| line |
true |
false |
branch |
|
93
|
1 |
1 |
unless defined $_readcor |
|
135
|
2 |
0 |
if (defined $_readcor) { } |
|
142
|
1 |
1 |
if ($map->core_exists) |
|
144
|
1 |
0 |
if (open my $CORE, '<', $corfile) { } |
|
158
|
2 |
18 |
if ($line =~ m[^//\s+fpc\s+project\s+(.+)]) |
|
159
|
2 |
18 |
if ($line =~ m[^//\s+([\d.]+)]) |
|
163
|
2 |
0 |
if ($line =~ /User:\s+(.+)/) |
|
166
|
2 |
18 |
if ($line =~ m[^//\s+Framework\s+(\w+)\s+(\w+)\s+([-\w]+)\s+(\w+)\s+(\w+)\s+(.+)$]) |
|
168
|
2 |
0 |
if $2 eq 'Label' |
|
169
|
2 |
0 |
if $4 eq 'Abbrev' |
|
172
|
2 |
18 |
unless $line =~ m[^//] |
|
175
|
0 |
2 |
unless (defined $map->group_type and defined $map->group_abbr) |
|
195
|
2 |
973 |
if $line =~ /^Markerdata/ |
|
203
|
30 |
943 |
if ($name =~ /sd1/) |
|
216
|
965 |
6294 |
if ($line =~ /^Map "ctg(\d+)" Ends (Left|Right) ([-\d]+)/) { } |
|
|
440 |
5854 |
elsif ($line =~ /^([a-zA-Z]+)_match_to_\w+\s+"(.+)"/) { } |
|
|
1079 |
4775 |
elsif ($line =~ /^Positive_(\w+)\s+"(.+)"/) { } |
|
|
973 |
3802 |
elsif ($line =~ /^Bands\s+(\d+)\s+(\d+)/ and not $bandsread) { } |
|
|
973 |
2829 |
elsif ($line =~ /^Gel_number\s+(.+)/) { } |
|
|
135 |
2694 |
elsif ($line =~ /^Remark\s+"(.+)"/) { } |
|
|
549 |
2145 |
elsif ($line =~ /^Fp_number\s+"(.+)"/) { } |
|
|
37 |
2108 |
elsif ($line =~ /^Shotgun\s+(\w+)\s+(\w+)/) { } |
|
|
162 |
1946 |
elsif ($line =~ /^Fpc_remark\s+"(.+)"/) { } |
|
230
|
43 |
922 |
if not exists $_contigs{$contigNumber}{'range'}{'start'} or $_contigs{$contigNumber}{'range'}{'start'} > $temp |
|
237
|
45 |
920 |
if not exists $_contigs{$contigNumber}{'range'}{'end'} or $_contigs{$contigNumber}{'range'}{'end'} < $3 |
|
256
|
355 |
618 |
if ($map->core_exists) { } |
|
267
|
8 |
965 |
if (exists $_contigs{'0'}{'clones'}{$name}) |
|
280
|
123 |
12 |
if ($seqclone == 1) |
|
281
|
30 |
93 |
if ($1 =~ /\,\s+Chr(\d+)\s+/) |
|
300
|
0 |
973 |
if $self->verbose and $curClone % 1000 == 0 |
|
310
|
2 |
165 |
unless $line =~ /^Marker_(\w+)\s+:\s+"(.+)"/ |
|
320
|
0 |
490 |
if ($line =~ /^Global_position\s+([\d.]+)\s*(Frame)?/) { } |
|
|
48 |
442 |
elsif ($line =~ /^Anchor_bin\s+"([\w\d.]+)"/) { } |
|
|
48 |
394 |
elsif ($line =~ /^Anchor_pos\s+([\d.]+)\s+(F|P)?/) { } |
|
|
0 |
394 |
elsif ($line =~ /^anchor$/) { } |
|
|
64 |
330 |
elsif ($line =~ /^Remark\s+"(.+)"/) { } |
|
328
|
0 |
0 |
if (defined $2) { } |
|
345
|
0 |
48 |
if $subgroup =~ /^\./ |
|
354
|
26 |
22 |
if ($2 eq 'F') { } |
|
370
|
0 |
165 |
if $self->verbose and $curMarker % 1000 == 0 |
|
384
|
12 |
19 |
if ($line =~ /^Ctg(\d+)/) { } |
|
|
0 |
19 |
elsif ($line =~ /^Chr_remark\s+"(-|\+|Chr(\d+))\s+(.+)"$/) { } |
|
|
2 |
17 |
elsif ($line =~ /^User_remark\s+"(.+)"/) { } |
|
|
1 |
16 |
elsif ($line =~ /^Trace_remark\s+"(.+)"/) { } |
|
|
4 |
12 |
elsif ($grpabbr and $line =~ /^Chr_remark\s+"(\W|$grpabbr((\d+)|(\w+)|([.\w\d]+)))\s*(\{(.*)\}|\[(.*)\])?"\s+(Pos\s+((\d.)+|NaN))(NOEDIT)?/) { } |
|
390
|
12 |
0 |
if ($line =~ /#\w*(.*)\w*$/) |
|
392
|
0 |
12 |
if ($line =~ /#\s+Chr(\d+)\s+/) |
|
401
|
0 |
0 |
if defined $3 |
|
403
|
0 |
0 |
if (defined $2) { } |
|
420
|
0 |
4 |
if ($pos eq 'NaN') |
|
428
|
4 |
0 |
if (defined $grpmatch) { } |
|
431
|
0 |
4 |
if ($grpmatch =~ /((\d+)((\D\d.\d+)|(.\d+)))|((\w+)(\.\d+))/) { } |
|
434
|
0 |
0 |
if $grpabbr eq 'Chr' |
|
435
|
0 |
0 |
if $grpabbr eq 'Chr' |
|
437
|
0 |
0 |
if $grpabbr eq 'Lg' |
|
438
|
0 |
0 |
if $grpabbr eq 'Lg' |
|
440
|
0 |
0 |
if $subgroup =~ /^\./ |
|
455
|
0 |
31 |
if $self->verbose and $curContig % 100 == 0 |
|
461
|
0 |
2 |
if $map->version < 7 |
|
462
|
0 |
2 |
if $map->version == 4.6 |