Does OptiType only predict alleles in "freq_alleles"
mourisl opened this issue · comments
Thank you for developing this super accurate HLA genotyper. I was going through the code, and found that the results seemed to be filtered by the alleles series listed in freq_alleles (
Line 136 in 07c49bf
| freq_alleles = '''A*01:01 A*01:02 A*01:03 A*01:06 A*01:09 A*01:23 A*01:38 A*01:44 A*02:01 A*02:02 A*02:03 A*02:04 A*02:05 A*02:06 A*02:07 A*02:08 A*02:09 A*02:10 A*02:11 A*02:12 A*02:13 A*02:133 A*02:14 A*02:141 A*02:146 A*02:15N A*02:16 A*02:17 A*02:18 A*02:19 A*02:20 A*02:21 A*02:22 A*02:226N A*02:24 A*02:25 A*02:26 A*02:27 A*02:28 A*02:29 A*02:30 A*02:33 A*02:34 A*02:35 A*02:36 A*02:37 A*02:38 A*02:40 A*02:42 A*02:44 A*02:45 A*02:46 A*02:48 A*02:49 A*02:51 A*02:53N A*02:54 A*02:55 A*02:57 A*02:58 A*02:60 A*02:64 A*02:67 A*02:74 A*02:85 A*02:90 A*02:93 A*03:01 A*03:02 A*03:05 A*03:07 A*03:08 A*03:10 A*03:12 A*03:22 A*03:25 A*03:65 A*03:69N A*03:97 A*11:01 A*11:02 A*11:03 A*11:04 A*11:05 A*11:06 A*11:08 A*11:10 A*11:12 A*11:13 A*11:18 A*11:19 A*11:20 A*11:29 A*11:40 A*23:01 A*23:02 A*23:03 A*23:04 A*23:05 A*23:09 A*24:02 A*24:03 A*24:04 A*24:05 A*24:06 A*24:07 A*24:08 A*24:09N A*24:10 A*24:13 A*24:14 A*24:15 A*24:17 A*24:18 A*24:20 A*24:21 A*24:22 A*24:23 A*24:24 A*24:25 A*24:26 A*24:27 A*24:28 A*24:29 A*24:31 A*24:35 A*24:46 A*24:51 A*24:56 A*24:63 A*24:93 A*25:01 A*25:02 A*25:04 A*26:01 A*26:02 A*26:03 A*26:04 A*26:05 A*26:06 A*26:07 A*26:08 A*26:09 A*26:10 A*26:11N A*26:12 A*26:14 A*26:15 A*26:16 A*26:17 A*26:18 A*26:20 A*26:49 A*29:01 A*29:02 A*29:03 A*29:04 A*29:10 A*29:12 A*30:01 A*30:02 A*30:03 A*30:04 A*30:06 A*30:08 A*30:09 A*30:10 A*30:11 A*30:12 A*30:16 A*31:01 A*31:02 A*31:03 A*31:04 A*31:05 A*31:06 A*31:08 A*31:09 A*31:12 A*32:01 A*32:02 A*32:03 A*32:04 A*32:05 A*32:06 A*32:08 A*32:13 A*32:20 A*32:22 A*33:01 A*33:03 A*33:04 A*33:05 A*33:10 A*33:26 A*34:01 A*34:02 A*34:03 A*34:05 A*36:01 A*36:03 A*43:01 A*66:01 A*66:02 A*66:03 A*68:01 A*68:02 A*68:03 A*68:04 A*68:05 A*68:06 A*68:07 A*68:08 A*68:12 A*68:13 A*68:15 A*68:16 A*68:17 A*68:18N A*68:23 A*68:24 A*68:38 A*69:01 A*74:01 A*74:02 A*74:03 A*74:04 