Branch Coverage

blib/lib/Bio/Trace/ABIF.pm
Criterion Covered Total %
branch 31 724 4.2


line true false branch
118 0 0 $IS_BIG_ENDIAN ? :
174 0 2 if (@_)
175 0 0 if shift()
181 0 2 unless open $self->{'_FH'}, $rw, $filename
183 0 2 unless ($self->is_abif_format)
192 0 2 unless (seek $self->{'_FH'}, 18, 0)
197 0 2 unless (read $self->{'_FH'}, $bytes, 12)
203 4 0 $_ < $LONG_MID ? :
218 0 5 unless (seek $self->{'_FH'}, $offset, 0)
223 1 4 unless (read $self->{'_FH'}, $field, 8)
228 0 4 if $tag_number >= $LONG_MID
248 1 2 if defined $self->{'_FH'}
250 11 3 if $k =~ /^\_/
283 0 2 unless (seek $self->{'_FH'}, 0, 0)
289 0 2 unless read $self->{'_FH'}, $file_signature, 4
291 0 2 if ($file_signature eq 'FIBA')
311 0 0 unless (defined $self->{'_ABIF_VERSION'})
313 0 0 unless seek $self->{'_FH'}, 4, 0
314 0 0 unless read $self->{'_FH'}, $version, 2
407 2 0 if ($self->search_tag($tag_name, $tag_number))
412 4 0 $_ < $SHORT_MID ? :
415 4 0 $_ < $LONG_MID ? :
418 0 2 if ($et > 1023) { }
431 1 1 if ($DirEntry{'DATA_SIZE'} > 4) { }
434 1 0 $_ < $LONG_MID ? :
481 2 0 if ($self->search_tag($tag_name, $tag_number))
485 2 0 $_ < $LONG_MID ? :
487 0 2 if ($data_size > 4) { }
490 0 0 $_ < $LONG_MID ? :
526 4 0 if (defined $offset) { }
609 0 0 if ($self->search_tag($tag_name, $tag_number))
611 0 0 $_ < $SHORT_MID ? :
614 0 0 $_ < $LONG_MID ? :
617 0 0 if $et > 1023
619 0 0 if $et == 9 or $et == 128 or $et == 256 or $et == 384
621 0 0 unless defined $elem_type
626 0 0 if ($elem_type eq 'float') { }
0 0 elsif ($elem_type eq 'double') { }
0 0 elsif ($elem_type eq 'date') { }
0 0 elsif ($elem_type eq 'time') { }
0 0 elsif ($elem_type eq 'pString') { }
0 0 elsif ($elem_type eq 'cString') { }
0 0 elsif ($elem_type eq 'char') { }
627 0 0 if (ref $data eq 'ARRAY') { }
0 0 elsif (ref $data) { }
644 0 0 if (ref $data eq 'ARRAY') { }
0 0 elsif (ref $data) { }
657 0 0 if ref $data
659 0 0 unless defined $yy and defined $mm and defined $dd
664 0 0 if ref $data
666 0 0 unless defined $hh and defined $min and defined $sec and defined $ms
671 0 0 if (ref $data eq 'SCALAR') { }
0 0 elsif (ref $data) { }
672 0 0 if length $$data > 255
681 0 0 if length $data > 255
688 0 0 if (ref $data eq 'SCALAR') { }
0 0 elsif (ref $data) { }
701 0 0 if (ref $data eq 'ARRAY') { }
0 0 elsif (ref $data eq 'SCALAR') { }
0 0 elsif (ref $data) { }
718 0 0 if (ref $data eq 'ARRAY') { }
0 0 elsif (ref $data) { }
738 0 0 if ($n_bytes <= 4) { }
0 0 elsif ($n_bytes <= $data_size) { }
811 0 0 if ($channel_number == 5) { }
817 0 0 if ($channel_number < 9 or $channel_number > 12 and $channel_number != 205)
822 0 0 unless (defined $self->{$key})
