| 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; |
| 45 |
|
//FZPipe(filter_multihits, false); |
| 46 |
+ |
ReadStream rdstream(flt_reads, NULL, true); |
| 47 |
+ |
/* |
| 48 |
|
FILE* rfile=fopen(flt_reads.c_str(),"r"); |
| 49 |
|
if (rfile==NULL) |
| 50 |
|
err_die("Error: cannot read file %s\n", flt_reads.c_str()); |
| 51 |
|
FLineReader fr(rfile); |
| 52 |
|
skip_lines(fr); //should not be needed, bowtie doesn't add extra header lines for this |
| 53 |
+ |
*/ |
| 54 |
|
Read read; |
| 55 |
< |
while (next_fastx_read(fr, read, reads_format)) { |
| 55 |
> |
//while (next_fastx_read(fr, read, reads_format)) { |
| 56 |
> |
while (rdstream.get_direct(read, reads_format)) { |
| 57 |
|
uint32_t rnum=(uint32_t)atol(read.name.c_str()); |
| 58 |
|
if (rnum>=(uint32_t) readmap.size()) |
| 59 |
|
readmap.resize(rnum+1, false); |
| 60 |
|
readmap[rnum] = true; |
| 61 |
|
} |
| 62 |
|
readmap_loaded=true; |
| 63 |
< |
fclose(rfile); |
| 63 |
> |
//fclose(rfile); |
| 64 |
|
} |
| 65 |
|
|
| 66 |
|
bool check_readmap(uint32_t read_id) { |
| 67 |
|
if (read_id>=readmap.size()) return false; |
| 68 |
|
else return readmap[read_id]; |
| 69 |
|
} |
| 70 |
< |
void flt_reads_and_hits(vector<FZPipe>& reads_files) { |
| 70 |
> |
|
| 71 |
> |
void flt_reads_and_hits(vector<string>& reads_files) { |
| 72 |
|
if (!readmap_loaded) |
| 73 |
|
err_die("Error: filtering reads not enabled, aborting."); |
| 74 |
|
if (aux_outfile.empty()) |
| 75 |
|
err_die("Error: auxiliary output file not provided."); |
| 76 |
+ |
//if (index_outfile.empty()) |
| 77 |
+ |
// err_die("Error: index output file not provided."); |
| 78 |
+ |
|
| 79 |
|
// -- filter mappings: |
| 80 |
|
string fext=getFext(flt_mappings); |
| 81 |
+ |
fprintf(stderr, "[[[ DEBUG: ]]] fext='%s'\n",fext.c_str()); |
| 82 |
|
if (fext=="bam") { |
| 83 |
< |
//TODO |
| 84 |
< |
//WRITEME: use samtools C API to write a quick bam filter |
| 85 |
< |
err_die("Error: cannot handle BAM files yet![WRITEME]"); |
| 86 |
< |
return; |
| 87 |
< |
} |
| 88 |
< |
bool is_sam=false; |
| 89 |
< |
string s(flt_mappings); |
| 90 |
< |
for(size_t i=0; i!=s.length(); ++i) |
| 91 |
< |
s[i] = std::tolower(s[i]); |
| 92 |
< |
if (fext=="sam" || s.rfind(".sam.")+fext.length()+5==s.length()) is_sam=true; |
| 93 |
< |
string unzcmd=getUnpackCmd(flt_mappings); |
| 94 |
< |
FZPipe hitsfile(flt_mappings, unzcmd); |
| 95 |
< |
FLineReader fh(hitsfile); |
| 96 |
< |
FZPipe outfile; |
| 97 |
< |
outfile.openWrite(aux_outfile.c_str(), zpacker); |
| 98 |
< |
if (outfile.file==NULL) err_die("Error: cannot create file %s", aux_outfile.c_str()); |
| 99 |
< |
const char* line; |
| 92 |
< |
while ((line=fh.nextLine())) { |
| 93 |
< |
if (is_sam && line[0]=='@') { |
| 94 |
< |
fprintf(outfile.file, "%s\n", line); |
