| line |
!l |
l&&!r |
l&&r |
condition |
|
731
|
30 |
18 |
691 |
$chr ne 'X' and $chr ne 'Y' |
|
|
48 |
654 |
37 |
$chr ne 'X' and $chr ne 'Y' and $chr == 17 |
|
735
|
0 |
37 |
0 |
$file_data[$n][3] != 2 and $file_data[$n][1] >= $TP53_start && $file_data[$n][1] <= $TP53_end || $file_data[$n][2] >= $TP53_start && $file_data[$n][2] <= $TP53_end |
|
797
|
2280 |
486 |
96 |
$file_data[$n][2] >= $file_data[$k][1] and $file_data[$n][2] <= $file_data[$k][2] |
|
802
|
2298 |
486 |
78 |
$file_data[$n][1] >= $file_data[$k][1] and $file_data[$n][1] <= $file_data[$k][2] |
|
807
|
486 |
2280 |
0 |
$file_data[$n][1] <= $file_data[$k][1] and $file_data[$n][2] >= $file_data[$k][2] |
|
821
|
0 |
96 |
0 |
$type eq 'cnv' and $file_data[$n][3] != $file_data[$k][3] |
|
838
|
18 |
0 |
78 |
$start_overlap == 1 and $end_overlap == 1 |
|
876
|
0 |
0 |
0 |
$type eq 'cnv' and $file_data[$n][3] != $file_data[$k][3] |
|
1167
|
5 |
105 |
631 |
$chr1 ne 'X' and $chr1 ne 'Y' |
|
|
110 |
630 |
1 |
$chr1 ne 'X' and $chr1 ne 'Y' and $chr1 == 17 |
|
1171
|
0 |
0 |
1 |
$file_data[$n][1] >= $TP53_start and $file_data[$n][1] <= $TP53_end |
|
|
0 |
0 |
0 |
$file_data[$n][2] >= $TP53_start and $file_data[$n][2] <= $TP53_end |
|
1188
|
0 |
376 |
365 |
$chr2 ne 'X' and $chr2 ne 'Y' |
|
|
376 |
365 |
0 |
$chr2 ne 'X' and $chr2 ne 'Y' and $chr2 == 17 |
|
1192
|
0 |
0 |
0 |
$file_data[$n][4] >= $TP53_start and $file_data[$n][4] <= $TP53_end |
|
|
0 |
0 |
0 |
$file_data[$n][5] >= $TP53_start and $file_data[$n][5] <= $TP53_end |
|
1339
|
0 |
0 |
0 |
$line_data[1] =~ /^[0-9]+$/ && $line_data[0] =~ /^(chr)?(1[0-9]|2[0-2]|X|Y|x|y|[1-9])/ |
|
1378
|
0 |
0 |
0 |
$line_data[1] < $bp + 10 and $line_data[1] > $bp - 10 |
|
1384
|
0 |
0 |
0 |
$chr ne 'X' and $chr ne 'Y' |
|
|
0 |
0 |
0 |
$chr ne 'X' and $chr ne 'Y' and $chr == 17 |
|
1388
|
0 |
0 |
0 |
$line_data[1] >= $TP53_start and $line_data[1] <= $TP53_end |
|
1553
|
0 |
0 |
0 |
$chr ne 'X' and $chr ne 'Y' |
|
|
0 |
0 |
0 |
$chr ne 'X' and $chr ne 'Y' and $chr == 17 |
|
1557
|
0 |
0 |
0 |
$file_data[$n][1] >= $TP53_start and $file_data[$n][1] <= $TP53_end |
|
|
0 |
0 |
0 |
$file_data[$n][2] >= $TP53_start and $file_data[$n][2] <= $TP53_end |
|
2219
|
88404 |
4620762 |
66812 |
$region_z_score < $outlier_deviation and $region_z_score >= $outlier_deviation - 1 |
|
2588
|
0 |
0 |
0 |
defined $loh_size and defined $hz_size |
|
2661
|
0 |
0 |
0 |
$tp53_mutated and $tp53_mutation_found |
|
3299
|
0 |
0 |
0 |
$val > $start and $val < $end |
|
3420
|
0 |
0 |
0 |
$size < $translocation_cut_off_count and $size > 2 |
|
3592
|
0 |
0 |
0 |
defined $chromosome_cnv_breakpoints_hash{$chr} and defined $chromosome_loh_breakpoints_hash{$chr} |
|
3627
|
0 |
0 |
0 |
$cnv_breakpoints[$cnv_end] >= $start and $cnv_breakpoints[$cnv_end] <= $end |
|
3632
|
0 |
0 |
0 |
$cnv_breakpoints[$cnv_start] >= $start and $cnv_breakpoints[$cnv_start] <= $end |
