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Errors in missing vs pad values in VCF #1190

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Mar 5, 2024
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Errors in missing vs pad values in VCF #1190

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b61a09b
Errors in missing vs pad values in VCF
jeromekelleher Feb 8, 2024
43d2f75
Skip tests for reported bugs #1195, #1196
jeromekelleher Feb 15, 2024
355ea2b
Mask VCF missing rather than fill values
jeromekelleher Feb 16, 2024
b5708ed
Enable tests, and skip problematic round trip
jeromekelleher Feb 16, 2024
a0edba7
Skip problematic fields in scikit-allel comparison
jeromekelleher Feb 16, 2024
b03b952
Remove all-missing fields from example VCF
jeromekelleher Feb 16, 2024
c58bb62
Simplify VCF reader logic
jeromekelleher Feb 16, 2024
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18 changes: 13 additions & 5 deletions docs/changelog.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -36,8 +36,16 @@ Improvements
- Improve performance of :func:`variant_stats` and :func:`sample_stats` functions.
(:user:`timothymillar`, :pr:`1119`, :issue:`1116`)

.. Bug fixes
.. ~~~~~~~~~
Bug fixes
~~~~~~~~~

- Fix error in missing data handling for VCF. Missing values for most
fields were marked as the corresponding "fill" value. For example, missing
string values were stored as the empty string (string fill value) rather
than "." (string missing value). Similarly for integer fields, missing
values were stored as -2 (int fill) rather than -1 (int missing)
(:user:`jeromekelleher`, :pr:`1190`, :issue:`1192`).


.. Documentation
.. ~~~~~~~~~~~~~
Expand Down Expand Up @@ -106,7 +114,7 @@ Deprecations
parameter now expects a full sized kinship matrix in which non-founder values are
ignored.
(:user:`timothymillar`, :pr:`1075`, :issue:`1061`)

Improvements
~~~~~~~~~~~~

Expand Down Expand Up @@ -190,9 +198,9 @@ Breaking changes
(:user:`timothymillar`, :pr:`995`, :issue:`875`)
- The ``genotype_count`` variable has been removed in favour of
:data:`sgkit.variables.variant_genotype_count_spec` which follows VCF ordering
(i.e., homozygous reference, heterozygous, homozygous alternate for biallelic,
(i.e., homozygous reference, heterozygous, homozygous alternate for biallelic,
diploid genotypes).
:func:`hardy_weinberg_test` now defaults to using
:func:`hardy_weinberg_test` now defaults to using
:data:`sgkit.variables.variant_genotype_count_spec` for the ``genotype_count``
parameter. (:user:`timothymillar`, :issue:`911`, :pr:`1002`)

Expand Down
21 changes: 6 additions & 15 deletions sgkit/io/vcf/vcf_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -278,17 +278,11 @@ class InfoAndFormatFieldHandler(VcfFieldHandler):

def add_variant(self, i: int, variant: Any) -> None:
if self.category == "INFO":
try:
val = variant.INFO[self.key]
present = True
except KeyError:
present, val = False, None

if present:
val = variant.INFO.get(self.key, None)
self.array[i] = self.missing_value
if val is not None:
assert self.array.ndim in (1, 2)
if self.array.ndim == 1:
if val is None:
val = self.missing_value
self.array[i] = val
elif self.array.ndim == 2:
self.array[i] = self.fill_value
Expand All @@ -300,11 +294,8 @@ def add_variant(self, i: int, variant: Any) -> None:
v if v is not None else self.missing_value
)
except TypeError: # val is a scalar
self.array[i, 0] = (
val if val is not None else self.missing_value
)
else:
self.array[i] = self.fill_value
self.array[i, 0] = val

elif self.category == "FORMAT":
val = variant.format(self.key)
if val is not None:
Expand All @@ -327,7 +318,7 @@ def add_variant(self, i: int, variant: Any) -> None:
a = a[..., : self.array.shape[-1]] # trim to fit
self.array[i, ..., : a.shape[-1]] = a
else:
self.array[i] = self.fill_value
self.array[i] = self.missing_value

def truncate_array(self, length: int) -> None:
self.array = self.array[:length]
Expand Down
8 changes: 4 additions & 4 deletions sgkit/io/vcf/vcf_writer_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -494,16 +494,16 @@ def vcf_genotypes_to_byte_buf_size(call_genotype):