| 95 |
< |
continue; |
| 96 |
< |
} |
| 97 |
< |
char* tab=strchr((char*)line, '\t'); |
| 98 |
< |
if (tab==NULL) |
| 99 |
< |
err_die("Error: cannot find tab character in %s mappings line:\n%s", |
| 100 |
< |
flt_mappings.c_str(),line); |
| 101 |
< |
*tab=0; |
| 102 |
< |
uint32_t rid = (uint32_t) atol(line); |
| 103 |
< |
if (rid==0) |
| 104 |
< |
err_die("Error: invalid read ID (%s) parsed from mapping file %s", |
| 105 |
< |
line, flt_mappings.c_str()); |
| 106 |
< |
*tab='\t'; |
| 107 |
< |
if (check_readmap(rid)) { |
| 108 |
< |
fprintf(outfile.file, "%s\n", line); |
| 109 |
< |
} |
| 83 |
> |
samfile_t* fbam=samopen(flt_mappings.c_str(), "rb", 0); |
| 84 |
> |
if (fbam==NULL) |
| 85 |
> |
err_die("Error opening BAM file %s!\n", flt_mappings.c_str()); |
| 86 |
> |
bam1_t *b = bam_init1(); |
| 87 |
> |
string aux_index(aux_outfile); |
| 88 |
> |
aux_index+=".index"; |
| 89 |
> |
GBamWriter wbam(aux_outfile.c_str(), fbam->header, aux_index); |
| 90 |
> |
while (samread(fbam, b) > 0) { |
| 91 |
> |
char* rname = bam1_qname(b); |
| 92 |
> |
uint32_t rid=(uint32_t)atol(rname); |
| 93 |
> |
if (check_readmap(rid)) { |
| 94 |
> |
//write this mapping into the output file |
| 95 |
> |
wbam.write(b, rid); |
| 96 |
> |
} |
| 97 |
> |
} |
| 98 |
> |
bam_destroy1(b); |
| 99 |
> |
samclose(fbam); |
| 100 |
|
} |
| 101 |
< |
outfile.close(); |
| 102 |
< |
hitsfile.close(); |
| 101 |
> |
else { |
| 102 |
> |
bool is_sam=false; |
| 103 |
> |
string s(flt_mappings); |
| 104 |
> |
for(size_t i=0; i!=s.length(); ++i) |
| 105 |
> |
s[i] = std::tolower(s[i]); |
| 106 |
> |
if (fext=="sam" || s.rfind(".sam.")+fext.length()+5==s.length()) is_sam=true; |
| 107 |
> |
string unzcmd=getUnpackCmd(flt_mappings); |
| 108 |
> |
FZPipe hitsfile(flt_mappings, unzcmd); |
| 109 |
> |
FLineReader fh(hitsfile); |
| 110 |
> |
FZPipe outfile; |
| 111 |
> |
outfile.openWrite(aux_outfile.c_str(), zpacker); |
| 112 |
> |
if (outfile.file==NULL) err_die("Error: cannot create file %s", aux_outfile.c_str()); |
| 113 |
> |
const char* line; |
| 114 |
> |
while ((line=fh.nextLine())) { |
| 115 |
> |
if (is_sam && line[0]=='@') { |
| 116 |
> |
//copy the header |
| 117 |
> |
fprintf(outfile.file, "%s\n", line); |
| 118 |
> |
continue; |
| 119 |
> |
} |
| 120 |
> |
char* tab=strchr((char*)line, '\t'); |
| 121 |
> |
if (tab==NULL) |
| 122 |
> |
err_die("Error: cannot find tab character in %s mappings line:\n%s", |
| 123 |
> |
flt_mappings.c_str(),line); |
| 124 |
> |
*tab=0; |
| 125 |
> |
uint32_t rid = (uint32_t) atol(line); |
| 126 |
> |
if (rid==0) |
| 127 |
> |
err_die("Error: invalid read ID (%s) parsed from mapping file %s", |
| 128 |
> |
line, flt_mappings.c_str()); |
| 129 |
> |
*tab='\t'; |
| 130 |
> |
