| line |
true |
false |
branch |
|
189
|
0 |
0 |
if ($_ =~ /^-reference$/) { } |
|
203
|
0 |
0 |
if ($line_num % 2 != 0) |
|
204
|
0 |
0 |
unless ($_ =~ /^>\S+$/) |
|
208
|
0 |
0 |
if ($line_num % 2 == 0) |
|
209
|
0 |
0 |
unless ($_ =~ /^[AGTCNRYMKSWHBVD]+$/i) |
|
232
|
0 |
0 |
if ($_ =~ /^-front_enzyme$/) { } |
|
|
0 |
0 |
elsif ($_ =~ /^-behind_enzyme$/) { } |
|
246
|
0 |
0 |
if ($_ =~ /^$$self{'enzyme1'}$/i) |
|
249
|
0 |
0 |
if ($_ =~ /^$$self{'enzyme2'}$/i) |
|
253
|
0 |
0 |
if ($enzyme1_exists > 0) { } |
|
258
|
0 |
0 |
if ($enzyme2_exists > 0) { } |
|
285
|
0 |
0 |
if ($_ =~ /^-enzyme_name$/) { } |
|
|
0 |
0 |
elsif ($_ =~ /^-recognition_site$/) { } |
|
290
|
0 |
0 |
unless ($new_enzyme_site =~ /|/) |
|
316
|
0 |
0 |
if ($_ =~ /^-start$/) { } |
|
|
0 |
0 |
elsif ($_ =~ /^-end$/) { } |
|
326
|
0 |
0 |
if ($$self{'range_start'} < $$self{'range_end'}) { } |
|
346
|
0 |
0 |
if ($_ =~ /^-front$/) { } |
|
|
0 |
0 |
elsif ($_ =~ /^-behind$/) { } |
|
|
0 |
0 |
elsif ($_ =~ /^-step$/) { } |
|
375
|
0 |
0 |
if ($_ =~ /^-output_dir$/) { } |
|
382
|
0 |
0 |
if (-d $$self{'output_dir'}) { } |
|
404
|
0 |
0 |
if ($ref) { } |
|
411
|
0 |
0 |
if ($front_enzyme) { } |
|
418
|
0 |
0 |
if ($later_enzyme) { } |
|
428
|
0 |
0 |
if ($output_dir) { } |
|
453
|
0 |
0 |
if ($_ =~ /^$front_enzyme$/i) |
|
456
|
0 |
0 |
if ($_ =~ /^$later_enzyme$/i) |
|
472
|
0 |
0 |
if ($_ =~ /\|/) { } |
|
481
|
0 |
0 |
if ($_ =~ /\|/) { } |
|
492
|
0 |
0 |
if ($_ =~ /N/) |
|
493
|
0 |
0 |
if ($_ =~ /R/) |
|
494
|
0 |
0 |
if ($_ =~ /Y/) |
|
495
|
0 |
0 |
if ($_ =~ /M/) |
|
496
|
0 |
0 |
if ($_ =~ /K/) |
|
497
|
0 |
0 |
if ($_ =~ /S/) |
|
498
|
0 |
0 |
if ($_ =~ /W/) |
|
499
|
0 |
0 |
if ($_ =~ /H/) |
|
500
|
0 |
0 |
if ($_ =~ /B/) |
|
501
|
0 |
0 |
if ($_ =~ /V/) |
|
502
|
0 |
0 |
if ($_ =~ /D/) |
|
511
|
0 |
0 |
if ($_ =~ /N/) |
|
512
|
0 |
0 |
if ($_ =~ /R/) |
|
513
|
0 |
0 |
if ($_ =~ /Y/) |
|
514
|
0 |
0 |
if ($_ =~ /M/) |
|
515
|
0 |
0 |
if ($_ =~ /K/) |
|
516
|
0 |
0 |
if ($_ =~ /S/) |
|
517
|
0 |
0 |
if ($_ =~ /W/) |
|
518
|
0 |
0 |
if ($_ =~ /H/) |
|
519
|
0 |
0 |
if ($_ =~ /B/) |
|
520
|
0 |
0 |
if ($_ =~ /V/) |
|
521
|
0 |
0 |
if ($_ =~ /D/) |
|
542
|
0 |
0 |
if ($_ =~ /^>/) { } |
|
559
|
0 |
0 |
if ($string =~ /^(\w+)$/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\](\w+)/) { } |
|
|
0 |
0 |