def create_mask(arr):
"""Return a mask array of shape ``arr.shape[0]` for masking out fill values."""
"""Return a mask array of shape ``arr.shape[0]` for masking out missing values."""
axis = tuple(range(1, len(arr.shape)))
if arr.dtype == bool:
return ~arr
elif arr.dtype in (np.int8, np.int16, np.int32):
return np.all(arr == INT_FILL, axis=axis)
return np.all(arr == INT_MISSING, axis=axis)
elif arr.dtype == np.float32:
return np.all(arr.view("i4") == FLOAT32_FILL_AS_INT32, axis=axis)
return np.all(arr.view("i4") == FLOAT32_MISSING_AS_INT32, axis=axis)
elif arr.dtype.kind == "S":
return np.all(arr == STR_FILL_BYTE, axis=axis)
return np.all(arr == STR_MISSING_BYTE, axis=axis)
else:
raise ValueError(f"Unsupported dtype: {arr.dtype}")

Expand Down
94 changes: 47 additions & 47 deletions sgkit/tests/io/vcf/data/all_fields.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -49,20 +49,20 @@
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s1 s2
1 1 . G A,C . PASS IB0 . . .
1 2 . A G,G . PASS II1=126 . . .
1 3 . A G,G . PASS II1=. . . .
1 3 . A G,G . PASS . . . .
1 4 . T A,C . PASS II2=459,-140 . . .
1 5 . T A,C . PASS II2=.,-140 . . .
1 6 . T A,C . PASS II2=459,. . . .
1 7 . T A,C . PASS II2=.,. . . .
1 7 . T A,C . PASS . . . .
1 8 . A A,G . PASS IIA=294,130 . . .
1 9 . A A,G . PASS IIA=.,130 . . .
1 10 . A A,G . PASS IIA=294,. . . .
1 11 . A A,G . PASS IIA=.,. . . .
1 11 . A A,G . PASS . . . .
1 12 . A A,G . PASS IIR=95,724,44 . . .
1 13 . A A,G . PASS IIR=.,724,44 . . .
1 14 . A A,G . PASS IIR=95,.,44 . . .
1 15 . A A,G . PASS IIR=95,724,. . . .
1 16 . A A,G . PASS IIR=.,.,. . . .
1 16 . A A,G . PASS . . . .
1 17 . G A,G . PASS IID=-879,-534,238,-670,482,-913,396 . . .
1 18 . G A,G . PASS IID=.,-534,238,-670,482,-913,396 . . .
1 19 . G A,G . PASS IID=-879,.,238,-670,482,-913,396 . . .
Expand All @@ -71,28 +71,28 @@
1 22 . G A,G . PASS IID=-879,-534,238,-670,.,-913,396 . . .
1 23 . G A,G . PASS IID=-879,-534,238,-670,482,.,396 . . .
1 24 . G A,G . PASS IID=-879,-534,238,-670,482,-913,. . . .
1 25 . G A,G . PASS IID=.,.,.,.,.,.,. . . .
1 25 . G A,G . PASS . . . .
1 26 . G A,G . PASS IID=-129,687,-870,685 . . .
1 27 . G A,G . PASS IID=.,687,-870,685 . . .
1 28 . G A,G . PASS IID=-129,.,-870,685 . . .
1 29 . G A,G . PASS IID=-129,687,.,685 . . .
1 30 . G A,G . PASS IID=-129,687,-870,. . . .
1 31 . G A,G . PASS IID=.,.,.,. . . .
1 31 . G A,G . PASS . . . .
1 32 . T A,T . PASS IF1=-887.177 . . .
1 33 . T A,T . PASS IF1=. . . .
1 33 . T A,T . PASS . . . .
1 34 . G C,A . PASS IF2=443.998,877.105 . . .
1 35 . G C,A . PASS IF2=.,877.105 . . .
1 36 . G C,A . PASS IF2=443.998,. . . .
