| 39 |
|
bool readmap_loaded=false; |
| 40 |
|
vector<bool> readmap; //for filter_multihits |
| 41 |
|
|
| 42 |
– |
|
| 42 |
|
void load_readmap() { |
| 43 |
|
readmap_loaded=false; |
| 44 |
|
if (flt_reads.empty()) return; |
| 68 |
|
err_die("Error: filtering reads not enabled, aborting."); |
| 69 |
|
if (aux_outfile.empty()) |
| 70 |
|
err_die("Error: auxiliary output file not provided."); |
| 71 |
+ |
if (index_outfile.empty()) |
| 72 |
+ |
err_die("Error: index output file not provided."); |
| 73 |
+ |
|
| 74 |
|
// -- filter mappings: |
| 75 |
|
string fext=getFext(flt_mappings); |
| 76 |
|
if (fext=="bam") { |
| 135 |
|
{ |
| 136 |
|
//TODO: add the option to write the garbage reads into separate file(s) |
| 137 |
|
int num_reads_chucked = 0; |
| 138 |
< |
int multimap_chucked=0; |
| 138 |
> |
int multimap_chucked = 0; |
| 139 |
|
int min_read_len = 20000000; |
| 140 |
|
int max_read_len = 0; |
| 141 |
|
uint32_t next_id = 0; |
| 142 |
+ |
uint64_t file_offset = 0; |
| 143 |
|
FILE* fw=NULL; |
| 144 |
|
if (!aux_outfile.empty()) { |
| 145 |
|
fw=fopen(aux_outfile.c_str(), "w"); |
| 147 |
|
err_die("Error: cannot create file %s\n",aux_outfile.c_str()); |
| 148 |
|
} |
| 149 |
|
|
| 150 |
+ |
FILE* findex = NULL; |
| 151 |
+ |
if (!index_outfile.empty()) { |
| 152 |
+ |
findex = fopen(index_outfile.c_str(), "w"); |
| 153 |
+ |
if (findex == NULL) |
| 154 |
+ |
err_die("Error: cannot create file %s\n", index_outfile.c_str()); |
| 155 |
+ |
} |
| 156 |
+ |
|
| 157 |
|
for (size_t fi = 0; fi < reads_files.size(); ++fi) |
| 158 |
|
{ |
| 159 |
|
Read read; |
| 160 |
< |
FLineReader fr(reads_files[fi]); |
| 161 |
< |
skip_lines(fr); |
| 162 |
< |
FZPipe fq; |
| 160 |
> |
//FLineReader fr(reads_files[fi]); |
| 161 |
> |
//skip_lines(fr); |
| 162 |
> |
FZPipe* fq=NULL; |
| 163 |
|
if (quals) |
| 164 |
< |
fq = quals_files[fi]; |
| 165 |
< |
FLineReader frq(fq); |
| 166 |
< |
skip_lines(frq); |
| 164 |
> |
fq = & quals_files[fi]; |
| 165 |
> |
ReadStream reads; |
| 166 |
> |
reads.init(reads_files[fi], fq); |
| 167 |
|
|
| 168 |
< |
while (!fr.isEof()) { |
| 169 |
< |
//read.clear(); |
| 168 |
> |
while (reads.get_direct(read, reads_format)) { |
| 169 |
> |
// read.clear(); |
| 170 |
|
// Get the next read from the file |
| 171 |
< |
if (!next_fastx_read(fr, read, reads_format, ((quals) ? &frq : NULL))) |
| 172 |
< |
break; |
| 171 |
> |
//if (!next_fastx_read(fr, read, reads_format, ((quals) ? &frq : NULL))) |
| 172 |
> |
// break; |
| 173 |
|
|
| 174 |
|
++next_id; |
| 175 |
|
//IMPORTANT: to keep paired reads in sync, this must be |
| 195 |
|
++multimap_chucked; |
| 196 |
|
continue; |
| 197 |
|
} |
| 198 |
< |
format_qual_string(read.qual); |
| 198 |
> |
format_qual_string(read.qual); |
| 199 |
|
std::transform(read.seq.begin(), read.seq.end(), read.seq.begin(), ::toupper); |
| 200 |
|
char counts[256]; |
| 201 |
|
memset(counts, 0, sizeof(counts)); |
| 227 |
|
} |
| 228 |
|
else |
| 229 |
|
{ |
| 230 |
+ |
// daehwan - we should not use buf in printf function |
| 231 |
+ |
// because it may contain some control characters such as "\" from quality values. |
| 232 |
+ |
// Here, buf is only used for calculating the file offset |
| 233 |
+ |