823 0 0 $_ < $SHORT_MID ? :
825 0 0 @data ? :
843 0 0 unless (defined $self->{'_APrN1'})
862 0 0 unless (defined $self->{'_APrV1'})
881 0 0 unless (defined $self->{'_APrX1'})
900 0 0 unless (defined $self->{'_APXV1'})
921 0 0 unless (defined $self->{'_ARTN1'})
922 0 0 $_ < $LONG_MID ? :
943 0 0 unless (defined $self->{'_SPAC1'})
946 0 0 if defined $s
966 0 0 unless (defined $self->{'_ASPF1'})
967 0 0 $_ < $SHORT_MID ? :
988 0 0 unless (defined $self->{'_SPAC2'})
1009 0 0 unless (defined $self->{'_SVER2'})
1032 0 0 unless (defined $self->{'_BCTS1'})
1053 0 0 unless (defined $self->{'_PLOC2'})
1054 0 0 $_ < $SHORT_MID ? :
1056 0 0 @bl ? :
1076 0 0 unless (defined $self->{'_PLOC1'})
1077 0 0 $_ < $SHORT_MID ? :
1079 0 0 @bl ? :
1103 0 0 unless (defined $self->{'_FWO_1'})
1105 0 0 if (defined $bases) { }
1131 0 0 unless (defined $self->{'_SPAC3'})
1134 0 0 if defined $s
1153 0 0 unless (defined $self->{'_BufT1'})
1154 0 0 $_ < $SHORT_MID ? :
1156 0 0 @T ? :
1174 0 0 unless (defined $self->{'_LANE1'})
1175 0 0 $_ < $SHORT_MID ? :
1197 0 0 unless $base =~ /^[ACGTacgt]$/
1219 0 0 unless (defined $self->{'_phCH1'})
1243 0 0 if @_
1245 0 0 unless (defined $self->{$tag_code})
1264 0 0 unless (defined $self->{'_CTTL1'})
1283 0 0 unless (defined $self->{'_CTID1'})
1304 0 0 unless (defined $self->{'_CTNM1'})
1323 0 0 unless (defined $self->{'_CTOw1'})
1342 0 0 unless (defined $self->{'_DATA6'})
1343 0 0 $_ < $SHORT_MID ? :
1345 0 0 @c ? :
1363 0 0 unless (defined $self->{'_MODF1'})
1382 0 0 unless (defined $self->{'_SVER1'})
1401 0 0 unless (defined $self->{'_SVER3'})
1420 0 0 unless (defined $self->{'_RUND3'})
1422 0 0 if (defined $d)
1424 0 0 if $y >= $SHORT_MID
1444 0 0 unless (defined $self->{'_RUNT3'})
1446 0 0 if defined $nn
1464 0 0 unless (defined $self->{'_RUND4'})
1466 0 0 if (defined $d)
1467 0 0 if $y >= $SHORT_MID
1487 0 0 unless (defined $self->{'_RUNT4'})
1489 0 0 if defined $nn
1507 0 0 unless (defined $self->{'_DCHT1'})
1508 0 0 $_ < $SHORT_MID ? :
1527 0 0 unless (defined $self->{'_DSam1'})
1528 0 0 $_ < $SHORT_MID ? :
1551 0 0 unless (defined $self->{$k})
1552 0 0 if ($n > 0 and $n <= 5)
1572 0 0 unless (defined $self->{'_DySN1'})
1595 0 0 unless (defined $self->{$k})
1596 0 0 if ($n > 0 and $n <= 5)
1620 0 0 unless (defined $self->{'_phDY1'})
1643 0 0 unless (defined $self->{$k})
1644 0 0 if ($n > 0 and $n <= 5)
1645 0 0 $_ < $SHORT_MID ? :
1667 0 0 unless (defined $self->{'_PCON1'})
1669 0 0 @qv ? :
1689 0 0 unless (defined $self->{'_PCON1'})
1691 0 0 @qv ? :
1711 0 0 unless (defined $self->{'_PBAS1'})
1729 0 0 unless defined $seq