1 37 . G C,A . PASS IF2=.,. . . .
1 37 . G C,A . PASS . . . .
1 38 . T C,A . PASS IFA=-998.442,984.423 . . .
1 39 . T C,A . PASS IFA=.,984.423 . . .
1 40 . T C,A . PASS IFA=-998.442,. . . .
1 41 . T C,A . PASS IFA=.,. . . .
1 41 . T C,A . PASS . . . .
1 42 . A T,G . PASS IFR=234.963,223.306,-985.867 . . .
1 43 . A T,G . PASS IFR=.,223.306,-985.867 . . .
1 44 . A T,G . PASS IFR=234.963,.,-985.867 . . .
1 45 . A T,G . PASS IFR=234.963,223.306,. . . .
1 46 . A T,G . PASS IFR=.,.,. . . .
1 46 . A T,G . PASS . . . .
1 47 . T G,G . PASS IFD=-417.542,223.706,-721.012,-415.711,-267.276,-87.86,570.352,-600.652,28.4689 . . .
1 48 . T G,G . PASS IFD=.,223.706,-721.012,-415.711,-267.276,-87.86,570.352,-600.652,28.4689 . . .
1 49 . T G,G . PASS IFD=-417.542,.,-721.012,-415.711,-267.276,-87.86,570.352,-600.652,28.4689 . . .
Expand All @@ -103,7 +103,7 @@
1 54 . T G,G . PASS IFD=-417.542,223.706,-721.012,-415.711,-267.276,-87.86,.,-600.652,28.4689 . . .
1 55 . T G,G . PASS IFD=-417.542,223.706,-721.012,-415.711,-267.276,-87.86,570.352,.,28.4689 . . .
1 56 . T G,G . PASS IFD=-417.542,223.706,-721.012,-415.711,-267.276,-87.86,570.352,-600.652,. . . .
1 57 . T G,G . PASS IFD=.,.,.,.,.,.,.,.,. . . .
1 57 . T G,G . PASS . . . .
1 58 . T G,G . PASS IFD=-907.099,215.09,-658.952,-869.897,897.771,931.264,616.795,-390.772,-804.656 . . .
1 59 . T G,G . PASS IFD=.,215.09,-658.952,-869.897,897.771,931.264,616.795,-390.772,-804.656 . . .
1 60 . T G,G . PASS IFD=-907.099,.,-658.952,-869.897,897.771,931.264,616.795,-390.772,-804.656 . . .
Expand All @@ -114,28 +114,28 @@
1 65 . T G,G . PASS IFD=-907.099,215.09,-658.952,-869.897,897.771,931.264,.,-390.772,-804.656 . . .
1 66 . T G,G . PASS IFD=-907.099,215.09,-658.952,-869.897,897.771,931.264,616.795,.,-804.656 . . .
1 67 . T G,G . PASS IFD=-907.099,215.09,-658.952,-869.897,897.771,931.264,616.795,-390.772,. . . .
1 68 . T G,G . PASS IFD=.,.,.,.,.,.,.,.,. . . .
1 68 . T G,G . PASS . . . .
1 69 . T C,G . PASS IC1=f . . .
1 70 . T C,G . PASS IC1=. . . .
1 70 . T C,G . PASS . . . .
1 71 . G T,G . PASS IC2=e,a . . .
1 72 . G T,G . PASS IC2=.,a . . .
1 73 . G T,G . PASS IC2=e,. . . .
1 74 . G T,G . PASS IC2=.,. . . .
1 74 . G T,G . PASS . . . .
1 75 . A C,A . PASS ICA=b,a . . .
1 76 . A C,A . PASS ICA=.,a . . .
1 77 . A C,A . PASS ICA=b,. . . .
1 78 . A C,A . PASS ICA=.,. . . .
1 78 . A C,A . PASS . . . .
1 79 . C G,C . PASS ICR=c,b,b . . .
1 80 . C G,C . PASS ICR=.,b,b . . .
1 81 . C G,C . PASS ICR=c,.,b . . .
1 82 . C G,C . PASS ICR=c,b,. . . .
1 83 . C G,C . PASS ICR=.,.,. . . .
1 83 . C G,C . PASS . . . .
1 84 . T G,G . PASS ICD=b,f,b,c . . .
1 85 . T G,G . PASS ICD=.,f,b,c . . .