if (check_readmap(rid)) { |
| 131 |
> |
fprintf(outfile.file, "%s\n", line); |
| 132 |
> |
} |
| 133 |
> |
} |
| 134 |
> |
outfile.close(); |
| 135 |
> |
hitsfile.close(); |
| 136 |
> |
} |
| 137 |
|
// -- now filter reads |
| 138 |
+ |
//FILE* findex = NULL; |
| 139 |
+ |
GBamWriter* wbam=NULL; |
| 140 |
+ |
FILE* fout=NULL; |
| 141 |
+ |
if (std_outfile.empty()) { |
| 142 |
+ |
fout=stdout; |
| 143 |
+ |
} |
| 144 |
+ |
else { //output file name explicitely given |
| 145 |
+ |
if (getFext(std_outfile)=="bam") { |
| 146 |
+ |
if (sam_header.empty()) err_die("Error: sam header file not provided.\n"); |
| 147 |
+ |
wbam = new GBamWriter(std_outfile.c_str(), sam_header.c_str(), index_outfile); |
| 148 |
+ |
//wbam = new GBamWriter(std_outfile, index_outfile); |
| 149 |
+ |
} |
| 150 |
+ |
else { |
| 151 |
+ |
fout = fopen(std_outfile.c_str(), "w"); |
| 152 |
+ |
if (fout==NULL) |
| 153 |
+ |
err_die("Error: cannot create file %s\n", std_outfile.c_str()); |
| 154 |
+ |
} |
| 155 |
+ |
} |
| 156 |
+ |
/* |
| 157 |
+ |
if (wbam==NULL && !index_outfile.empty()) { |
| 158 |
+ |
findex = fopen(index_outfile.c_str(), "w"); |
| 159 |
+ |
if (findex == NULL) |
| 160 |
+ |
err_die("Error: cannot create file %s\n", index_outfile.c_str()); |
| 161 |
+ |
} |
| 162 |
+ |
*/ |
| 163 |
|
for (size_t fi = 0; fi < reads_files.size(); ++fi) { |
| 164 |
|
//only one file expected here, this is not the initial prep_reads |
| 165 |
|
Read read; |
| 166 |
< |
FLineReader fr(reads_files[fi]); |
| 166 |
> |
ReadStream readstream(reads_files[fi], NULL, true); |
| 167 |
|
//skip_lines(fr); |
| 168 |
< |
while (next_fastx_read(fr, read)) { |
| 168 |
> |
while (readstream.get_direct(read)) { |
| 169 |
|
uint32_t rnum=(uint32_t)atol(read.name.c_str()); |
| 170 |
< |
if (check_readmap(rnum)) |
| 171 |
< |
printf("@%s\n%s\n+%s\n%s\n", |
| 172 |
< |
read.name.c_str(), |
| 173 |
< |
read.seq.c_str(), |
| 174 |
< |
read.alt_name.c_str(), |
| 175 |
< |
read.qual.c_str()); |
| 170 |
> |
if (check_readmap(rnum)) { |
| 171 |
> |
if (wbam) { |
| 172 |
> |
GBamRecord bamrec(read.name.c_str(), -1, 0, false, |
| 173 |
> |
read.seq.c_str(), NULL, read.qual.c_str()); |
| 174 |
> |
wbam->write(bamrec.get_b(), rnum); |
| 175 |
> |
} |
| 176 |
> |
else { |
| 177 |
> |
fprintf(fout, "@%s\n%s\n+%s\n%s\n", |
| 178 |
> |
read.name.c_str(), |
| 179 |
> |
read.seq.c_str(), |
| 180 |
> |
read.alt_name.c_str(), |
| 181 |
> |
read.qual.c_str()); |
| 182 |
> |
} |
| 183 |
|
} |
| 184 |
< |
} |
| 184 |
> |
} |
| 185 |
> |
} |
| 186 |
> |
if (wbam) delete wbam; |
| 187 |
> |
if (fout && fout!=stdout) fclose(fout); |
| 188 |
|
} |
| 189 |
|
|
| 190 |
|
|
| 191 |
< |
void process_reads(vector<FZPipe>& reads_files, vector<FZPipe>& quals_files) |
| 191 |
> |
