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Searched refs:base_quality (Results 1 – 25 of 100) sorted by relevance

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/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/
H A DtwoSamples.MT.g.vcf5 ##FILTER=<ID=base_quality,Description="alt median base quality">
384 …base_quality;t_lod CONTQ=93.00;DP=6987 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD ././.:3245,7,0:3.055e…
520 …base_quality;t_lod CONTQ=93.00;DP=7613 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD ././.:3631,52,0:3.160…
582 …base_quality;t_lod CONTQ=93.00;DP=10284 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD ././.:5069,21,0:2.59…
695 …base_quality;t_lod CONTQ=93.00;DP=13272 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD ././.:6480,7,0:2.802…
698 …base_quality;t_lod CONTQ=93.00;DP=13420 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD ././.:6554,10,0:1.52…
1045 …base_quality;t_lod CONTQ=93.00;DP=13189 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD ././.:6449,20,0:2.67…
1050 …base_quality;t_lod CONTQ=93.00;DP=13162 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD ././.:6419,6,0:1.825…
1959 …base_quality;t_lod CONTQ=93.00;DP=12989 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD ././.:6326,5,0:1.630…
1964 …base_quality;t_lod CONTQ=93.00;DP=12966 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD ././.:6317,10,0:1.75…
[all …]
H A DtwoSamples.MT.vcf5 ##FILTER=<ID=base_quality,Description="alt median base quality">
386 …base_quality;t_lod CONTQ=93.00;DP=6987;MFRL=315;MPOS=7;POPAF=7.30;SAAF=0.010;SAPP=0.378 GT:AD:AF:D…
522 …base_quality;t_lod CONTQ=93.00;DP=7613;MFRL=319;MPOS=26;POPAF=7.30;SAAF=0.010;SAPP=0.074 GT:AD:AF:…
584 …base_quality;t_lod CONTQ=93.00;DP=10284;MFRL=329;MPOS=28;POPAF=7.30;SAAF=0.010;SAPP=1.639e-03 GT:A…
697 …base_quality;t_lod CONTQ=93.00;DP=13272;MFRL=339;MPOS=22;POPAF=7.30;SAAF=0.010;SAPP=6.565e-04 GT:A…
700 …base_quality;t_lod CONTQ=93.00;DP=13420;MFRL=336;MPOS=31;POPAF=7.30;SAAF=0.010;SAPP=1.489e-03 GT:A…
1047 …base_quality;t_lod CONTQ=93.00;DP=13189;MFRL=348;MPOS=32;POPAF=7.30;SAAF=0.010;SAPP=1.666e-03 GT:A…
1052 …base_quality;t_lod CONTQ=93.00;DP=13162;MFRL=348;MPOS=24;POPAF=7.30;SAAF=0.010;SAPP=1.445e-03 GT:A…
1961 …base_quality;t_lod CONTQ=93.00;DP=12989;MFRL=345;MPOS=29;POPAF=7.30;SAAF=0.010;SAPP=5.681e-04 GT:A…
6549 …base_quality;t_lod CONTQ=93.00;DP=8011;MFRL=330;MPOS=6;POPAF=7.30;SAAF=0.010;SAPP=0.028 GT:AD:AF:D…
[all …]
H A DNA19240.MT.filtered.g.vcf5 ##FILTER=<ID=base_quality,Description="alt median base quality">
215 MT 136 . G T,<NON_REF> . base_quality;t_lod CONTQ=93;DP=5034;ECNT=33;MBQ=28,12,0;MFRL=417,476,0;MMQ…
217 MT 141 . C A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=5229;ECNT=33;MBQ=29,8,0;MFRL=416,8215,0;MMQ…
227 MT 163 . G T,<NON_REF> . base_quality;t_lod CONTQ=93;DP=5696;ECNT=33;MBQ=25,13,0;MFRL=392,484,0;MMQ…
231 MT 185 . G T,<NON_REF> . base_quality;t_lod CONTQ=93;DP=5738;ECNT=33;MBQ=28,12,0;MFRL=364,331,0;MMQ…
233 MT 187 . G T,<NON_REF> . base_quality;t_lod CONTQ=93;DP=5740;ECNT=33;MBQ=25,5,0;MFRL=362,8166,0;MMQ…
236 MT 190 . C A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=5774;ECNT=33;MBQ=28,2,0;MFRL=358,332,0;MMQ=…