1 86 . T G,G . PASS ICD=b,.,b,c . . .
1 87 . T G,G . PASS ICD=b,f,.,c . . .
1 88 . T G,G . PASS ICD=b,f,b,. . . .
1 89 . T G,G . PASS ICD=.,.,.,. . . .
1 89 . T G,G . PASS . . . .
1 90 . T G,G . PASS ICD=g,e,d,e,f,f,b . . .
1 91 . T G,G . PASS ICD=.,e,d,e,f,f,b . . .
1 92 . T G,G . PASS ICD=g,.,d,e,f,f,b . . .
Expand All @@ -144,22 +144,22 @@
1 95 . T G,G . PASS ICD=g,e,d,e,.,f,b . . .
1 96 . T G,G . PASS ICD=g,e,d,e,f,.,b . . .
1 97 . T G,G . PASS ICD=g,e,d,e,f,f,. . . .
1 98 . T G,G . PASS ICD=.,.,.,.,.,.,. . . .
1 98 . T G,G . PASS . . . .
1 99 . A C,C . PASS IS1=bc . . .
1 100 . A C,C . PASS IS1=. . . .
1 100 . A C,C . PASS . . . .
1 101 . T T,C . PASS IS2=hij,d . . .
1 102 . T T,C . PASS IS2=.,d . . .
1 103 . T T,C . PASS IS2=hij,. . . .
1 104 . T T,C . PASS IS2=.,. . . .
1 104 . T T,C . PASS . . . .
1 105 . T C,C . PASS ISA=bc,efg . . .
1 106 . T C,C . PASS ISA=.,efg . . .
1 107 . T C,C . PASS ISA=bc,. . . .
1 108 . T C,C . PASS ISA=.,. . . .
1 108 . T C,C . PASS . . . .
1 109 . C G,T . PASS ISR=d,bc,op . . .
1 110 . C G,T . PASS ISR=.,bc,op . . .
1 111 . C G,T . PASS ISR=d,.,op . . .
1 112 . C G,T . PASS ISR=d,bc,. . . .
1 113 . C G,T . PASS ISR=.,.,. . . .
1 113 . C G,T . PASS . . . .
1 114 . G A,A . PASS ISD=ab,hij,klmn,d,ab,d,op,efg . . .
1 115 . G A,A . PASS ISD=.,hij,klmn,d,ab,d,op,efg . . .
1 116 . G A,A . PASS ISD=ab,.,klmn,d,ab,d,op,efg . . .
Expand All @@ -169,89 +169,89 @@
1 120 . G A,A . PASS ISD=ab,hij,klmn,d,ab,.,op,efg . . .
1 121 . G A,A . PASS ISD=ab,hij,klmn,d,ab,d,.,efg . . .
1 122 . G A,A . PASS ISD=ab,hij,klmn,d,ab,d,op,. . . .
1 123 . G A,A . PASS ISD=.,.,.,.,.,.,.,. . . .
1 123 . G A,A . PASS . . . .
1 124 . G A,A . PASS ISD=op,op,ab . . .
1 125 . G A,A . PASS ISD=.,op,ab . . .
1 126 . G A,A . PASS ISD=op,.,ab . . .
1 127 . G A,A . PASS ISD=op,op,. . . .
1 128 . G A,A . PASS ISD=.,.,. . . .
1 128 . G A,A . PASS . . . .
2 129 . G G,G . PASS . FI1 -795 .
2 130 . C G,A . PASS . FI2 104,955 .,955
2 131 . C G,A . PASS . FI2 104,. .,.
2 131 . C G,A . PASS . FI2 104,. .
2 132 . C C,T . PASS . FIA 585,895 .,895
2 133 . C C,T . PASS . FIA 585,. .,.
2 133 . C C,T . PASS . FIA 585,. .
2 134 . T C,G . PASS . FIR 411,25,21 .,25,21
2 135 . T C,G . PASS . FIR 411,.,21 411,25,.
2 136 . T C,G . PASS . FIR .,.,. .,.,.
2 136 . T C,G . PASS . FIR . .
2 137 . A T,T . PASS . FIG 413,-435,129,795,845,500 .,-435,129,795,845,500
2 138 . A T,T . PASS . FIG 413,.,129,795,845,500 413,-435,.,795,845,500
2 139 . A T,T . PASS . FIG 413,-435,129,.,845,500 413,-435,129,795,.,500
2 140 . A T,T . PASS . FIG 413,-435,129,795,845,. .,.,.,.,.,.
2 140 . A T,T . PASS . FIG 413,-435,129,795,845,. .