elsif ($string =~ /^\[(\w+)\](\w+)\[(\w+)\]$/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\](\w+)\[(\w+)\](\w+)/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\]\[(\w+)\]\[(\w+)\](\w+)/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\]\[(\w+)\](\w+)/) { } |
|
562
|
0 |
0 |
unless ($loc_in_array == -1) |
|
567
|
0 |
0 |
unless ($loc_in_array == -1) |
|
582
|
0 |
0 |
unless ($loc_in_array == -1) |
|
587
|
0 |
0 |
unless ($loc_in_array == -1) |
|
605
|
0 |
0 |
unless ($loc_in_array == -1) |
|
610
|
0 |
0 |
unless ($loc_in_array == -1) |
|
631
|
0 |
0 |
unless ($loc_in_array == -1) |
|
636
|
0 |
0 |
unless ($loc_in_array == -1) |
|
658
|
0 |
0 |
unless ($loc_in_array == -1) |
|
663
|
0 |
0 |
unless ($loc_in_array == -1) |
|
683
|
0 |
0 |
unless ($loc_in_array == -1) |
|
688
|
0 |
0 |
unless ($loc_in_array == -1) |
|
702
|
0 |
0 |
if ($string =~ /^(\w+)$/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\](\w+)/) { } |
|
|
0 |
0 |
elsif ($string =~ /^\[(\w+)\](\w+)\[(\w+)\]$/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\](\w+)\[(\w+)\](\w+)/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\]\[(\w+)\]\[(\w+)\](\w+)/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\]\[(\w+)\](\w+)/) { } |
|
705
|
0 |
0 |
unless ($loc_in_array == -1) |
|
710
|
0 |
0 |
unless ($loc_in_array == -1) |
|
724
|
0 |
0 |
unless ($loc_in_array == -1) |
|
729
|
0 |
0 |
unless ($loc_in_array == -1) |
|
747
|
0 |
0 |
unless ($loc_in_array == -1) |
|
752
|
0 |
0 |
unless ($loc_in_array == -1) |
|
773
|
0 |
0 |
unless ($loc_in_array == -1) |
|
778
|
0 |
0 |
unless ($loc_in_array == -1) |
|
800
|
0 |
0 |
unless ($loc_in_array == -1) |
|
805
|
0 |
0 |
unless ($loc_in_array == -1) |
|
825
|
0 |
0 |
unless ($loc_in_array == -1) |
|
830
|
0 |
0 |
unless ($loc_in_array == -1) |
|
865
|
0 |
0 |
unless ($enzyme_before eq $enzyme_after) |
|
894
|
0 |
0 |
if ($front_enzyme =~ /$before_enzyme/i) { } |
|
|
0 |
0 |
elsif ($later_enzyme =~ /$before_enzyme/i) { } |
|
912
|
0 |
0 |
if ($before_enzyme =~ /$front_enzyme/i) { } |
|
|
0 |
0 |
elsif ($before_enzyme =~ /$later_enzyme/i) { } |
|
918
|
0 |
0 |
if ($length_of_fragment >= $range1) |
|
919
|
0 |
0 |
if ($length_of_fragment <= $range2) |
|
964
|
0 |
0 |
if ($lengths_distribution_tmp == $lengths_distribution_start) { } |
|
|
0 |
0 |
elsif ($lengths_distribution_tmp < $lengths_distribution_end) { } |
|
979
|
0 |
0 |
if ($lengths_distribution_tmp + $lengths_distribution_step < $lengths_distribution_end) { } |
