| line |
true |
false |
branch |
|
477
|
1 |
3 |
if ($key eq 'IGNORE_TAGS') |
|
563
|
5 |
70 |
if ($line =~ /^>(.*?)$/) |
|
565
|
4 |
1 |
if ($currid ne '') |
|
570
|
4 |
0 |
if (defined $fh2) |
|
573
|
5 |
60 |
if ($line2 =~ /^>(.*?)$/) |
|
575
|
1 |
4 |
if ($currscoreid eq '') |
|
576
|
0 |
4 |
if ($currid ne $currscoreid) |
|
580
|
56 |
4 |
if ($scores ne '') |
|
585
|
0 |
4 |
if ($scores eq '') |
|
586
|
0 |
4 |
if ($this->process_read($currseq, $scores) == 0) |
|
589
|
0 |
0 |
defined $scores ? : |
|
603
|
1 |
0 |
if ($currid ne '') |
|
608
|
1 |
0 |
if (defined $fh2) |
|
611
|
0 |
10 |
if ($line2 =~ /^>(.*?)$/) |
|
613
|
0 |
0 |
if ($currscoreid eq '') |
|
614
|
0 |
0 |
if ($currid ne $currscoreid) |
|
618
|
9 |
1 |
if ($scores ne '') |
|
623
|
0 |
1 |
if ($scores eq '') |
|
624
|
0 |
1 |
if ($this->process_read($currseq, $scores) == 0) |
|
689
|
0 |
5 |
unless (defined $read_sequence) |
|
690
|
0 |
5 |
if ($read_sequence eq '') |
|
692
|
0 |
5 |
if ($Bio::SAGE::DataProcessing::DEBUG >= 1) |
|
739
|
0 |
2 |
if ($$this{'keep_duplicates'} == 1) |
|
796
|
0 |
122 |
if ($$this{'keep_duplicates'} == 1) { } |
|
805
|
0 |
122 |
if ($scores eq '') |
|
812
|
0 |
244 |
if ($ignoreTag eq $tag1) |
|
817
|
0 |
122 |
if ($bIgnore == 1) { } |
|
820
|
0 |
122 |
if (not $tag1 =~ /^[ACGT]+$/) { } |
|
824
|
122 |
0 |
if ($scores ne '') |
|
827
|
120 |
2 |
if ($$this{'tag_filter'}->is_valid($tag1, $tagScores)) { } |
|
841
|
0 |
244 |
if ($ignoreTag eq $tag2) |
|
846
|
0 |
122 |
if ($bIgnore == 1) { } |
|
849
|
0 |
122 |
if (not $tag2 =~ /^[ACGT]+$/) { } |
|
853
|
122 |
0 |
if ($scores ne '') |
|
857
|
122 |
0 |
if ($$this{'tag_filter'}->is_valid($tag2, $tagScores)) { } |
|
1009
|
61 |
0 |
if ($minLength <= length $ditag and length $ditag <= $maxLength) |
|
1021
|
61 |
0 |
if ($minLength <= length $ditag and length $ditag <= $maxLength) |
|
1165
|
1 |
0 |
unless ($tag =~ /^$enzyme/ and length $tag == $$this{'protocol'}{'TAG_LENGTH'} + length($enzyme)) |
|
1166
|
1 |
0 |
if (length $tag == $$this{'protocol'}{'TAG_LENGTH'}) { } |
|
1182
|
0 |
61 |
if ($minDitagLength >= length $ditag) |
|
1186
|
1 |
60 |
if ($ditag =~ /^$tag/) |
|
1190
|
1 |
59 |
if ($ditag =~ /$revtag$/) |
|
1313
|
5 |
0 |
if (defined $read_scores) |
|
1318
|
0 |
5 |
if ($Bio::SAGE::DataProcessing::DEBUG >= 1) |
|
1340
|
3 |
98 |
unless ($ditag_sequence =~ /^[ACGT]+$/) |
|
1344
|
4 |
94 |
if (length $ditag_sequence < $minLength) |
|
1348
|
4 |
90 |
if (length $ditag_sequence > $maxLength) |
|
1353
|
90 |
0 |
if (defined $read_scores) |
|
1356
|
29 |
61 |
unless ($$this{'ditag_filter'}->is_valid($ditag_sequence, $ditag_scores)) |
|
1362
|
0 |
61 |
if (defined ${$$this{'ditags'};}{$ditag_sequence} and $$this{'keep_duplicates'} == 0) |
|
1364
|
0 |
0 |
if (defined $read_scores) |
|
1366
|
0 |
0 |
if ($result <= -1) |
|
1375
|
0 |
61 |
if ($$this{'keep_duplicates'} == 1) |