char buf[2048] = {0}; |
| 234 |
|
if (reads_format == FASTQ or (reads_format == FASTA && quals)) |
| 235 |
|
{ |
| 236 |
< |
|
| 237 |
< |
printf("@%u\n%s\n+%s\n%s\n", |
| 238 |
< |
next_id, |
| 239 |
< |
read.seq.c_str(), |
| 240 |
< |
read.name.c_str(), |
| 241 |
< |
read.qual.c_str()); |
| 236 |
> |
sprintf(buf, "@%u\n%s\n+%s\n%s\n", |
| 237 |
> |
next_id, |
| 238 |
> |
read.seq.c_str(), |
| 239 |
> |
read.name.c_str(), |
| 240 |
> |
read.qual.c_str()); |
| 241 |
> |
|
| 242 |
> |
printf("@%u\n%s\n+%s\n%s\n", |
| 243 |
> |
next_id, |
| 244 |
> |
read.seq.c_str(), |
| 245 |
> |
read.name.c_str(), |
| 246 |
> |
read.qual.c_str()); |
| 247 |
|
} |
| 248 |
|
else if (reads_format == FASTA) |
| 249 |
|
{ |
| 253 |
|
else |
| 254 |
|
qual = string(read.seq.length(), 'I').c_str(); |
| 255 |
|
|
| 256 |
< |
printf("@%u\n%s\n+%s\n%s\n", |
| 257 |
< |
next_id, |
| 258 |
< |
read.seq.c_str(), |
| 259 |
< |
read.name.c_str(), |
| 260 |
< |
qual.c_str()); |
| 256 |
> |
sprintf(buf, "@%u\n%s\n+%s\n%s\n", |
| 257 |
> |
next_id, |
| 258 |
> |
read.seq.c_str(), |
| 259 |
> |
read.name.c_str(), |
| 260 |
> |
qual.c_str()); |
| 261 |
> |
|
| 262 |
> |
printf("@%u\n%s\n+%s\n%s\n", |
| 263 |
> |
next_id, |
| 264 |
> |
read.seq.c_str(), |
| 265 |
> |
read.name.c_str(), |
| 266 |
> |
qual.c_str()); |
| 267 |
|
} |
| 268 |
+ |
else |
| 269 |
+ |
{ |
| 270 |
+ |
assert(0); |
| 271 |
+ |
} |
| 272 |
+ |
|
| 273 |
+ |
if (findex != NULL) |
| 274 |
+ |
{ |
| 275 |
+ |
if ((next_id - num_reads_chucked) % 1000 == 0) |
| 276 |
+ |
fprintf(findex, "%d\t%lu\n", next_id, file_offset); |
| 277 |
+ |
} |
| 278 |
+ |
|
| 279 |
+ |
file_offset += strlen(buf); |
| 280 |
|
} |
| 281 |
|
} //while !fr.isEof() |
| 282 |
< |
fr.close(); |
| 283 |
< |
frq.close(); |
| 282 |
> |
//fr.close(); |
| 283 |
> |
//frq.close(); |
| 284 |
|
} //for each input file |
| 285 |
|
fprintf(stderr, "%u out of %u reads have been filtered out\n", |
| 286 |
|
num_reads_chucked, next_id); |
| 294 |
|
fprintf(fw, "reads_out=%d\n",next_id-num_reads_chucked); |
| 295 |
|
fclose(fw); |
| 296 |
|
} |
| 297 |
+ |
|
| 298 |
+ |
if (findex != NULL) |
| 299 |
+ |
fclose(findex); |
| 300 |
|
} |
| 301 |
|
|
| 302 |
|
void print_usage() |
| 330 |
|
for (size_t i = 0; i < reads_file_names.size(); ++i) |
| 331 |
|
{ |
| 332 |
|
string fname=reads_file_names[i]; |
| 333 |
< |
string pipecmd=guess_packer(fname, true); |
| 294 |
< |
if (!pipecmd.empty()) pipecmd.append(" -cd"); |
| 295 |
< |
FZPipe seg_file(fname,pipecmd); |
| 333 |
> |
FZPipe seg_file(fname, true); //guess unpacker |
| 334 |
|
if (seg_file.file == NULL) { |
| 335 |
|
fprintf(stderr, "Error: cannot open reads file %s for reading\n", |
| 336 |
|
reads_file_names[i].c_str()); |
| 347 |
|
tokenize(quals_file_list, ",", quals_file_names); |
| 348 |
|
for (size_t i = 0; i < quals_file_names.size(); ++i) |
| 349 |
|
{ |
| 350 |
< |
string fname(quals_file_names[i]); |
| 313 |
< |
string pipecmd=guess_packer(fname, true); |
| 314 |
< |
FZPipe seg_file(fname, pipecmd); |
| 350 |
> |
FZPipe seg_file(quals_file_names[i], true); |
| 351 |
|
if (seg_file.file == NULL) |
| 352 |
|
{ |
| 353 |
|
fprintf(stderr, "Error: cannot open reads file %s for reading\n", |