void writePrepBam(GBamWriter* wbam, Read& read, uint32_t rid, char trashcode=0) { |
| 192 |
> |
if (wbam==NULL) return; |
| 193 |
> |
string rnum; |
| 194 |
> |
str_appendUInt(rnum,rid); |
| 195 |
> |
string rname(read.name); |
| 196 |
> |
size_t pl=rname.length()-1; |
| 197 |
> |
GBamRecord bamrec(rnum.c_str(), -1, 0, false, read.seq.c_str(), NULL, read.qual.c_str()); |
| 198 |
> |
int matenum=0; |
| 199 |
> |
if (rname[pl-1]=='/') { |
| 200 |
> |
if (rname[pl]=='1') { |
| 201 |
> |
bamrec.set_flag(BAM_FREAD1); |
| 202 |
> |
matenum=1; |
| 203 |
> |
} |
| 204 |
> |
else if (rname[pl]=='2') { |
| 205 |
> |
bamrec.set_flag(BAM_FREAD2); |
| 206 |
> |
matenum=2; |
| 207 |
> |
} |
| 208 |
> |
if (matenum) rname.resize(pl-1); |
| 209 |
> |
} |
| 210 |
> |
|
| 211 |
> |
bamrec.add_aux("ZN", 'Z',read.name.length(),(uint8_t*)rname.c_str()); |
| 212 |
> |
if (trashcode) { |
| 213 |
> |
bamrec.set_flag(BAM_FQCFAIL); |
| 214 |
> |
bamrec.add_aux("ZT", 'A', 1, (uint8_t*)&trashcode); |
| 215 |
> |
} |
| 216 |
> |
wbam->write(bamrec.get_b(), rid); |
| 217 |
> |
} |
| 218 |
> |
|
| 219 |
> |
void process_reads(vector<string>& reads_files, vector<FZPipe>& quals_files) |
| 220 |
|
{ |
| 221 |
|
//TODO: add the option to write the garbage reads into separate file(s) |
| 222 |
|
int num_reads_chucked = 0; |
| 223 |
< |
int multimap_chucked=0; |
| 223 |
> |
int multimap_chucked = 0; |
| 224 |
|
int min_read_len = 20000000; |
| 225 |
|
int max_read_len = 0; |
| 226 |
|
uint32_t next_id = 0; |
| 227 |
+ |
uint64_t file_offset = 0; |
| 228 |
|
FILE* fw=NULL; |
| 229 |
|
if (!aux_outfile.empty()) { |
| 230 |
|
fw=fopen(aux_outfile.c_str(), "w"); |
| 232 |
|
err_die("Error: cannot create file %s\n",aux_outfile.c_str()); |
| 233 |
|
} |
| 234 |
|
|
| 235 |
+ |
FILE* findex = NULL; |
| 236 |
+ |
GBamWriter* wbam=NULL; |
| 237 |
+ |
FILE* fout=NULL; |
| 238 |
+ |
if (std_outfile.empty()) { |
| 239 |
+ |
fout=stdout; |
| 240 |
+ |
} |
| 241 |
+ |
else { //output file name explicitely given |
| 242 |
+ |
if (getFext(std_outfile)=="bam") { |
| 243 |
+ |
if (sam_header.empty()) err_die("Error: sam header file not provided.\n"); |
| 244 |
+ |
wbam = new GBamWriter(std_outfile.c_str(), sam_header.c_str(), index_outfile); |
| 245 |
+ |
//wbam = new GBamWriter(std_outfile, index_outfile); |
| 246 |
+ |
} |
| 247 |
+ |
else { |
| 248 |
+ |
fout = fopen(std_outfile.c_str(), "w"); |
| 249 |
+ |
if (fout==NULL) |
| 250 |
+ |
err_die("Error: cannot create file %s\n", std_outfile.c_str()); |
| 251 |
+ |
} |
| 252 |
+ |
} |
| 253 |
+ |
if (wbam==NULL && !index_outfile.empty()) { |
| 254 |
+ |
findex = fopen(index_outfile.c_str(), "w"); |
| 255 |
+ |
if (findex == NULL) |
| 256 |
+ |
err_die("Error: cannot create file %s\n", index_outfile.c_str()); |
| 257 |
+ |
