| line |
true |
false |
branch |
|
263
|
0 |
0 |
if (load_config_file($config_file_path) != 1) |
|
270
|
0 |
0 |
if (defined $insertion_directory) |
|
274
|
0 |
0 |
if (defined $loh_directory) |
|
286
|
0 |
0 |
if (scalar @cnv_files == 0 or scalar @trans_files == 0) |
|
290
|
0 |
0 |
if (defined $insertion_directory) |
|
294
|
0 |
0 |
if (defined $loh_directory) |
|
303
|
0 |
0 |
if (scalar @insertion_files == 0) { } |
|
310
|
0 |
0 |
if (scalar @loh_files == 0) { } |
|
319
|
0 |
0 |
unless -d "$output_directory" |
|
322
|
0 |
0 |
unless (-e $output_directory) |
|
335
|
0 |
0 |
if (defined $insertion_directory) |
|
346
|
0 |
0 |
if (defined $loh_directory) |
|
357
|
0 |
0 |
if ($size % 2 != 0) |
|
433
|
0 |
0 |
if ($argv[0] eq '--help') { } |
|
443
|
0 |
0 |
if ($argv[$pos] eq '--cnv') { } |
|
446
|
0 |
0 |
unless (substr($$cnv_directory_ref, -1, 1) eq '/') |
|
456
|
0 |
0 |
if ($argv[$pos] eq '--trans') { } |
|
459
|
0 |
0 |
unless (substr($$trans_directory_ref, -1, 1) eq '/') |
|
468
|
0 |
0 |
if ($argv[$pos] eq '--insrt') |
|
471
|
0 |
0 |
unless (substr($$insertion_directory_ref, -1, 1) eq '/') |
|
478
|
0 |
0 |
if ($argv[$pos] eq '--loh') |
|
481
|
0 |
0 |
unless (substr($$loh_directory_ref, -1, 1) eq '/') |
|
488
|
0 |
0 |
if ($argv[$pos] eq '--tp53') |
|
493
|
0 |
0 |
if ($argv[$pos] eq '--config') { } |
|
502
|
0 |
0 |
if ($argv[$pos] eq '--output') { } |
|
505
|
0 |
0 |
unless (substr($$output_directory_ref, -1, 1) eq '/') |
|
514
|
0 |
0 |
if ($pos != $ARGC - 1) |
|
595
|
1 |
10 |
if ($#cnv_files == -1) |
|
601
|
1 |
15 |
unless open $CURRENT_FILE, '<', $file |
|
604
|
0 |
15 |
if (eof $CURRENT_FILE) |
|
614
|
1 |
14 |
unless ($line =~ /^#chr\tstart\tend\tnumber\tquality$/) |
|
626
|
1 |
835 |
unless ($line =~ /^(chr)?(1[0-9]|2[0-2]|X|Y|[1-9])\t[0-9]+\t[0-9]+\t[0-9]+\t([0-9]+|\.)$/) |
|
645
|
6 |
1 |
unless -d "$output_directory" . 'TP53' |
|
646
|
0 |
7 |
unless (-e "$output_directory" . 'TP53') |
|
651
|
0 |
7 |
unless open $TP53_FILE, '>', "$output_directory" . 'TP53/TP53.spc' |
|
665
|
0 |
739 |
unless ($file_data[$n][0] =~ /^(chr)?(1[0-9]|2[0-2]|X|Y|[1-9])$/) |
|
692
|
0 |
0 |
if (not defined @{$genome_hash{$source_chr};}[$index]) { } |
|
705
|
739 |
0 |
if (not defined @{$genome_cnv_data{$chr};}[$start_index]) { } |
|
719
|
738 |
1 |
if (not defined @{$genome_cnv_data{$chr};}[$end_index]) { } |
|
731
|
37 |
672 |
if ($chr ne 'X' and $chr ne 'Y' and $chr == 17) |
|
735
|
1 |
36 |
if ($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] <= $TP53_end) |
|
746
|
4 |
1 |
if ($i != scalar(@{$file_data[$n];}) - 1) |
|
794
|
2862 |
52794 |
if ($file_data[$n][0] eq $file_data[$k][0]) |
|
797
|
96 |
2766 |
if ($file_data[$n][2] >= $file_data[$k][1] and $file_data[$n][2] <= $file_data[$k][2]) |
|
802
|
78 |
2784 |