2 141 . C G,G . PASS . FID -271,579 .,579
2 142 . C G,G . PASS . FID -271,. .,.
2 142 . C G,G . PASS . FID -271,. .
2 143 . C G,G . PASS . FID -799,981 .,981
2 144 . C G,G . PASS . FID -799,. .,.
2 144 . C G,G . PASS . FID -799,. .
2 145 . A T,G . PASS . FF1 853.318 .
2 146 . T G,A . PASS . FF2 454.544,-346.918 .,-346.918
2 147 . T G,A . PASS . FF2 454.544,. .,.
2 147 . T G,A . PASS . FF2 454.544,. .
2 148 . C A,T . PASS . FFA 140.888,41.6685 .,41.6685
2 149 . C A,T . PASS . FFA 140.888,. .,.
2 149 . C A,T . PASS . FFA 140.888,. .
2 150 . T T,C . PASS . FFR 922.344,689.068,494.64 .,689.068,494.64
2 151 . T T,C . PASS . FFR 922.344,.,494.64 922.344,689.068,.
2 152 . T T,C . PASS . FFR .,.,. .,.,.
2 152 . T T,C . PASS . FFR . .
2 153 . A T,T . PASS . FFG 79.3843,173.502,930.511,214.068,-448.002,-407.453 .,173.502,930.511,214.068,-448.002,-407.453
2 154 . A T,T . PASS . FFG 79.3843,.,930.511,214.068,-448.002,-407.453 79.3843,173.502,.,214.068,-448.002,-407.453
2 155 . A T,T . PASS . FFG 79.3843,173.502,930.511,.,-448.002,-407.453 79.3843,173.502,930.511,214.068,.,-407.453
2 156 . A T,T . PASS . FFG 79.3843,173.502,930.511,214.068,-448.002,. .,.,.,.,.,.
2 156 . A T,T . PASS . FFG 79.3843,173.502,930.511,214.068,-448.002,. .
2 157 . A C,A . PASS . FFD -968.727 .
2 158 . A C,A . PASS . FFD 544.49,-602.569,-988.956,630.923,413.715,458.014,542.541,-851.911,-283.069 .,-602.569,-988.956,630.923,413.715,458.014,542.541,-851.911,-283.069
2 159 . A C,A . PASS . FFD 544.49,.,-988.956,630.923,413.715,458.014,542.541,-851.911,-283.069 544.49,-602.569,.,630.923,413.715,458.014,542.541,-851.911,-283.069
2 160 . A C,A . PASS . FFD 544.49,-602.569,-988.956,.,413.715,458.014,542.541,-851.911,-283.069 544.49,-602.569,-988.956,630.923,.,458.014,542.541,-851.911,-283.069
2 161 . A C,A . PASS . FFD 544.49,-602.569,-988.956,630.923,413.715,.,542.541,-851.911,-283.069 544.49,-602.569,-988.956,630.923,413.715,458.014,.,-851.911,-283.069
2 162 . A C,A . PASS . FFD 544.49,-602.569,-988.956,630.923,413.715,458.014,542.541,.,-283.069 544.49,-602.569,-988.956,630.923,413.715,458.014,542.541,-851.911,.
2 163 . A C,A . PASS . FFD .,.,.,.,.,.,.,.,. .,.,.,.,.,.,.,.,.
2 163 . A C,A . PASS . FFD . .
2 164 . T T,A . PASS . FC1 d .
2 165 . G C,T . PASS . FC2 c,b .,b
2 166 . G C,T . PASS . FC2 c,. .,.
2 166 . G C,T . PASS . FC2 c,. .
2 167 . G G,A . PASS . FCA c,g .,g
2 168 . G G,A . PASS . FCA c,. .,.
2 168 . G G,A . PASS . FCA c,. .
2 169 . G C,G . PASS . FCR a,b,c .,b,c
2 170 . G C,G . PASS . FCR a,.,c a,b,.
2 171 . G C,G . PASS . FCR .,.,. .,.,.
2 171 . G C,G . PASS . FCR . .
2 172 . G A,A . PASS . FCG a,e,b,g,g,a .,e,b,g,g,a