253 MT 214 . A C,<NON_REF> . base_quality;t_lod CONTQ=93;DP=5909;ECNT=33;MBQ=29,6,0;MFRL=338,311,0;MMQ=…
259 MT 224 . T G,<NON_REF> . base_quality;t_lod CONTQ=93;DP=5952;ECNT=33;MBQ=29,9,0;MFRL=334,287,0;MMQ=…
295 MT 292 . T A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=3553;ECNT=24;MBQ=28,2,0;MFRL=315,383,0;MMQ=…
[all …]
H A DNA12891.MT.filtered.g.vcf5 ##FILTER=<ID=base_quality,Description="alt median base quality">
179 MT 38 . G A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=1595;ECNT=3;MBQ=29,16,0;MFRL=511,402,0;MMQ=6…
181 MT 44 . C A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=1862;ECNT=3;MBQ=29,15,0;MFRL=503,16179,0;MMQ…
182 MT 45 . A C,<NON_REF> . base_quality;t_lod CONTQ=93;DP=1905;ECNT=3;MBQ=29,10,0;MFRL=502,16210,0;MMQ…
244 MT 187 . G T,<NON_REF> . base_quality;t_lod CONTQ=93;DP=6157;ECNT=28;MBQ=27,13,0;MFRL=415,508,0;MMQ…
254 MT 203 . G T,<NON_REF> . base_quality;t_lod CONTQ=93;DP=5698;ECNT=28;MBQ=29,14,0;MFRL=392,470,0;MMQ…
256 MT 239 . T C,<NON_REF> . base_quality;t_lod CONTQ=93;DP=4739;ECNT=28;MBQ=30,10,0;MFRL=345,341,0;MMQ…
288 MT 298 . C A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=3683;ECNT=28;MBQ=29,7,0;MFRL=328,434,0;MMQ=…
289 MT 299 . C A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=3670;ECNT=28;MBQ=28,2,0;MFRL=329,345,0;MMQ=…
290 MT 300 . A C,<NON_REF> . base_quality;t_lod CONTQ=93;DP=3688;ECNT=28;MBQ=28,4,0;MFRL=329,319,0;MMQ=…
[all …]
H A DNA12878.MT.filtered.g.vcf5 ##FILTER=<ID=base_quality,Description="alt median base quality">
176 MT 37 . A G,<NON_REF> . base_quality;t_lod CONTQ=93;DP=1594;ECNT=4;MBQ=27,6,0;MFRL=575,15999,0;MMQ=…
224 MT 124 . G T,<NON_REF> . base_quality;t_lod CONTQ=93;DP=5406;ECNT=17;MBQ=28,12,0;MFRL=500,411,0;MMQ…
238 MT 167 . C A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=6646;ECNT=17;MBQ=28,13,0;MFRL=410,450,0;MMQ…
241 MT 171 . G A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=6617;ECNT=17;MBQ=25,12,0;MFRL=404,394,0;MMQ…
243 MT 175 . A C,<NON_REF> . base_quality;t_lod CONTQ=93;DP=6592;ECNT=17;MBQ=29,8,0;MFRL=395,385,0;MMQ=…
266 MT 231 . C A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=4801;ECNT=23;MBQ=28,7,0;MFRL=342,266,0;MMQ=…
302 MT 292 . T A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=3434;ECNT=23;MBQ=28,12,0;MFRL=318,269,0;MMQ…
306 MT 296 . C A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=3398;ECNT=23;MBQ=28,2,0;MFRL=317,539,0;MMQ=…
2013 MT 4783 . A C,<NON_REF> . base_quality;t_lod CONTQ=93;DP=958;ECNT=8;MBQ=28,9,0;MFRL=335,327,0;MMQ=6…
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/
H A DthreeSamples.MT.g.vcf5 ##FILTER=<ID=base_quality,Description="alt median base quality">
580 …base_quality;t_lod CONTQ=93.00;DP=11345 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:SAAF:SAPP:TLOD ././.:3631…
602 …base_quality;strand_artifact;t_lod CONTQ=93.00;DP=11613 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:SAAF:SAPP…
608 …base_quality;t_lod CONTQ=93.00;DP=11389 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:SAAF:SAPP:TLOD ./.:3760,0…
779 …base_quality;t_lod CONTQ=93.00;DP=20398 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:SAAF:SAPP:TLOD ././.:6554…
