int validate_interleaved(char *f) {
unsigned long cline=1;
unsigned long nreads1=0;
gzFile fd1=NULL;
fprintf(stderr,"Paired-end interleaved\n");
fd1=open_fastq(f);
gzFile fdf=open_fixed_fastq(f);
while(!gzeof(fd1)) {
long start_pos=gztell(fd1);
// Read 1
char *hdr1=READ_LINE_HDR(fd1);
if ( hdr1==NULL) break;
int len;
char *seq1=READ_LINE_SEQ(fd1);
char *hdr1_2=READ_LINE_HDR2(fd1);
char *qual1=READ_LINE_QUAL(fd1);
// Read 2
char *hdr2=READ_LINE_HDR2_1(fd1);
char *seq2=READ_LINE_SEQ2(fd1);
char *hdr2_2=READ_LINE_HDR2_2(fd1);
char *qual2=READ_LINE_QUAL2(fd1);
if ( seq1==NULL || hdr1_2==NULL || qual1==NULL ||
hdr2==NULL || seq2==NULL || hdr2_2==NULL || qual2==NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: file truncated?\n",f,cline);
return(1);
}
if (validate_entry(hdr1,hdr1_2,seq1,qual1,cline,f)!=0) {
return(1);
}
if (validate_entry(hdr2,hdr2_2,seq2,qual2,cline+4,f)!=0) {
return(1);
}
char* readname1=get_readname(hdr1,&len,cline,f);
char* readname2=get_readname(hdr2,&len,cline+4,f);
if ( strcmp(readname1,readname2) ) {
fprintf(stderr,"\nError in file %s, line %lu: unpaired read - %s\n",f,cline,readname1);
return(1);
}
PRINT_READS_PROCESSED(cline/4);
replace_dots(start_pos,seq1,hdr1,hdr1_2,qual1,fdf);
replace_dots(start_pos,seq2,hdr2,hdr2_2,qual2,fdf);
//
cline+=8;
nreads1+=2;
}
printf("\n");
close_fixed_fastq(fdf);
gzclose(fd1);
return(nreads1);
}
void index_file(char *filename,hashtable sn_index,long start_offset,long length) {
gzFile fd1=open_fastq(filename);
gzFile fdf=open_fixed_fastq(filename);
if (fd1==NULL) {
fprintf(stderr,"\nError: Unable to open %s\n",filename);
exit(1);
}
// move to the right position
if(length>0) {
fprintf(stderr, "\nInternal error: Not implemented\n");
exit(2);
}
long cline=1;
// sn_index creation could be done in parallel
while(!gzeof(fd1)) {
long long start_pos=gztell(fd1);
char *hdr=READ_LINE_HDR(fd1);
if ( hdr==NULL) break;
int len;
//fprintf(stderr,"sn_index: =%s=\n",readname);
// get seq
//printf("cline=%ld\nLEN=%ld hdr=%s\n",cline,len,hdr);
char *seq=READ_LINE_SEQ(fd1);
char *hdr2=READ_LINE_HDR2(fd1);
char *qual=READ_LINE_QUAL(fd1);
char* readname=get_readname(hdr,&len,cline,filename);
if (seq==NULL || hdr2==NULL || qual==NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: file truncated?\n",filename,cline);
exit(1);
}
if (validate_entry(hdr,hdr2,seq,qual,cline,filename)!=0) {
exit(1);
}
// check for duplicates
if ( lookup_header(sn_index,readname)!=NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: duplicated sequence %s\n",filename,cline,readname);
exit(1);
}
if ( new_indexentry(sn_index,readname,len,start_pos)==NULL) {
fprintf(stderr,"\nError in file %s, line %lu: malloc failed?",filename,cline);
exit(1);
}
replace_dots(start_pos,seq,hdr,hdr2,qual,fdf);
PRINT_READS_PROCESSED(cline/4);
//
cline+=4;
}
close_fixed_fastq(fdf);
gzclose(fd1);
return;
}
int
main(int argc, char *argv[])
{
if (argc < 3) {
printf("not enough arguments\n");
return 1;
}
FILE *fp_h = fopen(argv[1], "w");
if (!fp_h) {
printf("can't open %s\n", argv[1]);
return 2;
}
FILE *fp_c = fopen(argv[2], "w");
if (!fp_c) {
fclose(fp_h);
printf("can't open %s\n", argv[2]);
return 2;
}
fprintf(fp_h,
"// generated file, all changes will be lost\n"
"#ifndef FPP_GENERATED_TXT_RESOURCES_H\n"
"#define FPP_GENERATED_TXT_RESOURCES_H\n"
"\n"
"\n");
for (int k = 3; k < argc; k ++) {
char *fname = strdup(argv[k]);
char *bname = basename(fname);
replace_dots(bname);
fprintf(fp_h, "extern const char *resource_text_%s;\n", bname);
free(fname);
}
fprintf(fp_h, "\n\n#endif\n");
fclose(fp_h);
fprintf(fp_c,
"// generated file, all changes will be lost\n"
"#include \"%s\"\n"
"\n", argv[1]);
for (int k = 3; k < argc; k ++) {
unsigned char buf[4096];
char *fname = strdup(argv[k]);
char *bname = basename(fname);
replace_dots(bname);
fprintf(fp_c, "const char *resource_text_%s = \"", bname);
size_t fsize = 0;
FILE *tmp = fopen(argv[k], "rb");
if (!tmp) {
printf("can't open %s\n", argv[k]);
free(fname);
goto err_1;
}
while (!feof(tmp)) {
size_t read_bytes = fread(buf, 1, sizeof(buf), tmp);