} |
| 258 |
+ |
|
| 259 |
|
for (size_t fi = 0; fi < reads_files.size(); ++fi) |
| 260 |
|
{ |
| 261 |
|
Read read; |
| 262 |
< |
FLineReader fr(reads_files[fi]); |
| 151 |
< |
skip_lines(fr); |
| 152 |
< |
FZPipe fq; |
| 262 |
> |
FZPipe* fq=NULL; |
| 263 |
|
if (quals) |
| 264 |
< |
fq = quals_files[fi]; |
| 265 |
< |
FLineReader frq(fq); |
| 156 |
< |
skip_lines(frq); |
| 264 |
> |
fq = & quals_files[fi]; |
| 265 |
> |
ReadStream reads(reads_files[fi], fq, true); |
| 266 |
|
|
| 267 |
< |
while (!fr.isEof()) { |
| 268 |
< |
//read.clear(); |
| 267 |
> |
while (reads.get_direct(read, reads_format)) { |
| 268 |
> |
// read.clear(); |
| 269 |
|
// Get the next read from the file |
| 270 |
< |
if (!next_fastx_read(fr, read, reads_format, ((quals) ? &frq : NULL))) |
| 271 |
< |
break; |
| 270 |
> |
//if (!next_fastx_read(fr, read, reads_format, ((quals) ? &frq : NULL))) |
| 271 |
> |
// break; |
| 272 |
|
|
| 273 |
|
++next_id; |
| 274 |
|
//IMPORTANT: to keep paired reads in sync, this must be |
| 275 |
|
//incremented BEFORE any reads are chucked ! |
| 167 |
– |
|
| 276 |
|
if (read.seq.length()<12) { |
| 277 |
|
++num_reads_chucked; |
| 278 |
+ |
writePrepBam(wbam, read, next_id, 'S'); |
| 279 |
|
continue; |
| 280 |
|
} |
| 281 |
|
if ((int)read.seq.length()<min_read_len) |
| 286 |
|
// daehwan - check this later, it's due to bowtie |
| 287 |
|
if (color && read.seq[1] == '4') { |
| 288 |
|
++num_reads_chucked; |
| 289 |
+ |
writePrepBam(wbam, read, next_id, 'c'); |
| 290 |
|
continue; |
| 291 |
|
} |
| 292 |
|
|
| 293 |
|
if (readmap_loaded && check_readmap(next_id)) { |
| 294 |
|
++num_reads_chucked; |
| 295 |
|
++multimap_chucked; |
| 296 |
+ |
writePrepBam(wbam, read, next_id, 'M'); |
| 297 |
|
continue; |
| 298 |
|
} |
| 299 |
< |
format_qual_string(read.qual); |
| 299 |
> |
format_qual_string(read.qual); |
| 300 |
|
std::transform(read.seq.begin(), read.seq.end(), read.seq.begin(), ::toupper); |
| 301 |
|
char counts[256]; |
| 302 |
|
memset(counts, 0, sizeof(counts)); |
| 316 |
|
|
| 317 |
|
// Chuck the read if there are at least 5 'N's or if it's mostly |
| 318 |
|
// (>90%) 'N's and 'A's |
| 319 |
< |
|
| 319 |
> |
char trash_code=0; |
| 320 |
|
if (percent_A > 0.9 || |
| 321 |
|
percent_C > 0.9 || |
| 322 |
|
percent_G > 0.9 || |
| 323 |
< |
percent_T > 0.9 || |
| 324 |
< |
percent_N >= 0.1 || |
| 325 |
< |
percent_4 >= 0.1) |
| 326 |
< |
{ |
| 327 |
< |
++num_reads_chucked; |
| 328 |
< |
} |
| 329 |
< |
else |
| 330 |
< |
{ |
| 331 |
< |
if (reads_format == FASTQ or (reads_format == FASTA && quals)) |
| 332 |
< |
{ |
| 323 |
> |
percent_T > 0.9) |
| 324 |
> |
trash_code='L'; |
| 325 |
> |
else if (percent_N >= 0.1 || percent_4 >=0.1) |
| 326 |
> |
trash_code='N'; |
| 327 |
> |