if ($file_data[$n][1] >= $file_data[$k][1] and $file_data[$n][1] <= $file_data[$k][2]) |
|
807
|
96 |
2766 |
if ($start_overlap == 1 or $end_overlap == 1) { } |
|
|
0 |
3252 |
elsif ($file_data[$n][1] <= $file_data[$k][1] and $file_data[$n][2] >= $file_data[$k][2]) { } |
|
810
|
0 |
96 |
if ($type eq 'trans') |
|
815
|
0 |
96 |
if ($type eq 'loh') |
|
821
|
0 |
96 |
if ($type eq 'cnv' and $file_data[$n][3] != $file_data[$k][3]) { } |
|
|
0 |
96 |
elsif ($collapse_regions == 0) { } |
|
|
96 |
0 |
elsif ($collapse_regions == 1) { } |
|
838
|
78 |
18 |
if ($start_overlap == 1 and $end_overlap == 1) { } |
|
|
0 |
18 |
elsif ($start_overlap == 1) { } |
|
|
18 |
0 |
elsif ($end_overlap == 1) { } |
|
853
|
96 |
0 |
if ($start_overlap == 1 or $end_overlap == 1) |
|
867
|
0 |
0 |
if ($type eq 'trans') |
|
871
|
0 |
0 |
if ($type eq 'loh') |
|
876
|
0 |
0 |
if ($type eq 'cnv' and $file_data[$n][3] != $file_data[$k][3]) { } |
|
|
0 |
0 |
elsif ($collapse_regions == 0) { } |
|
|
0 |
0 |
elsif ($collapse_regions == 1) { } |
|
980
|
1 |
9 |
if ($#trans_files == -1) |
|
986
|
0 |
14 |
unless open $CURRENT_FILE, '<', $file |
|
989
|
1 |
13 |
if (eof $CURRENT_FILE) |
|
999
|
1 |
12 |
unless ($line =~ /^#chr1\tstart\tend\tchr2\tstart\tend\tquality$/) |
|
1011
|
1 |
741 |
unless ($line =~ /^(chr)?(1[0-9]|2[0-2]|X|Y|[1-9])\t[0-9]+\t[0-9]+\t(chr)?(1[0-9]|2[0-2]|X|Y|[1-9])\t[0-9]+\t[0-9]+\t([0-9]+|\.)$/) |
|
1020
|
240 |
501 |
if ($line_data[1] >= $line_data[2] or $line_data[4] >= $line_data[5]) |
|
1040
|
2 |
4 |
unless -d "$output_directory" . 'TP53' |
|
1041
|
0 |
6 |
unless (-e "$output_directory" . 'TP53') |
|
1046
|
0 |
6 |
unless open $TP53_FILE, '>', "$output_directory" . 'TP53/TP53.spt' |
|
1061
|
0 |
741 |
unless ($file_data[$n][0] =~ /^(chr)?(1[0-9]|2[0-2]|X|Y|[1-9])$/) |
|
1069
|
0 |
741 |
unless ($file_data[$n][3] =~ /^(chr)?(1[0-9]|2[0-2]|X|Y|[1-9])$/) |
|
1095
|
0 |
0 |
if (not defined @{$genome_hash{$source_chr};}[$index]) { } |
|
1109
|
516 |
225 |
if (not defined @{$genome_trans_data{$chr1};}[$start_index1]) { } |
|
1120
|
275 |
466 |
if (not defined @{$genome_trans_data{$chr1};}[$end_index1]) { } |
|
1131
|
361 |
380 |
if (not defined @{$genome_trans_data{$chr2};}[$start_index2]) { } |
|
1142
|
160 |
581 |
if (not defined @{$genome_trans_data{$chr2};}[$end_index2]) { } |
|
1155
|
316 |
425 |
if ($chr1 ne $chr2) |
|
1167
|
1 |
735 |
if ($chr1 ne 'X' and $chr1 ne 'Y' and $chr1 == 17) |
|
1171
|
1 |
0 |
if ($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] <= $TP53_end) |
|
1180
|
6 |
1 |
if ($i != scalar(@{$file_data[$n];}) - 1) |
|
1188
|
0 |
741 |
if ($chr2 ne 'X' and $chr2 ne 'Y' and $chr2 == 17) |
|
1192
|
0 |
0 |
if ($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] <= $TP53_end) |
|
1199
|
0 |
0 |
if ($i != scalar(@{$file_data[$n];}) - 1) |
|
