerror(reti, ®ex, msgbuf, sizeof(msgbuf));
//fprintf(stderr, "Regex match failed: %s\n", msgbuf);
} */
regfree(®ex);
return is_casava_1_8;
}
int main(int argc, char **argv ) {
//printf("%d",sizeof(struct index_entry));
if (argc!=2) {
fprintf(stderr,"Usage: fastq_filter_n fastq1\n");
exit(1);
}
FILE *fd1=open_fastq(argv[1]);
// ************************************************************
unsigned long cline=1;
unsigned long cur_read=0;
//char tmp_buffer[MAX_READ_LENGTH];
// read the entry using another fd
cline=1;
while(!feof(fd1)) {
char *hdr=READ_LINE(fd1,1);
if ( hdr==NULL) break;
if ( hdr[0]!='@' ) {
fprintf(stderr,"line %lu: error in header %s",cline,hdr);
return 1;
}
//
char *seq=READ_LINE(fd1,2);
READ_LINE(fd1,3);
READ_LINE(fd1,4);
short n_found=0;
int k;
for ( k=0;k<MAX_READ_LENGTH;k++) {
if (seq[k]=='\n') break;
if (seq[k]=='N' || seq[k]=='n' ) {
n_found=1; break;
}
}
if ( ! n_found )
WRITE_READ(stdout);
cline+=4;
cur_read++;
}
fclose(fd1);
exit(0);
}
int main(int argc, char **argv ) {
long paired=0;
//printf("%d",sizeof(struct index_entry));
if (argc!=6) {
fprintf(stderr,"Usage: fastqinterleaved2pair.c fastq fastq1 fastq2\n");
//fprintf(stderr,"%d",argc);
exit(1);
}
FILE *fd=open_fastq(argv[1]);
// ************************************************************
off_t cur_offset=1;
unsigned long cline=1;
hashtable index=new_hashtable(HASHSIZE);
index_mem+=sizeof(hashtable);
index_file(argv[1],index,0,-1);
printf("\n");
// print some info
printf("Reads indexed: %ld\n",index->n_entries);
printf("Memory used in indexing: %ld MB\n",index_mem/1024/1024);
//
char *p1=argv[3];
char *p2=argv[4];
char *p3=argv[5];
fd1=open_fastq(argv[1]);
fd2=open_fastq(argv[2]);
FILE *fdw1=fopen(p1,"w");
FILE *fdw2=fopen(p2,"w");
FILE *fdw3=fopen(p3,"w");
unsigned long up2=0;
if ( fdw1==NULL || fdw2==NULL || fdw3==NULL ) {
fprintf(stderr,"Unable to create output files\n");
exit(1);
}
// read the entry using another fd
cline=1;
while(!feof(fd2)) {
long start_pos=ftell(fd2);
char *hdr=READ_LINE(fd2);
if ( hdr==NULL) break;
if ( hdr[0]!='@' ) {
fprintf(stderr,"line %ul: error in header %s",cline,hdr);
return 1;
}
// discard @ (one less byte)
hdr=&hdr[1];
int len=strlen(hdr);
len--;
hdr[len-1]='\0'; //
// lookup hdr in index
INDEX_ENTRY* e=lookup_header(index,hdr);
if (e==NULL) {
++up2;
copy_read(start_pos,fd2,fdw3);
} else {
long key=hashit(hdr);
// pair found
++paired;
copy_read(start_pos,fd2,fdw2);
copy_read(e->entry_start,fd1,fdw1);
// remove entry from index
if (delete(index,key,e)!=e) {
fprintf(stderr,"Unable to delete entry from index\n");
exit(1);
}
free_indexentry(e);
}
PRINT_READS_PROCESSED(cline/4);
cline+=4;
}
printf("\n");
printf("Recording %ld unpaired reads from %s\n",index->n_entries,argv[1]);fflush(stdout);
fclose(fd1);
// record the unpaired from argv[1]
fd1=open_fastq(argv[1]);
#ifndef SEQDISKACCESS
init_hash_traversal(index);
INDEX_ENTRY* e;
cline=1;
while((e=(INDEX_ENTRY*)next_hash_object(index))!=NULL) {
copy_read(e->entry_start,fd1,fdw3);
PRINT_READS_PROCESSED(cline);
++cline;
}
//
#else
//sequential disk access
//
cline=1;
unsigned long remaining=index->n_entries;
while(!feof(fd1) && remaining ) {
//long start_pos=ftell(fd2);
char *hdr=READ_LINE(fd1);
if ( hdr==NULL) break;
if ( hdr[0]!='@' ) {
fprintf(stderr,"line %ld %s: error in header %s",cline,argv[1],hdr);
return 1;
}
// discard @ (one less byte)
hdr=&hdr[1];
int len=strlen(hdr);
len--;
hdr[len-1]='\0'; //
// lookup hdr in index
INDEX_ENTRY* e=lookup_header(index,hdr);
if (e!=NULL) {
copy_read(e->entry_start,fd1,fdw3);
remaining--;
} else {
READ_LINE(fd1);//seq
READ_LINE(fd1);//qual
READ_LINE(fd1);//qual
}
PRINT_READS_PROCESSED(cline/4);
cline+=4;
}
fclose(fd1);
#endif
printf("\n");