1216 …base_quality;t_lod CONTQ=93.00;DP=19988 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:SAAF:SAPP:TLOD ././.:6449…
2377 …base_quality;t_lod CONTQ=93.00;DP=19676 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:SAAF:SAPP:TLOD ././.:6317…
7952 …base_quality;t_lod CONTQ=93.00;DP=12866 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:SAAF:SAPP:TLOD ././.:4213…
7953 …base_quality;t_lod CONTQ=93.00;DP=12893 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:SAAF:SAPP:TLOD ././.:4087…
7959 …base_quality;t_lod CONTQ=93.00;DP=13052 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:SAAF:SAPP:TLOD ././.:4186…
[all …]
H A DthreeSamples.MT.vcf5 ##FILTER=<ID=base_quality,Description="alt median base quality">
181 …base_quality;strand_artifact;t_lod CONTQ=93.00;DP=10123 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD 0/1:…
185 …base_quality;strand_artifact CONTQ=93.00;DP=10022 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:PGT:PID:PS:TLOD…
186 …base_quality;strand_artifact CONTQ=93.00;DP=11229 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:PGT:PID:PS:TLOD…
187 …base_quality CONTQ=93.00;DP=11622 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:PGT:PID:PS:TLOD 0:4386,0:0.00:4…
189 …base_quality;t_lod CONTQ=93.00;DP=17598 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD 0/1/2:6418,0,0:0.00,…
204 …base_quality;t_lod CONTQ=93.00;DP=19827 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD 0:6748,0,0:0.00,0.00…
224 …base_quality;t_lod CONTQ=93.00;DP=15745 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD 0/1:6044,0:0.00:6044…
226 …base_quality;t_lod CONTQ=93.00;DP=15649 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD 0/1:5858,0:0.00:5858…
239 …base_quality CONTQ=93.00;DP=15891 GT:AD:AF:DP:FT:MBQ:MFRL:MMQ:MPOS:TLOD 0:6421,0,0:0.00,0.00:6421:…
[all …]
H A DthreeSamples.2alts.vcf5 ##FILTER=<ID=base_quality,Description="alt median base quality">
179 …MMQ:TLOD 0/1:2505,360:0.045:2933:base_quality;strand_artifact:24,14:60,60:40.44 0/1:3125,192:8.308…
180 …base_quality:12,15,15:60,60,60:3307.49,64.62 0/./1/2/./.:50,1395,589:0.632,0.257:2485:PASS:29,22,2…
183 …+00 0:3397,0:0.00:3397:PASS:.,.:.,.:-3.533e+00 0|1:3361,74:0.011:3435:base_quality;strand_artifact…
184 …0:3487,0:0.00:3487:PASS:.,.:.,.:-3.541e+00 0|1:3490,69:9.096e-03:3559:base_quality;strand_artifact…
185 …0:3700,0:0.00:3700:PASS:.,.:.,.:-3.562e+00 0|1:3415,63:9.006e-03:3478:base_quality:29,2:60,60:21.06
199 …MMQ:TLOD 0/1:55,231:0.805:287:PASS:11,27:60,60:643.99 0:37,0:0.013:48:base_quality;t_lod:10,0:60,0…
200 …AF=0.990;SAPP=0.030 GT:AD:AF:DP:FT:MBQ:MMQ:TLOD 0:781,0:1.220e-03:783:base_quality;t_lod:29,0:60,0…
218 …D 0:7027,0:0.00:7027:PASS:.,.:.,.:-2.419e+00 0:6607,22:1.519e-04:6629:base_quality;t_lod:29,7:60,6…
222 …,.:.,.:5.07 0:4732,42:2.181e-04:4774:base_quality;t_lod:28,8:60,60:-3.361e+00 0:4590,38:2.922e-04:…
[all …]
/dports/multimedia/xvid/xvidcore/src/plugins/
H A Dplugin_single.c182 double base_quality; in rc_single_after() local
233 base_quality = rc->sequence_quality; in rc_single_after()
235 base_quality = 1.0 - (1.0 - base_quality) / quality_scale; in rc_single_after()
237 base_quality = 0.06452 + (base_quality - 0.06452) * quality_scale; in rc_single_after()