1301
|
0 |
0 |
unless -d "$output_directory" . 'TP53' |
|
1302
|
0 |
0 |
unless (-e "$output_directory" . 'TP53') |
|
1313
|
0 |
0 |
unless open $CURRENT_FILE, '<', $file |
|
1316
|
0 |
0 |
if (eof $CURRENT_FILE) |
|
1321
|
0 |
0 |
unless open $TP53_FILE, '>', "$output_directory" . "TP53/$file_name" . "$suffix" |
|
1339
|
0 |
0 |
if (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 $line_data[3]) |
|
1346
|
0 |
0 |
unless ($line) |
|
1355
|
0 |
0 |
if ($chr eq 'x') |
|
1358
|
0 |
0 |
if ($chr eq 'y') |
|
1367
|
0 |
0 |
if (not defined @{$genome_insertion_data{$chr};}[int $line_data[1] / $bin_size]) { } |
|
1378
|
0 |
0 |
if ($line_data[1] < $bp + 10 and $line_data[1] > $bp - 10) |
|
1384
|
0 |
0 |
if ($chr ne 'X' and $chr ne 'Y' and $chr == 17) |
|
1388
|
0 |
0 |
if ($line_data[1] >= $TP53_start and $line_data[1] <= $TP53_end) |
|
1399
|
0 |
0 |
unless ($line) |
|
1408
|
0 |
0 |
if ($insertion_found != 1) |
|
1484
|
0 |
0 |
unless open $CURRENT_FILE, '<', $file |
|
1487
|
0 |
0 |
if (eof $CURRENT_FILE) |
|
1497
|
0 |
0 |
unless ($line =~ /^#chr\tstart\tend\tquality$/) |
|
1510
|
0 |
0 |
unless ($line =~ /^(chr)?(1[0-9]|2[0-2]|X|Y|[1-9])\t[0-9]+\t[0-9]+\t([0-9]+|\.)$/) |
|
1527
|
0 |
0 |
unless -d "$output_directory" . 'TP53' |
|
1528
|
0 |
0 |
unless (-e "$output_directory" . 'TP53') |
|
1533
|
0 |
0 |
unless open $TP53_FILE, '>', "$output_directory" . 'TP53/TP53.spl' |
|
1541
|
0 |
0 |
unless ($file_data[$n][0] =~ /^(chr)?(1[0-9]|2[0-2]|X|Y|[1-9])$/) |
|
1553
|
0 |
0 |
if ($chr ne 'X' and $chr ne 'Y' and $chr == 17) |
|
1557
|
0 |
0 |
if ($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] <= $TP53_end) |
|
1567
|
0 |
0 |
if ($i != scalar(@{$file_data[$n];}) - 1) |
|
1638
|
0 |
2 |
unless open $OUTPUT_FILE, '>', "$output_directory/genome_localization.log" |
|
1806
|
2 |
0 |
unless -d "$output_directory" |
|
1807
|
0 |
2 |
unless (-e "$output_directory") |
|
1811
|
2 |
0 |
unless -d "$output_directory/cnv" |
|
1812
|
0 |
2 |
unless (-e "$output_directory") |
|
1816
|
2 |
0 |
unless -d "$output_directory/translocations" |
|
1817
|
0 |
2 |
unless (-e "$output_directory") |
|
1821
|
2 |
0 |
unless -d "$output_directory/all_types" |
|
1822
|
0 |
2 |
unless (-e "$output_directory") |
|
1832
|
40 |
0 |
if (scalar @current_chr_data > 0) |
|
1835
|
0 |
40 |
unless open $OUTPUT_FILE, '>', "$output_directory/cnv/chr$cnv_key" . '_cnv_localization.log' |
|
1844
|
399924 |
76 |
unless (defined $current_chr_data[$chr_pos]) |
|
1861
|
0 |
40 |
if (not defined @{$genome_cnv_data_windows{$cnv_key};}[0]) { } |
|
1875
|
24 |
4391040 |
if (($chr_pos + ($window_size - 1)) * $bin_size > $chromosome_length{$cnv_key}) |
|
1888
|
392 |
4390648 |
if (defined $current_chr_data[$chr_pos - 1]) |
|
1894
|
392 |
4390648 |
if (defined $current_chr_data[$chr_pos + ($window_size - 1)]) |