if (trash_code) { |
| 328 |
> |
++num_reads_chucked; |
| 329 |
> |
writePrepBam(wbam, read, next_id, trash_code); |
| 330 |
> |
continue; |
| 331 |
> |
} |
| 332 |
> |
|
| 333 |
> |
if (wbam) { |
| 334 |
> |
writePrepBam(wbam, read, next_id); |
| 335 |
> |
} |
| 336 |
> |
else { |
| 337 |
> |
// daehwan - we should not use buf in printf function |
| 338 |
> |
// because it may contain some control characters such as "\" from quality values. |
| 339 |
> |
// Here, buf is only used for calculating the file offset |
| 340 |
> |
char buf[2048] = {0}; |
| 341 |
> |
if (reads_format == FASTQ or (reads_format == FASTA && quals)) |
| 342 |
> |
{ |
| 343 |
> |
sprintf(buf, "@%u\n%s\n+%s\n%s\n", |
| 344 |
> |
next_id, |
| 345 |
> |
read.seq.c_str(), |
| 346 |
> |
read.name.c_str(), |
| 347 |
> |
read.qual.c_str()); |
| 348 |
> |
|
| 349 |
> |
fprintf(fout, "@%u\n%s\n+%s\n%s\n", |
| 350 |
> |
next_id, |
| 351 |
> |
read.seq.c_str(), |
| 352 |
> |
read.name.c_str(), |
| 353 |
> |
read.qual.c_str()); |
| 354 |
> |
} |
| 355 |
> |
else if (reads_format == FASTA) |
| 356 |
> |
{ |
| 357 |
> |
string qual; |
| 358 |
> |
if (color) |
| 359 |
> |
qual = string(read.seq.length()-1, 'I').c_str(); |
| 360 |
> |
else |
| 361 |
> |
qual = string(read.seq.length(), 'I').c_str(); |
| 362 |
> |
|
| 363 |
> |
sprintf(buf, "@%u\n%s\n+%s\n%s\n", |
| 364 |
> |
next_id, |
| 365 |
> |
read.seq.c_str(), |
| 366 |
> |
read.name.c_str(), |
| 367 |
> |
qual.c_str()); |
| 368 |
> |
|
| 369 |
> |
fprintf(fout, "@%u\n%s\n+%s\n%s\n", |
| 370 |
> |
next_id, |
| 371 |
> |
read.seq.c_str(), |
| 372 |
> |
read.name.c_str(), |
| 373 |
> |
qual.c_str()); |
| 374 |
> |
} |
| 375 |
> |
else |
| 376 |
> |
{ |
| 377 |
> |
assert(0); |
| 378 |
> |
} |
| 379 |
> |
|
| 380 |
> |
if (findex != NULL) |
| 381 |
> |
{ |
| 382 |
> |
if ((next_id - num_reads_chucked) % INDEX_REC_COUNT == 0) |
| 383 |
> |
fprintf(findex, "%d\t%lu\n", next_id, file_offset); |
| 384 |
> |
} |
| 385 |
|
|
| 386 |
< |
printf("@%u\n%s\n+%s\n%s\n", |
| 224 |
< |
next_id, |
| 225 |
< |
read.seq.c_str(), |
| 226 |
< |
read.name.c_str(), |
| 227 |
< |
read.qual.c_str()); |
| 228 |
< |
} |
| 229 |
< |
else if (reads_format == FASTA) |
| 230 |
< |
{ |
| 231 |
< |
string qual; |
| 232 |
< |
if (color) |
| 233 |
< |
qual = string(read.seq.length()-1, 'I').c_str(); |
| 234 |
< |
else |
| 235 |
< |
qual = string(read.seq.length(), 'I').c_str(); |
| 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 |
< |
qual.c_str()); |
| 242 |
< |
} |
| 386 |
> |
file_offset += strlen(buf); |
| 387 |
|
} |
| 388 |
|
} //while !fr.isEof() |
| 389 |
< |
fr.close(); |
| 390 |
< |
frq.close(); |
| 389 |
> |
//fr.close(); |
| 390 |
> |
//frq.close(); |
| 391 |
|
} //for each input file |
| 392 |
|