1746 0 0 unless (defined $self->{'_EPVt1'})
1747 0 0 $_ < $LONG_MID ? :
1766 0 0 unless (defined $self->{'_GTyp1'})
1785 0 0 unless (defined $self->{'_ANME1'})
1804 0 0 unless (defined $self->{'_PANL1'})
1823 0 0 unless (defined $self->{'_STYP1'})
1842 0 0 unless (defined $self->{'_SpNm1'})
1861 0 0 unless (defined $self->{'_InSc1'})
1862 0 0 $_ < $LONG_MID ? :
1881 0 0 unless (defined $self->{'_InVt1'})
1882 0 0 $_ < $LONG_MID ? :
1901 0 0 unless (defined $self->{'_HCFG1'})
1920 0 0 unless (defined $self->{'_HCFG2'})
1939 0 0 unless (defined $self->{'_MCHN1'})
1958 0 0 unless (defined $self->{'_HCFG4'})
1978 0 0 unless (defined $self->{'_CpEP1'})
1997 0 0 unless (defined $self->{'_LsrP1'})
1998 0 0 $_ < $LONG_MID ? :
2017 0 0 unless (defined $self->{'_LNTD1'})
2018 0 0 $_ < $SHORT_MID ? :
2039 0 0 unless (defined $self->{'_PDMF2'})
2059 0 0 unless (defined $self->{'_PDMF1'})
2078 0 0 unless (defined $self->{'_MODL1'})
2101 0 0 unless (defined $self->{'_NOIS1'})
2104 0 0 if (not defined $bits) { }
2132 0 0 unless (defined $self->{'_NLNE1'})
2133 0 0 $_ < $SHORT_MID ? :
2152 0 0 unless (defined $self->{'_Dye#1'})
2153 0 0 $_ < $SHORT_MID ? :
2172 0 0 unless (defined $self->{'_SCAN1'})
2173 0 0 $_ < $LONG_MID ? :
2192 0 0 unless (defined $self->{'_HCFG3'})
2217 0 0 unless (defined $self->{$t})
2219 0 0 @bytes ? :
2241 0 0 unless (defined $self->{'_OfSc1'})
2242 0 0 $_ < $LONG_MID ? :
2244 0 0 @off ? :
2264 0 0 unless (defined $self->{'_OB'})
2290 0 0 unless (defined $self->{'_B1Pt2'})
2291 0 0 $_ < $SHORT_MID ? :
2312 0 0 unless (defined $self->{'_B1Pt1'})
2313 0 0 $_ < $SHORT_MID ? :
2336 0 0 unless (defined $self->{'_phAR1'})
2339 0 0 if (defined $r)
2371 0 0 unless (defined $self->{$k})
2375 0 0 if defined $s
2390 0 0 @peak_array ? :
2408 0 0 unless (defined $self->{'_PXLB1'})
2409 0 0 $_ < $LONG_MID ? :
2428 0 0 unless (defined $self->{'_NAVG1'})
2429 0 0 $_ < $SHORT_MID ? :
2450 0 0 unless (defined $self->{'_PTYP1'})
2472 0 0 unless (defined $self->{'_PSZE1'})
2473 0 0 $_ < $LONG_MID ? :
2494 0 0 unless (defined $self->{'_SMED1'})
2515 0 0 unless (defined $self->{'_SMLt1'})
2534 0 0 unless (defined $self->{'_DATA7'})
2535 0 0 $_ < $SHORT_MID ? :
2537 0 0 @p ? :
2559 0 0 unless (defined $self->{'_phQL1'})
2560 0 0 $_ < $SHORT_MID ? :
2582 0 0 unless (defined $self->{'_PCON2'})
2585 0 0 @qv ? :
2606 0 0 unless (defined $self->{'_PCON2'})
2609 0 0 @qv ? :
2630 0 0 if ($channel_number == 5)
2633 0 0 if ($channel_number < 1 or $channel_number > 5 and $channel_number != 105)
2638 0 0 unless (defined $self->{$k})
2639 0 0 $_ < $SHORT_MID ? :
2641 0 0 @data ? :