251 base_quality + (base_quality - in rc_single_after()
/dports/japanese/timidity++-slang/TiMidity++-2.15.0/timidity/
H A Dw32g_vorbisenc_dll.c39 …edef int(*type_vorbis_encode_init_vbr)(vorbis_info *vi,long channels,long rate,float base_quality);
81 int vorbis_encode_init_vbr(vorbis_info *vi,long channels,long rate,float base_quality) in vorbis_encode_init_vbr() argument
84 return vorbisenc_dll.vorbis_encode_init_vbr(vi,channels,rate,base_quality); in vorbis_encode_init_vbr()
/dports/audio/ocp/ocp-0.2.90/playgmi/timidity-git/timidity/
H A Dw32g_vorbisenc_dll.c39 …edef int(*type_vorbis_encode_init_vbr)(vorbis_info *vi,long channels,long rate,float base_quality);
81 int vorbis_encode_init_vbr(vorbis_info *vi,long channels,long rate,float base_quality) in vorbis_encode_init_vbr() argument
84 return vorbisenc_dll.vorbis_encode_init_vbr(vi,channels,rate,base_quality); in vorbis_encode_init_vbr()
/dports/audio/timidity++-xaw/TiMidity++-2.15.0/timidity/
H A Dw32g_vorbisenc_dll.c39 …edef int(*type_vorbis_encode_init_vbr)(vorbis_info *vi,long channels,long rate,float base_quality);
81 int vorbis_encode_init_vbr(vorbis_info *vi,long channels,long rate,float base_quality)
84 return vorbisenc_dll.vorbis_encode_init_vbr(vi,channels,rate,base_quality);
/dports/audio/timidity++/TiMidity++-2.15.0/timidity/
H A Dw32g_vorbisenc_dll.c39 …edef int(*type_vorbis_encode_init_vbr)(vorbis_info *vi,long channels,long rate,float base_quality);
81 int vorbis_encode_init_vbr(vorbis_info *vi,long channels,long rate,float base_quality) in vorbis_encode_init_vbr() argument
84 return vorbisenc_dll.vorbis_encode_init_vbr(vi,channels,rate,base_quality); in vorbis_encode_init_vbr()
/dports/audio/timidity++-emacs/TiMidity++-2.15.0/timidity/
H A Dw32g_vorbisenc_dll.c39 …edef int(*type_vorbis_encode_init_vbr)(vorbis_info *vi,long channels,long rate,float base_quality);
81 int vorbis_encode_init_vbr(vorbis_info *vi,long channels,long rate,float base_quality)
84 return vorbisenc_dll.vorbis_encode_init_vbr(vi,channels,rate,base_quality);
/dports/audio/timidity++-motif/TiMidity++-2.15.0/timidity/
H A Dw32g_vorbisenc_dll.c39 …edef int(*type_vorbis_encode_init_vbr)(vorbis_info *vi,long channels,long rate,float base_quality);
81 int vorbis_encode_init_vbr(vorbis_info *vi,long channels,long rate,float base_quality) in vorbis_encode_init_vbr() argument
84 return vorbisenc_dll.vorbis_encode_init_vbr(vi,channels,rate,base_quality); in vorbis_encode_init_vbr()
/dports/audio/timidity++-xskin/TiMidity++-2.15.0/timidity/
H A Dw32g_vorbisenc_dll.c39 …edef int(*type_vorbis_encode_init_vbr)(vorbis_info *vi,long channels,long rate,float base_quality);
81 int vorbis_encode_init_vbr(vorbis_info *vi,long channels,long rate,float base_quality) in vorbis_encode_init_vbr() argument
84 return vorbisenc_dll.vorbis_encode_init_vbr(vi,channels,rate,base_quality); in vorbis_encode_init_vbr()
/dports/audio/timidity++-slang/TiMidity++-2.15.0/timidity/
H A Dw32g_vorbisenc_dll.c39 …edef int(*type_vorbis_encode_init_vbr)(vorbis_info *vi,long channels,long rate,float base_quality);
81 int vorbis_encode_init_vbr(vorbis_info *vi,long channels,long rate,float base_quality) in vorbis_encode_init_vbr() argument