|
|
0 |
0 |
elsif ($lengths_distribution_tmp + $lengths_distribution_step >= $lengths_distribution_end) { } |
|
1018
|
0 |
0 |
if ($num_pair < $num_last_pair) { } |
|
|
0 |
0 |
elsif ($num_pair == $num_last_pair) { } |
|
1019
|
0 |
0 |
if ($length >= $start and $length <= $end) |
|
1028
|
0 |
0 |
if ($length >= $start) |
|
1046
|
0 |
0 |
if ($num_all_frags > 0) { } |
|
1067
|
0 |
0 |
if ($_ =~ /^-SNPs$/) { } |
|
1086
|
0 |
0 |
if (keys %parameters) |
|
1088
|
0 |
0 |
if ($_ =~ /^-sequence_type$/) { } |
|
|
0 |
0 |
elsif ($_ =~ /^-sequence_end$/) { } |
|
1105
|
0 |
0 |
if ($SNPs) { } |
|
1118
|
0 |
0 |
if ($sequence_type =~ /^(\d+)pe$/i) { } |
|
|
0 |
0 |
elsif ($sequence_type =~ /^(\d+)se$/i) { } |
|
1121
|
0 |
0 |
if (not $sequence_length * 2 <= $range1) { } |
|
1131
|
0 |
0 |
if (not $sequence_length <= $range1) { } |
|
1147
|
0 |
0 |
if ($sequence_type_code == 1) |
|
1149
|
0 |
0 |
if ($se_sequence_end =~ /^front_enzyme$/i) { } |
|
|
0 |
0 |
elsif ($se_sequence_end =~ /^behind_enzyme$/i) { } |
|
1195
|
0 |
0 |
if ($sequence_type_code == 1) { } |
|
|
0 |
0 |
elsif ($sequence_type_code == 2) { } |
|
1196
|
0 |
0 |
if ($se_sequence_end_code == 1) { } |
|
|
0 |
0 |
elsif ($se_sequence_end_code == 2) { } |
|
1201
|
0 |
0 |
if ($fragment_name =~ /^>(.+)-(\d+)/) |
|
1204
|
0 |
0 |
if ($SNPs{$scaffold_name}) |
|
1206
|
0 |
0 |
if ($front_enzyme =~ /$enzyme1/i) { } |
|
|
0 |
0 |
elsif ($front_enzyme =~ /$enzyme2/i) { } |
|
1207
|
0 |
0 |
if ($SNP >= $pos1 and $SNP <= $pos1 + $se_sequence_length - 1) |
|
1213
|
0 |
0 |
if ($SNP >= $pos2 - $se_sequence_length + 1 and $SNP <= $pos2) |
|
1227
|
0 |
0 |
if ($fragment_name =~ /^>(.+)-(\d+)/) |
|
1230
|
0 |
0 |
if ($SNPs{$scaffold_name}) |
|
1232
|
0 |
0 |
if ($later_enzyme =~ /$enzyme1/i) { } |
|
|
0 |
0 |
elsif ($later_enzyme =~ /$enzyme2/i) { } |
|
1233
|
0 |
0 |
if ($SNP >= $pos1 and $SNP <= $pos1 + $se_sequence_length - 1) |
|
1239
|
0 |
0 |
if ($SNP >= $pos2 - $se_sequence_length + 1 and $SNP <= $pos2) |
|
1255
|
0 |
0 |
if ($fragment_name =~ /^>(.+)-(\d+)/) |
|
1258
|
0 |
0 |
if ($SNPs{$scaffold_name}) |
|
1260
|
0 |
0 |
if ($SNP >= $pos1 and $SNP <= $pos1 + $pe_sequence_length - 1 or $SNP >= $pos2 - $pe_sequence_length + 1 and $SNP <= $pos2) |
|
1275
|
0 |
0 |
if ($sequence_type_code == 1) { } |
|
|
0 |
0 |
elsif ($sequence_type_code == 2) { } |