2662 0 0 unless $base =~ /^[ACGTacgt]$/
2680 0 0 unless (defined $self->{'_Scal1'})
2683 0 0 if (defined $r)
2703 0 0 unless (defined $self->{'_RGNm1'})
2724 0 0 unless (defined $self->{'_RGCm1'})
2746 0 0 unless (defined $self->{'_RGOw1'})
2767 0 0 unless (defined $self->{'_RevC1'})
2768 0 0 $_ < $SHORT_MID ? :
2789 0 0 unless (defined $self->{'_RMdN1'})
2808 0 0 unless (defined $self->{'_RMdV1'})
2827 0 0 unless (defined $self->{'_RMXV1'})
2846 0 0 unless (defined $self->{'_RMdX1'})
2865 0 0 unless (defined $self->{'_RunN1'})
2884 0 0 unless (defined $self->{'_RPrN1'})
2903 0 0 unless (defined $self->{'_RPrV1'})
2922 0 0 unless (defined $self->{'_RUND1'})
2924 0 0 if (defined $d)
2925 0 0 if $y >= $SHORT_MID
2945 0 0 unless (defined $self->{'_RUNT1'})
2947 0 0 if defined $nn
2965 0 0 unless (defined $self->{'_RUND2'})
2967 0 0 if (defined $d)
2968 0 0 if $y >= $SHORT_MID
2988 0 0 unless (defined $self->{'_RUNT2'})
2990 0 0 if defined $nn
3008 0 0 unless (defined $self->{'_Tmpr1'})
3009 0 0 $_ < $LONG_MID ? :
3031 0 0 unless (defined $self->{'_SVER4'})
3050 0 0 unless (defined $self->{'_SMPL1'})
3069 0 0 unless (defined $self->{'_LIMS1'})
3091 0 0 unless (defined $self->{'_Rate1'})
3093 0 0 @bytes ? :
3115 0 0 unless (defined $self->{$k})
3116 0 0 $_ < $LONG_MID ? :
3118 0 0 @C ? :
3141 0 0 unless (defined $self->{'_Satd1'})
3142 0 0 $_ < $LONG_MID ? :
3144 0 0 @N ? :
3168 0 0 unless (defined $self->{$k})
3169 0 0 $_ < $LONG_MID ? :
3171 0 0 @I ? :
3192 0 0 unless (defined $self->{'_PROJ4'})
3214 0 0 unless (defined $self->{'_PRJT1'})
3236 0 0 unless (defined $self->{'_SPEC1'})
3257 0 0 unless (defined $self->{'_PBAS2'})
3275 0 0 unless defined $seq
3292 0 0 unless (defined $self->{'_APFN2'})
3315 0 0 unless (defined $self->{'_S/N%1'})
3316 0 0 $_ < $SHORT_MID ? :
3318 0 0 if (not @sl) { }
3346 0 0 unless (defined $self->{'_StdF1'})
3367 0 0 unless (defined $self->{'_SnpS1'})
3386 0 0 unless (defined $self->{'_EVNT3'})
3407 0 0 unless (defined $self->{'_ASPt2'})
3408 0 0 $_ < $SHORT_MID ? :
3429 0 0 unless (defined $self->{'_ASPt1'})
3430 0 0 $_ < $SHORT_MID ? :
3449 0 0 unless (defined $self->{'_EVNT1'})
3468 0 0 unless (defined $self->{'_EVNT4'})
3489 0 0 unless (defined $self->{'_AEPt2'})
3490 0 0 $_ < $SHORT_MID ? :
3511 0 0 unless (defined $self->{'_AEPt1'})
3512 0 0 $_ < $SHORT_MID ? :
3532 0 0 unless (defined $self->{'_EVNT2'})
3551 0 0 unless (defined $self->{'_DATA8'})
3552 0 0 $_ < $SHORT_MID ? :
3554 0 0 @t ? :
3574 0 0 unless $base =~ /^[ACGTacgt]$/
3594 0 0 unless (defined $self->{'_phTR2'})
3597 0 0 if defined $pr
3620 0 0 unless (defined $self->{'_phTR1'})
