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 $$self{'_FH'}, $bytes, 12)
202	4	0	$_ < $LONG_MID ? :
218	0	5	unless (seek $$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)