for (size_t j = 0; j < read_bytes; j ++)
fprintf(fp_c, "\\x%02x", buf[j]);
fsize += read_bytes;
}
fclose(tmp);
fprintf(fp_c, "\";\n");
free(fname);
}
fclose(fp_c);
return 0;
err_1:
fclose(fp_c);
return 3;
}
int main(int argc, char **argv ) {
//long paired=0;
unsigned long num_reads1=0,
num_reads2=0;
is_paired_data=FALSE;
is_interleaved=FALSE;
fix_dot=FALSE;
int nopt=0;
int c;
opterr = 0;
fprintf(stderr,"Version iRAP %s\n",VERSION);
while ((c = getopt (argc, argv, "f")) != -1)
switch (c)
{
case 'f':
fix_dot = TRUE;
fprintf(stderr,"Fixing (-f) enabled: Replacing . by N (creating .fix.gz files)\n");
++nopt;
break;
default:
++nopt;
fprintf(stderr,"ERROR: Option -%c invalid\n",optopt);
exit(1);
}
if (argc-nopt<2 || argc-nopt>3) {
fprintf(stderr,"Usage: fastq_info [-f] fastq1 [fastq2 file|pe]\n");
//fprintf(stderr,"%d",argc);
exit(1);
}
//gzFile fd1=NULL;
gzFile fd2=NULL;
if (argc-nopt ==3) {
is_paired_data=TRUE;
//fprintf(stderr,"%d %d %d %s\n",argc,nopt,argc-nopt,argv[2+nopt]);
if ( !strncmp(argv[2+nopt],"pe",2) ) {
is_interleaved=FALSE;
}
//else {
// fd2=open_fastq(argv[2+nopt]);
// gzclose(fd2);
//
}
// ************************************************************
if ( is_interleaved ) {
// interleaved
num_reads1=validate_interleaved(argv[1+nopt]);
} else {
// single or pair of fastq file(s)
unsigned long cline=1;
fprintf(stderr,"HASHSIZE=%lu\n",(long unsigned int)HASHSIZE);
//memset(&collisions[0],0,HASHSIZE+1);
hashtable sn_index=new_hashtable(HASHSIZE);
index_mem+=sizeof(hashtable);
index_file(argv[1+nopt],sn_index,0,-1);
num_reads1=sn_index->n_entries;
fprintf(stderr,"\n");
// print some info
fprintf(stderr,"Reads processed: %ld\n",sn_index->n_entries);
fprintf(stderr,"Memory used in indexing: ~%ld MB\n",index_mem/1024/1024);
// pair-end
if (argc-nopt ==3 ) {
fprintf(stderr,"File %s processed\n",argv[1+nopt]);
fprintf(stderr,"Next file %s\n",argv[2+nopt]);
// validate the second file and check if all reads are paired
fd2=open_fastq(argv[2+nopt]);
gzFile fdf=open_fixed_fastq(argv[2+nopt]);
INDEX_ENTRY* e;
// read the entry using another fd
cline=1;
// TODO: improve code - mostly duplicated:(
while(!gzeof(fd2)) {
long long start_pos=gztell(fd2);
char *hdr=READ_LINE_HDR(fd2);
if ( hdr==NULL) break;
int len;
char *seq=READ_LINE_SEQ(fd2);
char *hdr2=READ_LINE_HDR2(fd2);
char *qual=READ_LINE_QUAL(fd2);
char* readname=get_readname(hdr,&len,cline,argv[2+nopt]);
if (seq==NULL || hdr2==NULL || qual==NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: file truncated?\n",argv[2+nopt],cline);
exit(1);
}
if (validate_entry(hdr,hdr2,seq,qual,cline,argv[2+nopt])!=0) {
exit(1);
}
//fprintf(stderr,"Reads processed: %ld\n",sn_index->n_entries);
// check for duplicates
if ( (e=lookup_header(sn_index,readname))==NULL ) {
fprintf(stderr,"\nError in file %s, line %lu: unpaired read - %s\n",argv[2+nopt],cline,readname);
exit(1);
} else {
ulong key=hashit(readname);
// remove entry from sn_index
if (delete(sn_index,key,e)!=e) {
fprintf(stderr,"\nError in file %s, line %lu: unable to delete entry from sn_index - %s\n",argv[2+nopt],cline,readname);
exit(1);
}
free_indexentry(e);
}
PRINT_READS_PROCESSED(cline/4);
++num_reads2;
//
replace_dots(start_pos,seq,hdr,hdr2,qual,fdf);
cline+=4;
}
printf("\n");
close_fixed_fastq(fdf);
if (sn_index->n_entries>0 ) {
fprintf(stderr,"\nError in file %s: found %lu unpaired reads\n",argv[1+nopt],sn_index->n_entries);
exit(1);
}
}
}
FILE* out;
if (fix_dot) {
out=stderr;
} else {
out=stdout;
}
fprintf(out,"------------------------------------\n");
if ( num_reads2>0 ) {
fprintf(out,"Number of reads: %lu %lu\n",num_reads1,num_reads2);
} else {
fprintf(out,"Number of reads: %lu\n",num_reads1);
}
fprintf(out,"Quality encoding range: %lu %lu\n",min_qual,max_qual);
char *enc=qualRange2enc(min_qual,max_qual);
if ( enc == NULL ) {
fprintf(stderr,"\nERROR: Unable to determine quality encoding - unknown range [%lu,%lu]\n",min_qual,max_qual);
exit(1);
}
fprintf(out,"Quality encoding: %s\n",qualRange2enc(min_qual,max_qual));
fprintf(out,"Read length: %lu %lu\n",min_rl,max_rl);
fprintf(out,"OK\n");
exit(0);
}