|
1911
|
0 |
4391040 |
if (not defined @{$genome_cnv_data_windows{$cnv_key};}[$chr_pos]) { } |
|
1935
|
26 |
0 |
if (scalar @current_chr_data > 0) |
|
1938
|
0 |
26 |
unless open $OUTPUT_FILE, '>', "$output_directory/translocations/chr$trans_key" . '_translocation_localization.log' |
|
1948
|
259970 |
30 |
unless (defined $current_chr_data[$chr_pos]) |
|
1958
|
20 |
10 |
if (defined $region_hash{'in'}) |
|
1969
|
18 |
12 |
if (defined $region_hash{'out'}) |
|
1973
|
18 |
0 |
if ($key eq $trans_key) |
|
1993
|
0 |
26 |
if (not defined @{$genome_trans_data_windows{$trans_key};}[0]) { } |
|
2006
|
10 |
2520282 |
if (($chr_pos + ($window_size - 1)) * $bin_size > $chromosome_length{$trans_key}) |
|
2018
|
428 |
2519854 |
if (defined $current_chr_data[$chr_pos - 1]) |
|
2025
|
234 |
194 |
if (defined $prev_region_hash{'in'}) |
|
2035
|
278 |
150 |
if (defined $prev_region_hash{'out'}) |
|
2039
|
184 |
100 |
if ($key eq $trans_key) |
|
2051
|
456 |
2519826 |
if (defined $current_chr_data[$chr_pos + ($window_size - 1)]) |
|
2058
|
238 |
218 |
if (defined $next_region_hash{'in'}) |
|
2068
|
306 |
150 |
if (defined $next_region_hash{'out'}) |
|
2072
|
192 |
120 |
if ($key eq $trans_key) |
|
2096
|
0 |
2520282 |
if (not defined @{$genome_trans_data_windows{$trans_key};}[$chr_pos]) { } |
|
2116
|
42 |
6 |
if (scalar @{$genome_mutation_data_windows{$mutation_key};} > 0) |
|
2119
|
0 |
42 |
unless open $OUTPUT_FILE, '>', "$output_directory/all_types/chr$mutation_key" . '_mutation_localization.log' |
|
2130
|
0 |
4775978 |
if (not defined @{$genome_mutation_data_windows{$mutation_key};}[$chr_pos]) { } |
|
2161
|
42 |
6 |
if (scalar @{$genome_mutation_data_windows{$mutation_key};} > 0) |
|
2165
|
0 |
4775978 |
if (not defined @{$genome_mutation_data_windows{$mutation_key};}[$chr_pos]) { } |
|
2184
|
42 |
6 |
if (scalar @{$genome_mutation_data_windows{$mutation_key};} > 0) |
|
2190
|
0 |
4775978 |
if (not defined @{$genome_mutation_data_windows{$mutation_key};}[$chr_pos]) { } |
|
2201
|
88404 |
4687574 |
if ($region_z_score >= $outlier_deviation) { } |
|
|
8 |
4687566 |
elsif ($in_suspect_region == 1) { } |
|
2202
|
8 |
88396 |
if ($in_suspect_region != 1) |
|
2219
|
66812 |
4709166 |
if ($region_z_score < $outlier_deviation and $region_z_score >= $outlier_deviation - 1) { } |
|
|
24 |
4709142 |
elsif ($in_likely_region == 1) { } |
|
2223
|
26 |
66786 |
if ($in_likely_region != 1) |
|
2241
|
0 |
42 |
if ($in_suspect_region == 1) |
|
2249
|
2 |
40 |
if ($in_likely_region == 1) |
|
2289
|
0 |
1 |
unless open $OUTPUT_FILE, '>', "$output_directory/copy_number_count.log" |
|
2339
|
0 |
1 |
unless open $OUTPUT_FILE, '>', "$output_directory/copy_number_switches.log" |
|
2352
|
80 |
0 |
if ($CN != 2) |
|
2395
|
0 |
1 |