3621 0 0 $_ < $SHORT_MID ? :
3641 0 0 unless (defined $self->{'_DATA5'})
3642 0 0 $_ < $SHORT_MID ? :
3644 0 0 @v ? :
3664 0 0 unless (defined $self->{'_User1'})
3683 0 0 unless (defined $self->{'_TUBE1'})
3711 0 0 unless %sl
3713 0 0 unless %noise
3748 0 0 if (@_)
3777 0 0 if (@_)
3783 0 0 unless defined $qv_ref
3786 0 0 if $N < $window
3791 0 0 if ($qv_ref->[$j] < $threshold)
3796 0 0 if ($$qv_ref[$j - $window] < $threshold)
3799 0 0 if ($qv_ref->[$j] < $threshold)
3804 0 0 if $n >= $bad_bases
3829 0 0 if (@_)
3835 0 0 unless defined $qv_ref
3838 0 0 if $N < $window
3843 0 0 if ($qv_ref->[$j] < $threshold)
3848 0 0 if ($$qv_ref[$j + $window] < $threshold)
3851 0 0 if ($qv_ref->[$j] < $threshold)
3856 0 0 if $n >= $bad_bases
3889 0 0 if @_
3893 0 0 if $N < $window_width
3904 0 0 if $q >= $threshold
3908 0 0 if ($crl and $q < $threshold) { }
0 0 elsif (not $crl and $q >= $threshold) { }
3910 0 0 if ($stop - $start < $i - $new_start - 1)
3921 0 0 if ($crl and $stop - $start < $N - $new_start - 1)
3925 0 0 unless $trim
3929 0 0 if ($$qv_ref[$start + $j] < 10) { }
3939 0 0 if ($$qv_ref[$stop - $j] < 10) { }
3947 0 0 if ($stop - $start < 4)
3949 0 0 if ($qv_ref->[$k] < 10)
3991 0 0 if (@_)
3994 0 0 unless defined $qv_ref
4003 0 0 if ($N < $window)
4010 0 0 if ($method eq 'SequencingAnalysis') { }
4020 0 0 if ($sum < $threshold)
4035 0 0 if ($sum < $threshold)
4044 0 0 $stop > $start ? :
4058 0 0 if ($sum >= $threshold)
4067 0 0 if ($sum >= $threshold)
4100 0 0 if (@_) { }
4110 0 0 unless defined $qv_ref
4112 0 0 if ($start <= $stop) { }
4114 0 0 if ($qv_ref->[$i] <= $max)
4121 0 0 if ($qv <= $max)
4152 0 0 if (@_) { }
4162 0 0 unless defined $qv_ref
4164 0 0 if ($start <= $stop) { }
4166 0 0 if ($qv_ref->[$i] >= $min)
4173 0 0 if ($qv >= $min)
4209 0 0 if (@_) { }
4219 0 0 unless defined $qv_ref
4221 0 0 if ($start <= $stop) { }
4223 0 0 if ($qv_ref->[$i] >= $min and $qv_ref->[$i] <= $max)
4230 0 0 if ($qv >= $min and $qv <= $max)
4258 0 0 if (@_) { }
4270 0 0 unless $start >= 0 and $start <= $stop and defined $qv_ref
4356 1 0 substr($b, 0, 1) eq '0' ? :
4378 0 0 if ($decimal_number == 0)
4385 0 0 if (abs(($decimal_number - $ff) / $ff) < 0.0001)
4391 0 0 if ($decimal_number =~ /^-/)
4396 0 0 unless $i
4397 0 0 unless $f
4404 0 0 if ($mantissa =~ /1/g) { }
4411 0 0 $exp > 0 ? :
4415 0 0 unless $mantissa
4443 0 0 if @_
4461 0 0 $m < 10 ? :
4463 0 0 $d < 10 ? :
4471 0 0 $hh < 10 ? :
4473 0 0 $mm < 10 ? :
4475 0 0 $ss < 10 ? :
4477 0 0 $nn < 10 ? :
4483 0 0 unless @_ == 1
4485 0 0 if (ref $self) { }
4495 0 1 if ($Debugging or $self->{'_DEBUG'})
4501 0 2 if ($Debugging)