A*74:06 A*74:09 A*74:11 A*80:01 A*80:02 B*07:02 B*07:03 B*07:04 B*07:05 B*07:06 B*07:07 B*07:08 B*07:09 B*07:10 B*07:12 B*07:13 B*07:14 B*07:15 B*07:17 B*07:20 B*07:22 B*07:26 B*07:33 B*07:36 B*07:47 B*07:53 B*07:85 B*08:01 B*08:02 B*08:03 B*08:04 B*08:05 B*08:09 B*08:12 B*08:18 B*08:23 B*13:01 B*13:02 B*13:03 B*13:04 B*13:07N B*13:09 B*13:11 B*13:13 B*14:01 B*14:02 B*14:03 B*14:04 B*14:05 B*14:06 B*15:01 B*15:02 B*15:03 B*15:04 B*15:05 B*15:06 B*15:07 B*15:08 B*15:09 B*15:10 B*15:108 B*15:11 B*15:12 B*15:123 B*15:125 B*15:13 B*15:135 B*15:15 B*15:153 B*15:16 B*15:17 B*15:18 B*15:20 B*15:21 B*15:23 B*15:24 B*15:25 B*15:27 B*15:28 B*15:29 B*15:30 B*15:31 B*15:32 B*15:33 B*15:34 B*15:35 B*15:36 B*15:37 B*15:38 B*15:39 B*15:40 B*15:42 B*15:45 B*15:46 B*15:47 B*15:48 B*15:50 B*15:52 B*15:53 B*15:54 B*15:55 B*15:56 B*15:58 B*15:61 B*15:63 B*15:67 B*15:68 B*15:70 B*15:71 B*15:73 B*15:82 B*15:86 B*18:01 B*18:02 B*18:03 B*18:04 B*18:05 B*18:06 B*18:07 B*18:08 B*18:09 B*18:11 B*18:13 B*18:14 B*18:18 B*18:19 B*18:20 B*18:28 B*18:33 B*27:01 B*27:02 B*27:03 B*27:04 B*27:05 B*27:06 B*27:07 B*27:08 B*27:09 B*27:10 B*27:11 B*27:12 B*27:13 B*27:14 B*27:19 B*27:20 B*27:21 B*27:30 B*27:39 B*35:01 B*35:02 B*35:03 B*35:04 B*35:05 B*35:06 B*35:08 B*35:09 B*35:10 B*35:11 B*35:12 B*35:13 B*35:14 B*35:15 B*35:16 B*35:17 B*35:18 B*35:19 B*35:20 B*35:21 B*35:22 B*35:23 B*35:24 B*35:25 B*35:27 B*35:28 B*35:29 B*35:30 B*35:31 B*35:32 B*35:33 B*35:34 B*35:36 B*35:43 B*35:46 B*35:51 B*35:77 B*35:89 B*37:01 B*37:02 B*37:04 B*37:05 B*38:01 B*38:02 B*38:04 B*38:05 B*38:06 B*38:15 B*39:01 B*39:02 B*39:03 B*39:04 B*39:05 B*39:06 B*39:07 B*39:08 B*39:09 B*39:10 B*39:11 B*39:12 B*39:13 B*39:14 B*39:15 B*39:23 B*39:24 B*39:31 B*39:34 B*40:01 B*40:02 B*40:03 B*40:04 B*40:05 B*40:06 B*40:07 B*40:08 B*40:09 B*40:10 B*40:11 B*40:12 B*40:14 B*40:15 B*40:16 B*40:18 B*40:19 B*40:20 B*40:21 B*40:23 B*40:27 B*40:31 B*40:35 B*40:36 B*40:37 B*40:38 B*40:39 B*40:40 B*40:42 B*40:44 B*40:49 B*40:50 B*40:52 B*40:64 B*40:80 B*41:01 B*41:02 B*41:03 B*42:01 B*42:02 B*44:02 B*44:03 B*44:04 B*44:05 B*44:06 B*44:07 B*44:08 B*44:09 B*44:10 B*44:12 B*44:13 B*44:15 