unless open $OUTPUT_FILE, '>', "$output_directory/interchromosomal_translocation_rate.log" |
|
2490
|
0 |
0 |
if ($suspect_regions_size % 3 != 0) |
|
2495
|
0 |
0 |
unless -d "$output_directory" . 'suspect_regions' |
|
2496
|
0 |
0 |
unless (-e "$output_directory" . 'suspect_regions') |
|
2501
|
0 |
0 |
unless open $OUTPUT_FILE, '>', "$output_directory" . 'suspect_regions/suspect_regions.yml' |
|
2555
|
0 |
0 |
if (defined $cnv_number_hash_ref) { } |
|
2569
|
0 |
0 |
if (defined $intertranslocation_hash_ref) { } |
|
2580
|
0 |
0 |
if (defined $breakpoint_insertions_array_ref) |
|
2588
|
0 |
0 |
if (defined $loh_size and defined $hz_size) |
|
2621
|
0 |
0 |
if ($num_copy_num > 0) |
|
2635
|
0 |
0 |
if ($num_trans_chr > 0) |
|
2645
|
0 |
0 |
if (defined $breakpoint_insertions_array_ref) |
|
2653
|
0 |
0 |
if ($loh_size != -1) |
|
2661
|
0 |
0 |
if ($tp53_mutated and $tp53_mutation_found) { } |
|
|
0 |
0 |
elsif ($tp53_mutated) { } |
|
|
0 |
0 |
elsif ($tp53_mutation_found) { } |
|
2730
|
0 |
1 |
if ($likely_regions_size % 3 != 0) |
|
2736
|
1 |
0 |
unless -d "$output_directory" . 'suspect_regions' |
|
2737
|
0 |
1 |
unless (-e "$output_directory" . 'suspect_regions') |
|
2742
|
0 |
1 |
unless open $OUTPUT_FILE, '>', "$output_directory" . 'suspect_regions/likely_regions.log' |
|
2860
|
0 |
0 |
if (defined $genome_trans_insertion_breakpoints_hash_ref) |
|
2866
|
0 |
0 |
if (defined $chromosome_loh_breakpoints_hash_ref) |
|
2936
|
0 |
0 |
if (defined $genome_cnv_data_hash{$chr}) |
|
2943
|
0 |
0 |
unless (defined $chr_data[$i]) |
|
2949
|
0 |
0 |
if ($key eq 'BPcount') { } |
|
2968
|
0 |
0 |
if (scalar keys %cnv_number_hash == 0) |
|
2985
|
0 |
0 |
if ($SD == 0 or ($cnv_number_hash{$key} - $mean) / $SD >= -1 * $outlier_deviation) |
|
3056
|
0 |
0 |
if ($mean_density == 0 or $standard_deviation == 0) |
|
3070
|
0 |
0 |
if ($z_score < 0) |
|
3139
|
12 |
1 |
if (defined $genome_cnv_data_hash{$chr}) |
|
3145
|
145301 |
34 |
unless (defined $chr_data[$i]) |
|
3157
|
13 |
0 |
if (defined $genome_trans_data_hash{$chr}) |
|
3163
|
163313 |
93 |
unless (defined $chr_data[$i]) |
|
3258
|
0 |
0 |
if (defined $genome_trans_data_hash{$chr}) |
|
3265
|
0 |
0 |
unless (defined $chr_data[$i]) |
|
3273
|
0 |
0 |
if (defined $trans_hash{'in'}) |
|
3291
|
0 |
0 |
if (defined $trans_hash{'out'}) |
|
3297
|
0 |
0 |
if ($key eq $chr) |
|
3299
|
0 |
0 |
if ($val > $start and $val < $end) |
|
3319
|
0 |
0 |
if (keys %trans_number_hash == 0) |
|
3344
|
0 |
0 |
if ($SD == 0 or ($trans_number_hash{$key} - $mean) / $SD > -1 * $outlier_deviation) |
|
3376
|
0 |
0 |
if ($size == 1) { } |
|
3386
|
0 |
0 |
if ($SD == 0 or ($val - $mean) / $SD < $outlier_deviation) |
|
3402
|
0 |
0 |
if ($spread_factor == 0) |
|
3420
|
0 |
0 |
if ($size < $translocation_cut_off_count and $size > 2) |
|
3423
|
0 |