|
1276
|
0 |
0 |
if ($se_sequence_end_code == 1) { } |
|
|
0 |
0 |
elsif ($se_sequence_end_code == 2) { } |
|
1281
|
0 |
0 |
if ($fragment_name =~ /^>(.+)-(\d+)/) |
|
1284
|
0 |
0 |
if ($SNPs{$scaffold_name}) |
|
1286
|
0 |
0 |
if ($front_enzyme =~ /$enzyme1/i) { } |
|
|
0 |
0 |
elsif ($front_enzyme =~ /$enzyme2/i) { } |
|
1287
|
0 |
0 |
if ($SNP >= $pos1 and $SNP <= $pos1 + $se_sequence_length - 1) |
|
1293
|
0 |
0 |
if ($SNP >= $pos2 - $se_sequence_length + 1 and $SNP <= $pos2) |
|
1307
|
0 |
0 |
if ($fragment_name =~ /^>(.+)-(\d+)/) |
|
1310
|
0 |
0 |
if ($SNPs{$scaffold_name}) |
|
1312
|
0 |
0 |
if ($later_enzyme =~ /$enzyme1/i) { } |
|
|
0 |
0 |
elsif ($later_enzyme =~ /$enzyme2/i) { } |
|
1313
|
0 |
0 |
if ($SNP >= $pos1 and $SNP <= $pos1 + $se_sequence_length - 1) |
|
1319
|
0 |
0 |
if ($SNP >= $pos2 - $se_sequence_length + 1 and $SNP <= $pos2) |
|
1335
|
0 |
0 |
if ($fragment_name =~ /^>(.+)-(\d+)/) |
|
1338
|
0 |
0 |
if ($SNPs{$scaffold_name}) |
|
1340
|
0 |
0 |
if ($SNP >= $pos1 and $SNP <= $pos1 + $pe_sequence_length - 1 or $SNP >= $pos2 - $pe_sequence_length + 1 and $SNP <= $pos2) |
|
1365
|
0 |
0 |
if ($_ =~ /^-gff$/) { } |
|
1450
|
0 |
0 |
if ($gff) { } |
|
1463
|
0 |
0 |
if ($basename_loc_frags_file =~ /in_range/) { } |
|
1485
|
0 |
0 |
unless ($_ =~ /^#/) |
|
1487
|
0 |
0 |
if (@gff == 9) |
|
1489
|
0 |
0 |
if ($gff_type =~ /CDS|exon/) { } |
|
|
0 |
0 |
elsif ($gff_type =~ /mRNA|gene/) { } |
|
1491
|
0 |
0 |
if ($gff{$gff_scfd_name}{$gff_type}) { } |
|
1493
|
0 |
0 |
unless (grep {$gff_start == $_;} @{$gff{$gff_scfd_name}{$gff_type};}) |
|
1504
|
0 |
0 |
if ($gff{$gff_scfd_name}{$gff_type}) { } |
|
1505
|
0 |
0 |
unless (grep {$gff_start == $_;} @{$gff{$gff_scfd_name}{$gff_type};}) |
|
1528
|
0 |
0 |
if ($frgt_name =~ /^>(.+)-\d+$/) |
|
1541
|
0 |
0 |
if ($_ =~ /^>(\S+)$/) { } |
|
1552
|
0 |
0 |
if ($gff{$scfd_name}{'gene'}) { } |
|
1555
|
0 |
0 |
if (@gene_tmp % 2) |
|
1569
|
0 |
0 |
if ($gff{$scfd_name}{'exon'}) |
|
1572
|
0 |
0 |
if (@exon_tmp % 2) |
|
1595
|
0 |
0 |
if ($all_locs{$scfd_name}) |
|
1605
|
0 |
0 |
if ($gff{$scfd_name}{'gene'}) |
|
1610
|
0 |
0 |
if ($one >= $front and $one <= $behind) |
|
1618
|
0 |
0 |
if ($gff{$scfd_name}{'exon'}) |
|
1623
|
0 |
0 |
if ($one >= $front and $one <= $behind) |
|
1631
|
0 |
0 |
if ($gene_map_count == 0) { } |
|
|
0 |
0 |
elsif ($exon_map_count == 0) { } |
|
1645
|
0 |
0 |