B*44:18 B*44:20 B*44:21 B*44:22 B*44:26 B*44:27 B*44:29 B*44:31 B*44:59 B*45:01 B*45:02 B*45:04 B*45:06 B*46:01 B*46:02 B*46:13 B*47:01 B*47:02 B*47:03 B*48:01 B*48:02 B*48:03 B*48:04 B*48:05 B*48:06 B*48:07 B*48:08 B*49:01 B*49:02 B*49:03 B*50:01 B*50:02 B*50:04 B*50:05 B*51:01 B*51:02 B*51:03 B*51:04 B*51:05 B*51:06 B*51:07 B*51:08 B*51:09 B*51:10 B*51:12 B*51:13 B*51:14 B*51:15 B*51:18 B*51:21 B*51:22 B*51:27N B*51:29 B*51:31 B*51:32 B*51:33 B*51:34 B*51:36 B*51:37 B*51:63 B*51:65 B*52:01 B*52:02 B*52:06 B*53:01 B*53:02 B*53:03 B*53:04 B*53:05 B*53:07 B*53:08 B*54:01 B*54:02 B*55:01 B*55:02 B*55:03 B*55:04 B*55:07 B*55:08 B*55:10 B*55:12 B*55:16 B*55:46 B*56:01 B*56:02 B*56:03 B*56:04 B*56:05 B*56:06 B*56:07 B*56:09 B*56:11 B*57:01 B*57:02 B*57:03 B*57:04 B*57:05 B*57:06 B*57:10 B*58:01 B*58:02 B*58:06 B*59:01 B*67:01 B*67:02 B*73:01 B*78:01 B*78:02 B*78:03 B*78:05 B*81:01 B*81:02 B*82:01 B*82:02 B*83:01 C*01:02 C*01:03 C*01:04 C*01:05 C*01:06 C*01:08 C*01:14 C*01:17 C*01:30 C*01:32 C*02:02 C*02:03 C*02:04 C*02:06 C*02:08 C*02:09 C*02:10 C*02:19 C*02:20 C*02:27 C*03:02 C*03:03 C*03:04 C*03:05 C*03:06 C*03:07 C*03:08 C*03:09 C*03:10 C*03:13 C*03:14 C*03:15 C*03:16 C*03:17 C*03:19 C*03:21 C*03:32 C*03:42 C*03:43 C*03:56 C*03:67 C*03:81 C*04:01 C*04:03 C*04:04 C*04:05 C*04:06 C*04:07 C*04:10 C*04:11 C*04:14 C*04:15 C*04:24 C*04:29 C*04:33 C*04:37 C*05:01 C*05:03 C*05:04 C*05:07N C*05:09 C*06:02 C*06:03 C*06:04 C*06:06 C*06:08 C*06:09 C*06:17 C*06:24 C*06:53 C*07:01 C*07:02 C*07:03 C*07:04 C*07:05 C*07:06 C*07:07 C*07:08 C*07:09 C*07:10 C*07:109 C*07:123 C*07:13 C*07:14 C*07:17 C*07:18 C*07:19 C*07:21 C*07:22 C*07:27 C*07:29 C*07:32N C*07:37 C*07:43 C*07:46 C*07:49 C*07:56 C*07:66 C*07:67 C*07:68 C*07:80 C*07:95 C*08:01 C*08:02 C*08:03 C*08:04 C*08:05 C*08:06 C*08:13 C*08:15 C*08:20 C*08:21 C*08:27 C*12:02 C*12:03 C*12:04 C*12:05 C*12:07 C*12:12 C*12:15 C*12:16 C*14:02 C*14:03 C*14:04 C*15:02 C*15:03 C*15:04 C*15:05 C*15:06 C*15:07 C*15:08 C*15:09 C*15:11 C*15:12 C*15:13 C*15:17 C*16:01 C*16:02 C*16:04 C*16:08 C*16:09 C*17:01 C*17:02 C*17:03 C*17:04 C*18:01 C*18:02 A*30:07 B*15:64 B*18:12'''.split(' ') |