2 173 . G A,A . PASS . FCG a,.,b,g,g,a a,e,.,g,g,a
2 174 . G A,A . PASS . FCG a,e,b,.,g,a a,e,b,g,.,a
2 175 . G A,A . PASS . FCG a,e,b,g,g,. .,.,.,.,.,.
2 175 . G A,A . PASS . FCG a,e,b,g,g,. .
2 176 . A G,A . PASS . FCD a,g,d,d,f,f,b,a,d .,g,d,d,f,f,b,a,d
2 177 . A G,A . PASS . FCD a,.,d,d,f,f,b,a,d a,g,.,d,f,f,b,a,d
2 178 . A G,A . PASS . FCD a,g,d,.,f,f,b,a,d a,g,d,d,.,f,b,a,d
2 179 . A G,A . PASS . FCD a,g,d,d,f,.,b,a,d a,g,d,d,f,f,.,a,d
2 180 . A G,A . PASS . FCD a,g,d,d,f,f,b,.,d a,g,d,d,f,f,b,a,.
2 181 . A G,A . PASS . FCD .,.,.,.,.,.,.,.,. c,d,f,e,g,a,c
2 181 . A G,A . PASS . FCD . c,d,f,e,g,a,c
2 182 . A G,A . PASS . FCD .,d,f,e,g,a,c c,.,f,e,g,a,c
2 183 . A G,A . PASS . FCD c,d,.,e,g,a,c c,d,f,.,g,a,c
2 184 . A G,A . PASS . FCD c,d,f,e,.,a,c c,d,f,e,g,.,c
2 185 . A G,A . PASS . FCD c,d,f,e,g,a,. .,.,.,.,.,.,.
2 185 . A G,A . PASS . FCD c,d,f,e,g,a,. .
2 186 . C T,A . PASS . FS1 bc .
2 187 . C C,C . PASS . FS2 bc,op .,op
2 188 . C C,C . PASS . FS2 bc,. .,.
2 188 . C C,C . PASS . FS2 bc,. .
2 189 . C T,G . PASS . FSA ab,op .,op
2 190 . C T,G . PASS . FSA ab,. .,.
2 190 . C T,G . PASS . FSA ab,. .
2 191 . T T,T . PASS . FSR klmn,bc,efg .,bc,efg
2 192 . T T,T . PASS . FSR klmn,.,efg klmn,bc,.
2 193 . T T,T . PASS . FSR .,.,. .,.,.
2 193 . T T,T . PASS . FSR . .
2 194 . A C,A . PASS . FSG d,op,bc,klmn,efg,d .,op,bc,klmn,efg,d
2 195 . A C,A . PASS . FSG d,.,bc,klmn,efg,d d,op,.,klmn,efg,d
2 196 . A C,A . PASS . FSG d,op,bc,.,efg,d d,op,bc,klmn,.,d
2 197 . A C,A . PASS . FSG d,op,bc,klmn,efg,. .,.,.,.,.,.
2 197 . A C,A . PASS . FSG d,op,bc,klmn,efg,. .
2 198 . T T,G . PASS . FSD klmn,bc,d,op,hij,efg,klmn,ab,hij .,bc,d,op,hij,efg,klmn,ab,hij
2 199 . T T,G . PASS . FSD klmn,.,d,op,hij,efg,klmn,ab,hij klmn,bc,.,op,hij,efg,klmn,ab,hij
2 200 . T T,G . PASS . FSD klmn,bc,d,.,hij,efg,klmn,ab,hij klmn,bc,d,op,.,efg,klmn,ab,hij
2 201 . T T,G . PASS . FSD klmn,bc,d,op,hij,.,klmn,ab,hij klmn,bc,d,op,hij,efg,.,ab,hij
2 202 . T T,G . PASS . FSD klmn,bc,d,op,hij,efg,klmn,.,hij klmn,bc,d,op,hij,efg,klmn,ab,.
2 203 . T T,G . PASS . FSD .,.,.,.,.,.,.,.,. efg,klmn,bc,op,ab,bc,hij,hij
2 203 . T T,G . PASS . FSD . efg,klmn,bc,op,ab,bc,hij,hij
2 204 . T T,G . PASS . FSD .,klmn,bc,op,ab,bc,hij,hij efg,.,bc,op,ab,bc,hij,hij
2 205 . T T,G . PASS . FSD efg,klmn,.,op,ab,bc,hij,hij efg,klmn,bc,.,ab,bc,hij,hij
2 206 . T T,G . PASS . FSD efg,klmn,bc,op,.,bc,hij,hij efg,klmn,bc,op,ab,.,hij,hij
2 207 . T T,G . PASS . FSD efg,klmn,bc,op,ab,bc,.,hij efg,klmn,bc,op,ab,bc,hij,.
2 208 . T T,G . PASS . FSD .,.,.,.,.,.,.,. .,.,.,.,.,.,.,.
2 208 . T T,G . PASS . FSD . .
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