if (not $intergenic_length == 0) { } |
|
1651
|
0 |
0 |
if (not $gene_length == 0) { } |
|
1657
|
0 |
0 |
if (not $exon_length == 0) { } |
|
1663
|
0 |
0 |
if (not $intron_length == 0) { } |
|
1679
|
0 |
0 |
if ($all_gene_length == 0) { } |
|
1682
|
0 |
0 |
if ($all_exon_length == 0) { } |
|
1685
|
0 |
0 |
if ($all_intron_length == 0) { } |
|
1688
|
0 |
0 |
if ($all_intergenic_length == 0) { } |
|
1832
|
0 |
0 |
if ($_ =~ /^-reference$/) { } |
|
1846
|
0 |
0 |
if ($line_num % 2 != 0) |
|
1847
|
0 |
0 |
unless ($_ =~ /^>\S+$/) |
|
1851
|
0 |
0 |
if ($line_num % 2 == 0) |
|
1852
|
0 |
0 |
unless ($_ =~ /^[AGTCNRYMKSWHBVD]+$/i) |
|
1872
|
0 |
0 |
if ($_ =~ /^-enzyme$/) { } |
|
1883
|
0 |
0 |
if ($_ =~ /^$$self{'enzyme'}$/i) |
|
1887
|
0 |
0 |
if ($enzyme_exists > 0) { } |
|
1913
|
0 |
0 |
if ($_ =~ /^-enzyme_name$/) { } |
|
|
0 |
0 |
elsif ($_ =~ /^-recognition_site$/) { } |
|
1918
|
0 |
0 |
unless ($new_enzyme_site =~ /|/) |
|
1942
|
0 |
0 |
if ($_ =~ /^-start$/) { } |
|
|
0 |
0 |
elsif ($_ =~ /^-end$/) { } |
|
1952
|
0 |
0 |
if ($$self{'range_start'} < $$self{'range_end'}) { } |
|
1971
|
0 |
0 |
if ($_ =~ /^-front$/) { } |
|
|
0 |
0 |
elsif ($_ =~ /^-behind$/) { } |
|
|
0 |
0 |
elsif ($_ =~ /^-step$/) { } |
|
2000
|
0 |
0 |
if ($_ =~ /^-output_dir$/) { } |
|
2007
|
0 |
0 |
if (-d $$self{'output_dir'}) { } |
|
2029
|
0 |
0 |
if ($ref) { } |
|
2036
|
0 |
0 |
if ($enzyme) { } |
|
2046
|
0 |
0 |
if ($output_dir) { } |
|
2071
|
0 |
0 |
if ($_ =~ /^$enzyme$/i) |
|
2084
|
0 |
0 |
if ($_ =~ /\|/) { } |
|
2095
|
0 |
0 |
if ($_ =~ /N/) |
|
2096
|
0 |
0 |
if ($_ =~ /R/) |
|
2097
|
0 |
0 |
if ($_ =~ /Y/) |
|
2098
|
0 |
0 |
if ($_ =~ /M/) |
|
2099
|
0 |
0 |
if ($_ =~ /K/) |
|
2100
|
0 |
0 |
if ($_ =~ /S/) |
|
2101
|
0 |
0 |
if ($_ =~ /W/) |
|
2102
|
0 |
0 |
if ($_ =~ /H/) |
|
2103
|
0 |
0 |
if ($_ =~ /B/) |
|
2104
|
0 |
0 |
if ($_ =~ /V/) |
|
2105
|
0 |
0 |
if ($_ =~ /D/) |
|
2126
|
0 |
0 |
if ($_ =~ /^>/) { } |
|
2140
|
0 |
0 |
if ($string =~ /^(\w+)$/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\](\w+)/) { } |
|
|
0 |
0 |
elsif ($string =~ /^\[(\w+)\](\w+)\[(\w+)\]$/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\](\w+)\[(\w+)\](\w+)/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\]\[(\w+)\]\[(\w+)\](\w+)/) { } |
|
|
0 |
0 |
elsif ($string =~ /(\w+)\[(\w+)\]\[(\w+)\](\w+)/) { } |
|
2143
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2148
