| 101 |
|
int island_extension = 25; |
| 102 |
|
int segment_length = 25; |
| 103 |
|
int segment_mismatches = 2; |
| 104 |
< |
|
| 104 |
> |
int max_read_mismatches = 2; |
| 105 |
|
int max_splice_mismatches = 1; |
| 106 |
|
|
| 107 |
|
ReadFormat reads_format = FASTQ; |
| 108 |
|
|
| 109 |
|
bool verbose = false; |
| 110 |
|
|
| 111 |
< |
int max_multihits = 40; |
| 111 |
> |
unsigned int max_multihits = 40; |
| 112 |
|
bool no_closure_search = false; |
| 113 |
|
bool no_coverage_search = false; |
| 114 |
|
bool no_microexon_search = false; |
| 135 |
|
|
| 136 |
|
string gtf_juncs = ""; |
| 137 |
|
|
| 138 |
+ |
string flt_reads = ""; |
| 139 |
+ |
string flt_mappings = ""; |
| 140 |
+ |
|
| 141 |
|
eLIBRARY_TYPE library_type = LIBRARY_TYPE_NONE; |
| 142 |
|
|
| 143 |
|
extern void print_usage(); |
| 224 |
|
} |
| 225 |
|
|
| 226 |
|
|
| 227 |
< |
const char *short_options = "QCp:z:"; |
| 227 |
> |
const char *short_options = "QCp:z:N:"; |
| 228 |
|
|
| 229 |
|
enum |
| 230 |
|
{ |
| 244 |
|
OPT_NO_COVERAGE_SEARCH, |
| 245 |
|
OPT_NO_MICROEXON_SEARCH, |
| 246 |
|
OPT_SEGMENT_LENGTH, |
| 247 |
+ |
OPT_READ_MISMATCHES, |
| 248 |
|
OPT_SEGMENT_MISMATCHES, |
| 249 |
|
OPT_MIN_CLOSURE_EXON, |
| 250 |
|
OPT_MAX_CLOSURE_INTRON, |
| 272 |
|
OPT_ZPACKER, |
| 273 |
|
OPT_SAMTOOLS, |
| 274 |
|
OPT_AUX_OUT, |
| 275 |
< |
OPT_GTF_JUNCS |
| 275 |
> |
OPT_GTF_JUNCS, |
| 276 |
> |
OPT_FILTER_READS, |
| 277 |
> |
OPT_FILTER_HITS |
| 278 |
|
}; |
| 279 |
|
|
| 280 |
|
static struct option long_options[] = { |
| 296 |
|
{"no-microexon-search", no_argument, 0, OPT_NO_MICROEXON_SEARCH}, |
| 297 |
|
{"segment-length", required_argument, 0, OPT_SEGMENT_LENGTH}, |
| 298 |
|
{"segment-mismatches", required_argument, 0, OPT_SEGMENT_MISMATCHES}, |
| 299 |
+ |
{"max-mismatches", required_argument, 0, OPT_READ_MISMATCHES}, |
| 300 |
|
{"min-closure-exon", required_argument, 0, OPT_MIN_CLOSURE_EXON}, |
| 301 |
|
{"min-closure-intron", required_argument, 0, OPT_MIN_CLOSURE_INTRON}, |
| 302 |
|
{"max-closure-intron", required_argument, 0, OPT_MAX_CLOSURE_INTRON}, |
| 323 |
|
{"samtools", required_argument, 0, OPT_SAMTOOLS}, |
| 324 |
|
{"aux-outfile", required_argument, 0, OPT_AUX_OUT}, |
| 325 |
|
{"gtf-juncs", required_argument, 0, OPT_GTF_JUNCS}, |
| 326 |
+ |
{"flt-reads",required_argument, 0, OPT_FILTER_READS}, |
| 327 |
+ |
{"flt-hits",required_argument, 0, OPT_FILTER_HITS}, |
| 328 |
|
{0, 0, 0, 0} // terminator |
| 329 |
|
}; |
| 330 |
|
|
| 400 |
|
case OPT_SEGMENT_MISMATCHES: |
| 401 |
|
segment_mismatches = parseIntOpt(0, "--segment-mismatches arg must be at least 0", print_usage); |
| 402 |
|
break; |
| 403 |
+ |
case 'N': |
| 404 |
+ |
case OPT_READ_MISMATCHES: |
| 405 |
+ |
max_read_mismatches = parseIntOpt(0, "--max-mismatches arg must be at least 0", print_usage); |
| 406 |
+ |
break; |
| 407 |
|
case OPT_MIN_CLOSURE_EXON: |
| 408 |
|
min_closure_exon_length = parseIntOpt(1, "--min-closure-exon arg must be at least 1", print_usage); |
| 409 |
|
break; |
| 503 |
|
case OPT_GTF_JUNCS: |
| 504 |
|
gtf_juncs = optarg; |
| 505 |
|
break; |
| 506 |
+ |
case OPT_FILTER_READS: |
| 507 |
+ |
flt_reads = optarg; |
| 508 |
+ |
break; |
| 509 |
+ |
case OPT_FILTER_HITS: |
| 510 |
+ |
flt_mappings = optarg; |
| 511 |
+ |
break; |
| 512 |
|
default: |
| 513 |
|
print_usage(); |
| 514 |
|
return 1; |
| 619 |
|
//only needed for the primary input files (given by user) |
| 620 |
|
string picmd(""); |
| 621 |
|
string fext=getFext(fname); |
| 622 |
+ |
if (fext=="bam") { |
| 623 |
+ |
picmd="bam2fastx"; |
| 624 |
+ |
return picmd; |
| 625 |
+ |
} |
| 626 |
|
if (fext=="gz" || fext=="gzip" || fext=="z") { |
| 627 |
|
if (use_all_cpus && str_endsWith(zpacker,"pigz")) { |
| 628 |
|
picmd=zpacker; |
| 671 |
|
} |
| 672 |
|
|
| 673 |
|
string getUnpackCmd(const string& fname, bool use_all_cpus) { |
| 674 |
< |
//prep_reads should use guess_packer() instead |
| 674 |
> |
//prep_reads should use guess_packer() instead |
| 675 |
> |
//otherwise compressed files MUST have the .z extension, |
| 676 |
> |
//as they are all internally generated |
| 677 |
|
string pipecmd(""); |
| 678 |
< |
if (zpacker.empty() || getFext(fname)!="z") { |
| 679 |
< |
return pipecmd; |
| 678 |
> |
string fext=getFext(fname); |
| 679 |
> |
if (fext=="bam") { |
| 680 |
> |
pipecmd="bam2fastx"; |
| 681 |
> |
return pipecmd; |
| 682 |
> |
} |
| 683 |
> |
if (zpacker.empty() || fext!="z") { |
| 684 |
> |
return pipecmd; //no packer used |
| 685 |
|
} |
| 686 |
|
pipecmd=zpacker; |
| 687 |
|
if (str_endsWith(pipecmd, "pigz") ||str_endsWith(pipecmd, "pbzip2")) { |