|
3637
|
0 |
0 |
0 |
$start_overlap == 1 and $end_overlap == 1 |
|
|
0 |
0 |
0 |
$cnv_breakpoints[$cnv_start] < $start and $cnv_breakpoints[$cnv_end] > $end |
|
3688
|
0 |
0 |
0 |
$loh_breakpoints[$loh_end] >= $start and $loh_breakpoints[$loh_end] <= $end |
|
3693
|
0 |
0 |
0 |
$loh_breakpoints[$loh_start] >= $start and $loh_breakpoints[$loh_start] <= $end |
|
3698
|
0 |
0 |
0 |
$start_overlap_region_loh == 1 and $end_overlap_region_loh != 1 |
|
|
0 |
0 |
0 |
$end_overlap_region_loh == 1 and $start_overlap_region_loh != 1 |
|
|
0 |
0 |
0 |
$loh_breakpoints[$loh_start] < $start and $loh_breakpoints[$loh_end] > $end |
|
3710
|
0 |
0 |
0 |
$start_overlap_region_loh != 1 and $end_overlap_region_loh != 1 |
|
3731
|
0 |
0 |
0 |
$cnv_breakpoints[$cnv_end] >= $loh_start_breakpoint and $cnv_breakpoints[$cnv_end] <= $loh_end_breakpoint |
|
3736
|
0 |
0 |
0 |
$cnv_breakpoints[$cnv_start] >= $loh_start_breakpoint and $cnv_breakpoints[$cnv_start] <= $loh_end_breakpoint |
|
3741
|
0 |
0 |
0 |
$start_overlap_loh_cnv == 1 and $end_overlap_loh_cnv == 1 |
|
|
0 |
0 |
0 |
$cnv_breakpoints[$cnv_start] < $loh_start_breakpoint and $cnv_breakpoints[$cnv_end] > $loh_end_breakpoint |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
286
|
0 |
0 |
0 |
scalar @cnv_files == 0 or scalar @trans_files == 0 |
|
735
|
1 |
0 |
36 |
$file_data[$n][1] >= $TP53_start && $file_data[$n][1] <= $TP53_end || $file_data[$n][2] >= $TP53_start && $file_data[$n][2] <= $TP53_end |
|
807
|
78 |
18 |
2766 |
$start_overlap == 1 or $end_overlap == 1 |
|
853
|
78 |
18 |
0 |
$start_overlap == 1 or $end_overlap == 1 |
|
1020
|
240 |
0 |
501 |
$line_data[1] >= $line_data[2] or $line_data[4] >= $line_data[5] |
|
1171
|
1 |
0 |
0 |
$file_data[$n][1] >= $TP53_start and $file_data[$n][1] <= $TP53_end or $file_data[$n][2] >= $TP53_start and $file_data[$n][2] <= $TP53_end |
|
1192
|
0 |
0 |
0 |
$file_data[$n][4] >= $TP53_start and $file_data[$n][4] <= $TP53_end or $file_data[$n][5] >= $TP53_start and $file_data[$n][5] <= $TP53_end |
|
1339
|
0 |
0 |
0 |
not $line_data[1] =~ /^[0-9]+$/ && $line_data[0] =~ /^(chr)?(1[0-9]|2[0-2]|X|Y|x|y|[1-9])/ or length $line_data[4] <= length $line_data[3] |
|
1557
|
0 |
0 |
0 |
$file_data[$n][1] >= $TP53_start and $file_data[$n][1] <= $TP53_end or $file_data[$n][2] >= $TP53_start and $file_data[$n][2] <= $TP53_end |
|
2985
|
0 |
0 |
0 |
$SD == 0 or ($cnv_number_hash{$key} - $mean) / $SD >= -1 * $outlier_deviation |
|
3056
|
0 |
0 |
0 |
$mean_density == 0 or $standard_deviation == 0 |
|
3344
|
0 |
0 |
0 |
$SD == 0 or ($trans_number_hash{$key} - $mean) / $SD > -1 * $outlier_deviation |
|
3386
|
0 |
0 |
0 |
$SD == 0 or ($val - $mean) / $SD < $outlier_deviation |
|
3653
|
0 |
0 |
0 |
$remaining_heterozygous_size == 0 or $remaining_heterozygous_size == $original_heterozygous_size |