printf("Unpaired from %s: %ld\n",argv[1],index->n_entries);
printf("Unpaired from %s: %ld\n",argv[2],up2);
printf("Paired: %ld\n",paired);
/*fseek(fd2,start_pos,SEEK_SET);
printf("%s",READ_LINE(fd2));
printf("%s",READ_LINE(fd2));
printf("%s",READ_LINE(fd2));
printf("%s",READ_LINE(fd2));
*/
fclose(fdw1);
fclose(fdw2);
fclose(fdw3);
if ( paired == 0 ) {
fprintf(stderr,"!!!WARNING!!! 0 paired reads! are the headers ok?\n");
exit(1);
}
exit(0);
}
hash_t *HASH_load(disk_t *file){
wchar_t *line = L"";
while(STRING_starts_with(line, "#") || STRING_equals2(STRING_trim(line), L""))
line = READ_LINE(file);
int version;
if(STRING_equals(line,">> HASH MAP BEGIN")){
version = 1;
} else if (STRING_equals(line,">> HASH MAP V2 BEGIN")){
version = 2;
} else if (STRING_equals(line,">> HASH MAP V3 BEGIN")){
version = 3;
} else if (STRING_starts_with(line, ">> HASH MAP V")){
version = 3;
vector_t v = {0};
int try_anyway = VECTOR_push_back(&v, "Try anyway (program might crash and/or behave unstable)");
int ok = VECTOR_push_back(&v, "Ok");
int res = GFX_Message(&v, "Need a newer version of Radium to load this file");
if (res!=try_anyway)
return NULL;
(void)ok;
} else {
GFX_Message(NULL, "Trying to load something which is not a hash map. First line: \"%S\"", line);
return NULL;
}
line = READ_LINE(file);
int elements_size = STRING_get_int(line);
hash_t *hash=HASH_create(elements_size);
hash->version = version;
line = READ_LINE(file);
while(!STRING_equals(line,"<< HASH MAP END") && !STRING_equals(line,"<< HASH MAP V2 END") && !STRING_equals(line,"<< HASH MAP V3 END")){
const char *key = STRING_get_chars(line);
int i = 0;
if(version > 1){
line = READ_LINE(file);
i = STRING_get_int(line);
int new_size = i+1;
if(new_size > hash->num_array_elements)
hash->num_array_elements = new_size;
} else if(!strncmp(key,"<int hash>",strlen("<int hash>"))) {
sscanf(key, "<int hash> %d", &i);
key = "";
hash->num_array_elements++;
}
bool success;
dyn_t dyn = DYN_load(file, &success);
if (!success)
return NULL;
put_dyn(hash, key, i, dyn);
line = READ_LINE(file);
}
return hash;
}
static gboolean
gnm_glpk_read_solution_458 (GnmGlpk *lp,
GsfInputTextline *tl,
GnmSolverResult *result,
GnmSolverSensitivity *sensitivity,
gboolean has_integer)
{
GnmSubSolver *subsol = lp->parent;
const char *line;
unsigned cols, rows, c, r;
gnm_float val;
char pstat, dstat;
READ_LINE (tl, line);
if (has_integer) {
if (sscanf (line, "s %*s %u %u %c %" GNM_SCANF_g,
&rows, &cols, &pstat, &val) != 4)
goto fail;
} else {
if (sscanf (line, "s %*s %u %u %c %c %" GNM_SCANF_g,
&rows, &cols, &pstat, &dstat, &val) != 5)
goto fail;
}
if (cols != g_hash_table_size (subsol->cell_from_name))
goto fail;
result->value = val;
switch (pstat) {
case 'o':
result->quality = GNM_SOLVER_RESULT_OPTIMAL;
break;
case 'f':
result->quality = GNM_SOLVER_RESULT_FEASIBLE;
break;
case 'u':
case 'i':
case 'n':
result->quality = GNM_SOLVER_RESULT_INFEASIBLE;
break;
default:
goto fail;
}
for (r = 0; r < rows; r++) {
gnm_float pval, dval;
char rstat;
unsigned r1, cidx = r;
READ_LINE (tl, line);
if ((has_integer
? sscanf (line, "i %d %" GNM_SCANF_g,
&r1, &dval) != 2
: sscanf (line, "i %d %c %" GNM_SCANF_g " %" GNM_SCANF_g,
&r1, &rstat, &pval, &dval) != 4) ||
r1 != cidx + 1)
goto fail;
// rstat?
sensitivity->constraints[cidx].shadow_price = dval;
}
for (c = 0; c < cols; c++) {
gnm_float pval, dval;
char cstat;
unsigned c1, cidx = c;
READ_LINE (tl, line);
if ((has_integer
? sscanf (line, "j %d %" GNM_SCANF_g,
&c1, &pval) != 2
: sscanf (line, "j %d %c %" GNM_SCANF_g " %" GNM_SCANF_g,
&c1, &cstat, &pval, &dval) != 4) ||
c1 != cidx + 1)
goto fail;
// cstat?
result->solution[cidx] = pval;
}
// Success
return FALSE;
fail:
return TRUE;
}