84 return vorbisenc_dll.vorbis_encode_init_vbr(vi,channels,rate,base_quality); in vorbis_encode_init_vbr()
/dports/audio/timidity++-gtk/TiMidity++-2.15.0/timidity/
H A Dw32g_vorbisenc_dll.c39 …edef int(*type_vorbis_encode_init_vbr)(vorbis_info *vi,long channels,long rate,float base_quality);
81 int vorbis_encode_init_vbr(vorbis_info *vi,long channels,long rate,float base_quality) in vorbis_encode_init_vbr() argument
84 return vorbisenc_dll.vorbis_encode_init_vbr(vi,channels,rate,base_quality); in vorbis_encode_init_vbr()
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/mitochondria/
H A DNA12878.MT.filtered.g.vcf5 ##FILTER=<ID=base_quality,Description="alt median base quality">
178 MT 37 . A G,<NON_REF> . base_quality;t_lod CONTQ=93;DP=1594;ECNT=4;MBQ=27,6,0;MFRL=575,15999,0;MMQ=…
226 MT 124 . G T,<NON_REF> . base_quality;t_lod CONTQ=93;DP=5406;ECNT=17;MBQ=28,12,0;MFRL=500,411,0;MMQ…
240 MT 167 . C A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=6646;ECNT=17;MBQ=28,13,0;MFRL=410,450,0;MMQ…
249 MT 183 . A T,<NON_REF> . base_quality;t_lod CONTQ=93;DP=6554;ECNT=17;MBQ=29,13,0;MFRL=383,419,0;MMQ…
268 MT 231 . C A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=4801;ECNT=23;MBQ=28,7,0;MFRL=342,266,0;MMQ=…
275 MT 247 . G T,<NON_REF> . base_quality;t_lod CONTQ=93;DP=4357;ECNT=23;MBQ=28,12,0;MFRL=329,411,0;MMQ…
304 MT 292 . T A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=3434;ECNT=23;MBQ=28,12,0;MFRL=318,269,0;MMQ…
305 MT 293 . T A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=3426;ECNT=23;MBQ=28,12,0;MFRL=317,394,0;MMQ…
307 MT 295 . C A,<NON_REF> . base_quality;t_lod CONTQ=93;DP=3399;ECNT=23;MBQ=28,11,0;MFRL=317,319,0;MMQ…
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/main/python/org/broadinstitute/hellbender/vqsr_cnn/vqsr_cnn/
H A Dinference.py426 def base_quality_to_phred_array(base_quality: int, base: str, base_dict: Dict) -> np.ndarray:
428 exponent = float(-base_quality) / 10.0
437 phred[base_dict[b]] = base_quality
443 def base_quality_to_p_hot_array(base_quality: int, base: str, base_dict: Dict) -> np.ndarray:
444 not_p = not_p_lut[base_quality]
446 phot[base_dict[base]] = p_lut[base_quality]
451 def quality_from_mode(base_quality: int, base: str, base_dict: Dict, base_quality_mode: str) -> np.…
453 return base_quality_to_p_hot_array(base_quality, base, base_dict)
455 return base_quality_to_phred_array(base_quality, base, base_dict)
/dports/games/diaspora/Diaspora_R1_Linux/Diaspora/fs2_open/oggvorbis/include/vorbis/
H A Dvorbisenc.h55 float base_quality /* quality level from 0. (lo) to 1. (hi) */
/dports/multimedia/gpac-libgpac/gpac-1.0.0/extra_lib/include/vorbis/
H A Dvorbisenc.h55 float base_quality /* quality level from 0. (lo) to 1. (hi) */
/dports/multimedia/gpac-mp4box/gpac-1.0.0/extra_lib/include/vorbis/
H A Dvorbisenc.h55 float base_quality /* quality level from 0. (lo) to 1. (hi) */
/dports/games/ags/ags_linux_v.3.4.4.1/Common/libinclude/vorbis/
H A Dvorbisenc.h55 float base_quality /* quality level from 0. (lo) to 1. (hi) */
/dports/games/assaultcube/AssaultCube_v1.2.0.2/source/include/vorbis/
H A Dvorbisenc.h55 float base_quality /* quality level from 0. (lo) to 1. (hi) */

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