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2163
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2168
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2186
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2191
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2212
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2217
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2239
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2244
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2264
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2269
|
0 |
0 |
unless ($loc_in_array == -1) |
|
2284
|
0 |
0 |
if (@enzyme_locs) |
|
2288
|
0 |
0 |
if ($front_rec_loc == 0) { } |
|
2298
|
0 |
0 |
if (@enzyme_locs) { } |
|
2339
|
0 |
0 |
if ($length_of_fragment >= $range1) |
|
2340
|
0 |
0 |
if ($length_of_fragment <= $range2) |
|
2385
|
0 |
0 |
if ($lengths_distribution_tmp == $lengths_distribution_start) { } |
|
|
0 |
0 |
elsif ($lengths_distribution_tmp < $lengths_distribution_end) { } |
|
2400
|
0 |
0 |
if ($lengths_distribution_tmp + $lengths_distribution_step < $lengths_distribution_end) { } |
|
|
0 |
0 |
elsif ($lengths_distribution_tmp + $lengths_distribution_step >= $lengths_distribution_end) { } |
|
2439
|
0 |
0 |
if ($num_pair < $num_last_pair) { } |
|
|
0 |
0 |
elsif ($num_pair == $num_last_pair) { } |
|
2440
|
0 |
0 |
if ($length >= $start and $length <= $end) |
|
2449
|
0 |
0 |
if ($length >= $start) |
|
2467
|
0 |
0 |
if ($num_all_frags > 0) { } |
|
2489
|
0 |
0 |
if ($_ =~ /^-SNPs$/) { } |
|
2508
|
0 |
0 |
if (keys %parameters) |
|
2510
|
0 |
0 |
if ($_ =~ /^-sequence_type$/) { } |
|
2523
|
0 |
0 |
if ($SNPs) { } |
|
2535
|
0 |
0 |
if ($sequence_type =~ /^(\d+)pe$/i) { } |
|
|
0 |
0 |
elsif ($sequence_type =~ /^(\d+)se$/i) { } |
|
2538
|
0 |
0 |
if (not $sequence_length * 2 <= $range1) { } |
|
2548
|
0 |
0 |
if (not $sequence_length <= $range1) { } |
|
2585
|
0 |
0 |
if ($sequence_type_code == 2) |
|
2593
|
0 |
0 |
if ($sequence_type_code == 1) { } |
|
|
0 |
0 |
elsif ($sequence_type_code == 2) { } |
|
2598
|
0 |
0 |
if ($fragment_name =~ /^>(.+)-(\d+)/) |
|
2601
|
0 |
0 |
if ($SNPs{$scaffold_name}) |
|
2603
|
0 |
0 |
if ($SNP >= $pos1 and $SNP <= $pos1 + $se_sequence_length - 1 or $SNP >= $pos2 - $se_sequence_length + 1 and $SNP <= $pos2) |
|
2617
|
0 |
0 |
if ($fragment_name =~ /^>(.+)-(\d+)/) |