fprintf(stderr, "%u out of %u reads have been filtered out\n", |
| 393 |
|
num_reads_chucked, next_id); |
| 394 |
|
if (readmap_loaded) |
| 395 |
|
fprintf(stderr, "\t(%u filtered out due to %s)\n", |
| 396 |
|
multimap_chucked, flt_reads.c_str()); |
| 397 |
+ |
if (wbam) { delete wbam; } |
| 398 |
+ |
if (fout && fout!=stdout) fclose(fout); |
| 399 |
|
if (fw!=NULL) { |
| 400 |
|
fprintf(fw, "min_read_len=%d\n",min_read_len - (color ? 1 : 0)); |
| 401 |
|
fprintf(fw, "max_read_len=%d\n",max_read_len - (color ? 1 : 0)); |
| 403 |
|
fprintf(fw, "reads_out=%d\n",next_id-num_reads_chucked); |
| 404 |
|
fclose(fw); |
| 405 |
|
} |
| 406 |
+ |
|
| 407 |
+ |
if (findex != NULL) |
| 408 |
+ |
fclose(findex); |
| 409 |
|
} |
| 410 |
|
|
| 411 |
|
void print_usage() |
| 433 |
|
|
| 434 |
|
string reads_file_list = argv[optind++]; |
| 435 |
|
|
| 436 |
< |
vector<string> reads_file_names; |
| 437 |
< |
vector<FZPipe> reads_files; |
| 289 |
< |
tokenize(reads_file_list, ",",reads_file_names); |
| 290 |
< |
for (size_t i = 0; i < reads_file_names.size(); ++i) |
| 291 |
< |
{ |
| 292 |
< |
string fname=reads_file_names[i]; |
| 293 |
< |
string pipecmd=guess_packer(fname, true); |
| 294 |
< |
if (!pipecmd.empty()) pipecmd.append(" -cd"); |
| 295 |
< |
FZPipe seg_file(fname,pipecmd); |
| 296 |
< |
if (seg_file.file == NULL) { |
| 297 |
< |
fprintf(stderr, "Error: cannot open reads file %s for reading\n", |
| 298 |
< |
reads_file_names[i].c_str()); |
| 299 |
< |
exit(1); |
| 300 |
< |
} |
| 301 |
< |
reads_files.push_back(seg_file); |
| 302 |
< |
} |
| 303 |
< |
|
| 436 |
> |
vector<string> reads_filenames; |
| 437 |
> |
tokenize(reads_file_list, ",",reads_filenames); |
| 438 |
|
vector<string> quals_file_names; |
| 439 |
|
vector<FZPipe> quals_files; |
| 440 |
|
if (quals) |
| 443 |
|
tokenize(quals_file_list, ",", quals_file_names); |
| 444 |
|
for (size_t i = 0; i < quals_file_names.size(); ++i) |
| 445 |
|
{ |
| 446 |
< |
string fname(quals_file_names[i]); |
| 313 |
< |
string pipecmd=guess_packer(fname, true); |
| 314 |
< |
FZPipe seg_file(fname, pipecmd); |
| 446 |
> |
FZPipe seg_file(quals_file_names[i], true); |
| 447 |
|
if (seg_file.file == NULL) |
| 448 |
|
{ |
| 449 |
|
fprintf(stderr, "Error: cannot open reads file %s for reading\n", |
| 457 |
|
// Only print to standard out the good reads |
| 458 |
|
//TODO: a better, more generic read filtering protocol |
| 459 |
|
if (flt_mappings.empty()) |
| 460 |
< |
process_reads(reads_files, quals_files); |
| 460 |
> |
process_reads(reads_filenames, quals_files); |
| 461 |
|
else //special use case: filter previous bowtie results |
| 462 |
< |
flt_reads_and_hits(reads_files); |
| 462 |
> |
flt_reads_and_hits(reads_filenames); |
| 463 |
|
|
| 464 |
|
return 0; |
| 465 |
|
} |
