| line |
true |
false |
branch |
|
115
|
0 |
0 |
unless defined $args->{'-max_target_seqs'}
|
|
124
|
0 |
0 |
if $query_seqs->type eq "prot" and $blastdb->type eq "nucl"
|
|
139
|
0 |
0 |
unless $rp->debug_mode
|
|
166
|
0 |
0 |
if ($rp->ref_brh eq 'off') { }
|
|
179
|
0 |
0 |
if $homologous_seqs->type eq "nucl" and $blastdb->type eq "prot"
|
|
189
|
0 |
0 |
if $in_best_hits
|
|
191
|
0 |
0 |
unless $rp->debug_mode
|
|
211
|
0 |
0 |
unless ($rp->run_mode eq "metagenomic")
|
|
212
|
0 |
0 |
if ($rp->merge_orthologues eq "on")
|
|
231
|
0 |
0 |
unless $blastdb
|
|
238
|
0 |
0 |
if $orthologous_seqs->type eq "nucl" and $blastdb->type eq "prot"
|
|
253
|
0 |
0 |
unless $rp->debug_mode
|
|
267
|
0 |
0 |
unless $blastdb
|
|
274
|
0 |
0 |
if $orthologous_seqs->type eq "nucl" and $blastdb->type eq "prot"
|
|
281
|
0 |
0 |
unless $bo
|
|
287
|
0 |
0 |
unless $orthologue->count_hits
|
|
300
|
0 |
0 |
if $self->is_allowed($hit_id)
|
|
309
|
0 |
0 |
unless $rp->debug_mode
|
|
329
|
0 |
0 |
if $orthologous_seqs->type eq "nucl" and $blastdb->type eq "prot"
|
|
338
|
0 |
0 |
unless $bo
|
|
342
|
0 |
0 |
unless ($orthologue->count_hits)
|
|
350
|
0 |
0 |
unless $tax_line
|
|
355
|
0 |
0 |
if $contam_org
|
|
369
|
0 |
0 |
if $rp->run_mode eq "metagenomic"
|
|
372
|
0 |
0 |
if ($rp->aligner_mode eq "off")
|
|
396
|
0 |
0 |
if ($rp->ali_skip_self eq "on")
|
|
397
|
0 |
0 |
if ($template_id->full_org eq $transcript_seq->full_org)
|
|
409
|
0 |
0 |
if $coverage < $best_coverage * $rp->ali_cover_mul
|
|
425
|
0 |
0 |
unless (@templates)
|
|
433
|
0 |
0 |
if ($rp->aligner_mode =~ /exonerate|exoblast/msx)
|
|
454
|
0 |
0 |
if ($new_seq->seq_len) { }
|
|
455
|
0 |
0 |
$rp->aligner_mode eq 'exoblast' ? :
|
|
477
|
0 |
0 |
if ($rp->aligner_mode eq "blast" or $rp->aligner_mode eq "exoblast" and $failure)
|
|
485
|
0 |
0 |
unless $template_seq
|
|
508
|
0 |
0 |
if ($ap->query_seqs->type eq "nucl" and $blastdb->type eq "nucl" and $hsp->hit_strand == -1)
|
|
533
|
0 |
0 |
unless $rp->debug_mode
|
|
553
|
0 |
0 |
unless @seqs2cap
|
|
560
|
0 |
0 |
if (@seqs2cap < 2)
|
|
582
|
0 |
0 |
unless @contigs
|
|
623
|
0 |
0 |
if not defined $end and defined $start and $start =~ /\A \+\d+ \z/msx
|
|
636
|
0 |
0 |
if ($ap->para_blastdb)
|
|
638
|
0 |
0 |
if ($para_score > $temp_score)
|
|
645
|
0 |
0 |
if ($rp->tol_blastdb)
|
|
647
|
0 |
0 |
if ($tol_score > $temp_score)
|
|
664
|
0 |
0 |
if $family
|
|
683
|
0 |
0 |
if ($rp->tax_reports eq "on" or $self->_tax_filter)
|
|
710
|
0 |
0 |
if @relatives >= $rp->tax_max_hits
|
|
722
|
0 |
0 |
unless $tax
|
|
724
|
0 |
0 |
if $score < $rp->tax_min_score
|
|
725
|
0 |
0 |
if $score < $rp->tax_score_mul * $best_score
|
|
729
|
0 |
0 |
if $len < $rp->tax_min_len
|
|
731
|
0 |
0 |
if $ident < $rp->tax_min_ident
|
|
737
|
0 |
0 |
if (@taxonomy)
|
|
752
|
0 |
0 |
if (@relatives < $rp->tax_min_hits) { }
|
|
755
|
0 |
0 |
if ($self->_tax_filter)
|
|
768
|
0 |
0 |
if ($rp->tax_reports eq "on")
|
|
777
|
0 |
0 |
if ($self->_tax_filter and $rp->tol_check eq "off")
|
|
779
|
0 |
0 |
unless ($self->is_allowed($common_tax))
|
|
793
|
0 |
0 |
if ($count > 1)
|
|
800
|
0 |
0 |
if $more
|
|
805
|
0 |
0 |
$org =~ /$Bio::MUST::Apps::FortyTwo::OrgProcessor::PKEYONLY/ || $org =~ /$Bio::MUST::Apps::FortyTwo::OrgProcessor::GCAONLY/ ? :
|
|
839
|
0 |
0 |
if ($self->tax_filter)
|
|
841
|
0 |
0 |
if $tax
|
|
846
|
0 |
0 |
unless $self->homologous_seqs->all_long_ids
|
|
849
|
0 |
0 |
unless $self->orthologous_seqs->all_long_ids
|
|
852
|
0 |
0 |
unless $self->aligned_seqs->all_seq_ids
|