|
2620
|
0 |
0 |
if ($SNPs{$scaffold_name}) |
|
2622
|
0 |
0 |
if ($SNP >= $pos1 and $SNP <= $pos1 + $pe_sequence_length - 1 or $SNP >= $pos2 - $pe_sequence_length + 1 and $SNP <= $pos2) |
|
2635
|
0 |
0 |
if ($sequence_type_code == 1) { } |
|
|
0 |
0 |
elsif ($sequence_type_code == 2) { } |
|
2640
|
0 |
0 |
if ($fragment_name =~ /^>(.+)-(\d+)/) |
|
2643
|
0 |
0 |
if ($SNPs{$scaffold_name}) |
|
2645
|
0 |
0 |
if ($SNP >= $pos1 and $SNP <= $pos1 + $se_sequence_length - 1 or $SNP >= $pos2 - $se_sequence_length + 1 and $SNP <= $pos2) |
|
2659
|
0 |
0 |
if ($fragment_name =~ /^>(.+)-(\d+)/) |
|
2662
|
0 |
0 |
if ($SNPs{$scaffold_name}) |
|
2664
|
0 |
0 |
if ($SNP >= $pos1 and $SNP <= $pos1 + $pe_sequence_length - 1 or $SNP >= $pos2 - $pe_sequence_length + 1 and $SNP <= $pos2) |
|
2689
|
0 |
0 |
if ($_ =~ /^-gff$/) { } |
|
2771
|
0 |
0 |
if ($gff) { } |
|
2785
|
0 |
0 |
if ($basename_loc_frags_file =~ /in_range/) { } |
|
2805
|
0 |
0 |
unless ($_ =~ /^#/) |
|
2807
|
0 |
0 |
if (@gff == 9) |
|
2809
|
0 |
0 |
if ($gff_type =~ /CDS|exon/) { } |
|
|
0 |
0 |
elsif ($gff_type =~ /mRNA|gene/) { } |
|
2811
|
0 |
0 |
if ($gff{$gff_scfd_name}{$gff_type}) { } |
|
2812
|
0 |
0 |
unless (grep {$gff_start == $_;} @{$gff{$gff_scfd_name}{$gff_type};}) |
|
2822
|
0 |
0 |
if ($gff{$gff_scfd_name}{$gff_type}) { } |
|
2823
|
0 |
0 |
unless (grep {$gff_start == $_;} @{$gff{$gff_scfd_name}{$gff_type};}) |
|
2846
|
0 |
0 |
if ($frgt_name =~ /^>(.+)-\d+$/) |
|
2860
|
0 |
0 |
if ($_ =~ /^>(\S+)$/) { } |
|
2871
|
0 |
0 |
if ($gff{$scfd_name}{'gene'}) { } |
|
2884
|
0 |
0 |
if ($gff{$scfd_name}{'exon'}) |
|
2909
|
0 |
0 |
if ($all_locs{$scfd_name}) |
|
2919
|
0 |
0 |
if ($gff{$scfd_name}{'gene'}) |
|
2924
|
0 |
0 |
if ($one >= $front and $one <= $behind) |
|
2932
|
0 |
0 |
if ($gff{$scfd_name}{'exon'}) |
|
2937
|
0 |
0 |
if ($one >= $front and $one <= $behind) |
|
2945
|
0 |
0 |
if ($gene_map_count == 0) { } |
|
|
0 |
0 |
elsif ($exon_map_count == 0) { } |
|
2957
|
0 |
0 |
if (not $intergenic_length == 0) { } |
|
2963
|
0 |
0 |
if (not $gene_length == 0) { } |
|
2969
|
0 |
0 |
if (not $exon_length == 0) { } |
|
2975
|
0 |
0 |
if (not $intron_length == 0) { } |
|
2991
|
0 |
0 |
if ($all_gene_length == 0) { } |
|
2994
|
0 |
0 |
if ($all_exon_length == 0) { } |
|
2997
|
0 |
0 |
if ($all_intron_length == 0) { } |
|
3000
|
0 |
0 |
if ($all_intergenic_length == 0) { } |