0 |
if ($size >= $translocation_cut_off_count) |
|
3427
|
0 |
0 |
if ($translocation_score >= 1) |
|
3496
|
0 |
0 |
if (defined $genome_trans_data_hash{$chr}) |
|
3503
|
0 |
0 |
unless (defined $chr_data[$i]) |
|
3520
|
0 |
0 |
if ($breakpoint > $end) |
|
3523
|
0 |
0 |
if ($breakpoint > $start) |
|
3529
|
0 |
0 |
if ($total_breakpoints > 0) |
|
3533
|
0 |
0 |
if ($insertion_breakpoint_score > 1) |
|
3594
|
0 |
0 |
unless (defined $chromosome_cnv_breakpoints_hash{$chr} and defined $chromosome_loh_breakpoints_hash{$chr}) |
|
3624
|
0 |
0 |
if ($cnv_breakpoints[$cnv_start] > $end) |
|
3629
|
0 |
0 |
if ($cnv_breakpoints[$cnv_end] >= $start and $cnv_breakpoints[$cnv_end] <= $end) |
|
3634
|
0 |
0 |
if ($cnv_breakpoints[$cnv_start] >= $start and $cnv_breakpoints[$cnv_start] <= $end) |
|
3639
|
0 |
0 |
if ($start_overlap == 1 and $end_overlap == 1) { } |
|
|
0 |
0 |
elsif ($start_overlap == 1) { } |
|
|
0 |
0 |
elsif ($end_overlap == 1) { } |
|
|
0 |
0 |
elsif ($cnv_breakpoints[$cnv_start] < $start and $cnv_breakpoints[$cnv_end] > $end) { } |
|
3655
|
0 |
0 |
if ($remaining_heterozygous_size == 0 or $remaining_heterozygous_size == $original_heterozygous_size) |
|
3685
|
0 |
0 |
if ($loh_breakpoints[$loh_start] > $end) |
|
3690
|
0 |
0 |
if ($loh_breakpoints[$loh_end] >= $start and $loh_breakpoints[$loh_end] <= $end) |
|
3695
|
0 |
0 |
if ($loh_breakpoints[$loh_start] >= $start and $loh_breakpoints[$loh_start] <= $end) |
|
3700
|
0 |
0 |
if ($start_overlap_region_loh == 1 and $end_overlap_region_loh != 1) { } |
|
|
0 |
0 |
elsif ($end_overlap_region_loh == 1 and $start_overlap_region_loh != 1) { } |
|
|
0 |
0 |
elsif ($loh_breakpoints[$loh_start] < $start and $loh_breakpoints[$loh_end] > $end) { } |
|
3712
|
0 |
0 |
if ($start_overlap_region_loh != 1 and $end_overlap_region_loh != 1) |
|
3728
|
0 |
0 |
if ($cnv_breakpoints[$cnv_start] > $loh_end_breakpoint) |
|
3733
|
0 |
0 |
if ($cnv_breakpoints[$cnv_end] >= $loh_start_breakpoint and $cnv_breakpoints[$cnv_end] <= $loh_end_breakpoint) |
|
3738
|
0 |
0 |
if ($cnv_breakpoints[$cnv_start] >= $loh_start_breakpoint and $cnv_breakpoints[$cnv_start] <= $loh_end_breakpoint) |
|
3743
|
0 |
0 |
if ($start_overlap_loh_cnv == 1 and $end_overlap_loh_cnv == 1) { } |
|
|
0 |
0 |
elsif ($start_overlap_loh_cnv == 1) { } |
|
|
0 |
0 |
elsif ($end_overlap_loh_cnv == 1) { } |
|
|
0 |
0 |
elsif ($cnv_breakpoints[$cnv_start] < $loh_start_breakpoint and $cnv_breakpoints[$cnv_end] > $loh_end_breakpoint) { } |
|
3763
|
0 |
0 |
if ($loh_size > $remaining_heterozygous_size) |
|
3798
|
5 |
6 |
if ($type == 0) { } |
|
|
5 |
1 |
elsif ($type == 1) { } |
|
3801
|
1 |
2 |
if (scalar keys %hash == 0) |
|
3825
|
1 |
2 |
if ($size == 0) |
|
3860
|
0 |
0 |
if ($pos == $ARGC) |
|
3972
|
0 |
8 |
unless open $CONFIG, '<', "$path" |