| line |
true |
false |
branch |
|
138
|
0 |
0 |
if ($$cl_args{'data'}) { } |
|
141
|
0 |
0 |
if (-r $$cl_args{'data'}) { } |
|
148
|
0 |
0 |
if (-e $$cl_args{'binary'} and -r $$cl_args{'binary'}) { } |
|
165
|
0 |
0 |
if (@errors) { } |
|
178
|
0 |
0 |
wantarray ? : |
|
261
|
0 |
0 |
unless $cl_silent |
|
262
|
0 |
0 |
unless $cl_silent |
|
266
|
0 |
0 |
unless $cl_silent |
|
268
|
0 |
0 |
unless $cl_silent |
|
279
|
0 |
0 |
unless $cl_silent |
|
281
|
0 |
0 |
if $_ eq '>' |
|
287
|
0 |
0 |
if ($$self{'param'}{'pre_subst'} == 1) { } |
|
|
0 |
0 |
elsif ($$self{'param'}{'pre_subst'} == 2) { } |
|
294
|
0 |
0 |
unless $id and $sequence |
|
298
|
0 |
0 |
if length $id > $id_len |
|
303
|
0 |
0 |
if (exists $$oli2seqoffs{$oligo}) { } |
|
321
|
0 |
0 |
if (not $cl_silent and $seqnum % 5000 == 0) |
|
334
|
0 |
0 |
unless ($cl_silent) |
|
350
|
0 |
0 |
if ($@) |
|
353
|
0 |
0 |
unless ($bin_fh = 'IO::File'->new($cl_binary, 'w')) |
|
360
|
0 |
0 |
unless (defined $bin_fh) |
|
365
|
0 |
0 |
unless ($cl_silent) |
|
388
|
0 |
0 |
if $begpos =~ /^0/ |
|
478
|
0 |
0 |
unless $cl_silent |
|
506
|
0 |
0 |
if (exists $$cl_args{'valid_chars'}) { } |
|
513
|
0 |
0 |
if (exists $$cl_args{'pre_subst'}) { } |
|
521
|
0 |
0 |
if ($$cl_args{'minlen'}) { } |
|
523
|
0 |
0 |
if ($$cl_args{'minlen'} < 1) |
|
535
|
0 |
0 |
if ($$cl_args{'wordlen'}) { } |
|
536
|
0 |
0 |
if ($$cl_args{'wordlen'} < 1) |
|
539
|
0 |
0 |
if ($$cl_args{'wordlen'} > $$cl_args{'minlen'}) |
|
547
|
0 |
0 |
unless (defined $$cl_args{'silent'}) |
|
553
|
0 |
0 |
if (@errors) { } |
|
563
|
0 |
0 |
wantarray ? : |
|
676
|
0 |
0 |
if defined wantarray |
|
687
|
0 |
0 |
if ($@) |
|
689
|
0 |
0 |
unless ($bin_fh = 'IO::File'->new($$self{'param'}{'binary'}, 'r')) |
|
746
|
0 |
0 |
if ($void_context == 1 and $$self{'param'}{'outfile'}) |
|
749
|
0 |
0 |
unless $$self{'param'}{'silent'} |
|
760
|
0 |
0 |
if $_ eq '>' |
|
765
|
0 |
0 |
if ($$self{'param'}{'pre_subst'} == 1) { } |
|
|
0 |
0 |
elsif ($$self{'param'}{'pre_subst'} == 2) { } |
|
773
|
0 |
0 |
unless $query_sid and $sequence |
|
775
|
0 |
0 |
if ($$self{'param'}{'reverse'}) |
|
779
|
0 |
0 |
unless $silent |
|
793
|
0 |
0 |
if (defined($pos = $$oli2pos{$oligo}[0])) |
|
841
|
0 |
0 |
if ($scovec[$i]) |
|
847
|
0 |
0 |
if ($oli_count < $oli_counts[$i]) { } |
|
853
|
0 |
0 |
if ($score >= $minscore) |
|
855
|
0 |
0 |
if (scalar @scores < $outlen) { } |
|
|
0 |
0 |
elsif ($score > $scores[0][1]) { } |
|
870
|
0 |
0 |
if ($$cl_args{'noids'}) { } |
|
892
|
0 |
0 |
if ($void_context == 0) { } |
|
899
|
0 |
0 |
if (defined $out_fh) { } |
|
906
|
0 |
0 |
unless ($silent) |
|
916
|
0 |
0 |
if ($void_context == 0) { } |
|
946
|
0 |
0 |
if (exists $$cl_args{'valid_chars'}) { } |
|
953
|
0 |
0 |
if (exists $$cl_args{'pre_subst'}) { } |
|
962
|
0 |
0 |
if ($$cl_args{'outlen'}) { } |
|
964
|
0 |
0 |
if ($$cl_args{'outlen'} < 1) |
|
973
|
0 |
0 |
if ($$cl_args{'minpct'}) { } |
|
979
|
0 |
0 |
if ($$cl_args{'reverse'}) { } |
|
991
|
0 |
0 |
if ($$cl_args{'query'}) { } |
|
994
|
0 |
0 |
unless (-r $$cl_args{'query'}) |
|
1005
|
0 |
0 |
if ($$cl_args{'outfile'}) { } |
|
1007
|
0 |
0 |
if (-e $$cl_args{'outfile'}) |
|
1013
|
0 |
0 |
if (not -d $outdir) { } |
|
|
0 |
0 |
elsif (not -w $outdir) { } |
|
1024
|
0 |
0 |
if (defined $$cl_args{'silent'}) |
|
1027
|
0 |
0 |
unless (defined $$self{'param'}{'silent'}) |
|
1033
|
0 |
0 |
if (@errors) { } |
|
1045
|
0 |
0 |
wantarray ? : |
|
1076
|
0 |
0 |
if ($valid_chars) { } |
|
1086
|
0 |
0 |
if $span_len < $word_len |
|
1105
|
0 |
0 |
wantarray ? : |
|
1133
|
0 |
0 |
if ($$array[$cur][1] < $value) { } |
|
1158
|
0 |
0 |
if $_ =~ /^\>/ |