| Next changeset 1:335665e15630 (2021-09-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" |
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added:
macros.xml test-data/global_phylo.nh test-data/global_samples.vcf.gz test-data/mutation_annotation.pb test-data/new_samples.vcf.gz test-data/rename_samples.tabular test-data/sample_names.txt test-data/test_01_annotated_tree.pb test-data/test_01_condensed_tree.nh test-data/test_01_final_tree.nh test-data/test_02_mutation_path.nh test-data/test_02_uncondensed_tree.nh test-data/test_03_condensed_tree.nh test-data/test_03_final_tree.nh test-data/test_04_mutation_paths.txt test-data/test_04_subtree_1.nh test-data/test_04_subtree_1_expanded.txt test-data/test_04_subtree_1_mutations.txt test-data/test_04_uncondensed_tree.nh test-data/test_05_current_tree.nw test-data/test_05_parsimony_scores.tabular test-data/test_06_final_tree.nh test-data/test_06_mutation_paths.txt test-data/test_07_single_subtree.nh test-data/test_07_single_subtree_mutations.txt test-data/test_08_final_tree.nh test-data/test_08_mutation_path.nh test-data/test_09_final_tree.nh test-data/test_09_mutation_path.nh test-data/test_10_final_tree.nh test-data/test_10_mutation_path.nh test-data/test_11_final_tree.nh test-data/test_11_mutation_path.nh test-data/test_12_final_tree.nh test-data/test_12_mutation_path.nh test-data/test_13_path_clades.tabular test-data/test_13_path_mutations.tabular test-data/test_13_sample_names.txt test-data/test_14_all_paths.txt test-data/test_14_path_clades.tabular test-data/test_14_path_mutations.tabular test-data/test_14_sample_names.txt test-data/test_15_mutation_annotated_tree.pb test-data/test_15_subtree.json test-data/test_15_subtree_no_genotype.vcf test-data/test_15_tree.nh test-data/test_16_path_mutations.tabular test-data/test_16_sample_names.txt test-data/test_17_all_paths.txt test-data/test_17_path_clades.tabular test-data/test_17_path_mutations.tabular test-data/test_17_sample_names.txt test-data/test_18_all_paths.txt test-data/test_18_path_clades.tabular test-data/test_18_path_mutations.tabular test-data/test_18_sample_names.txt test-data/test_19_path_clades.tabular test-data/test_19_path_mutations.tabular test-data/test_19_sample_names.txt test-data/test_20_general_stats.txt test-data/test_21_aberrant_stats.tabular test-data/test_21_clades_stats.tabular test-data/test_21_mutations_stats.tabular test-data/test_21_sample_stats.tabular test-data/test_22_total_parsimony_tree.txt test-data/test_23_equally_parsimoniou.tabular test-data/test_23_neighbourhood.tabular test-data/test_24_restricted.pb test-data/test_25_renamed.pb usher.xml |
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| diff -r 000000000000 -r 524cb8f7a69a macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 11 17:53:49 2021 +0000 |
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| @@ -0,0 +1,33 @@ +<macros> + <token name="@TOOL_VERSION@">0.2.1</token> + <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0194</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0540</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">usher</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/2020.09.26.314971</citation> + <citation type="doi">10.1101/2021.04.03.438321</citation> + </citations> + </xml> + <macro name="sanitize_string" > + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_"/> + <add value="-"/> + <add value="."/> + <add value=":"/> + </valid> + </sanitizer> + </macro> +</macros> |
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| diff -r 000000000000 -r 524cb8f7a69a test-data/global_phylo.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/global_phylo.nh Tue May 11 17:53:49 2021 +0000 |
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| b'@@ -0,0 +1,1 @@\n+((Shanghai_SH0007_2020,Hangzhou_ZJU-07_2020,Wuhan_IPBCAMS-WH-03_2019,Wuhan_WH01_2019,Wuhan_WIV07_2019,Shanghai_SH0093_2020,Wuhan_HBCDC-HB-01_2019,Wuhan_IPBCAMS-WH-01_2019,Wuhan_IVDC-HB-04_2020,Wuhan_IVDC-HB-05_2019,Wuhan_WIV05_2019,Sweden_01_2020,Taiwan_2_2020,USA_CA2_2020,Shanghai_SH0040_2020,Singapore_7_2020,Australia_VIC02_2020,France_IDF0515_2020,Hangzhou_ZJU-01_2020,Shanghai_SH0037_2020,Nepal_61_2020,Wuhan_HBCDC-HB-03_2019,Wuhan_IVDC-HB-01_2019,Wuhan_WIV06_2019,Wuhan_WIV04_2019,China_WH-09_2020,Wuhan_IPBCAMS-WH-04_2019,Wuhan_IPBCAMS-WH-02_2019,Wuhan_WH03_2020,Jiangxi_IVDC-JX-002_2020,Zhejiang_WZ-01_2020,Japan_KY-V-029_2020,Hangzhou_ZJU-03_2020,Zhejiang_WZ-02_2020,Netherlands_Utrecht_12_2020,Nonthaburi_61_2020,Nonthaburi_74_2020,Hangzhou_ZJU-05_2020,Hangzhou_HZ-1_2020,Singapore_1_2020,Taiwan_NTU02_2020,England_SHEF-BFD36_2020,France_IDF0626_2020,Malaysia_MKAK-CL-2020-7554_2020,Cambodia_0012_2020,Finland_1_2020,England_200641094_2020,England_200690756_2020,(USA_CA-CDPH-UC2_2020,(USA_CA9_2020,(USA_CA-CDPH-UC3_2020,USA_CA-CDPH-UC4_2020)5)4)3,(Australia_NSW08_2020,Australia_NSW10_2020)6,(Germany_NRW-10_2020,Germany_NRW-09_2020,Poland_PL_P1_2020,(Germany_NRW-04_2020,Germany_NRW-07_2020,(Germany_NRW-08_2020,(Germany_NRW-01_2020,Netherlands_Limburg_4_2020)10)9)8,(Germany_NRW-05_2020,Germany_NRW-03_2020,Germany_NRW-02-1_2020,Germany_NRW-06_2020,Brazil_SPBR-11_2020)11)7,(Malaysia_MKAK-CL-2020-5045_2020,(Singapore_2_2020,(Singapore_6_2020,Malaysia_MKAK-CL-2020-5047_2020)15)14)13,(Jiangsu_JS01_2020,Shanghai_SH0031_2020)16,(Australia_NSW02_2020,(Hangzhou_ZJU-06_2020,(Shanghai_SH0085_2020,Shanghai_SH0094_2020)19)18)17,(India_1-27_2020,Shanghai_SH0011_2020,Fujian_13_2020,(Singapore_11_2020,USA_WI1_2020)21)20,(Wuhan_HBCDC-HB-05_2020,Shandong_IVDC-SD-001_2020,England_200960041_2020,Australia_NSW05_2020,(Georgia_Tb-82_2020,Australia_NSW09_2020,(Canada_BC_25211_2020,Kuwait_KU09_2020)24,(Kuwait_KU18_2020,Kuwait_KU12_2020,Australia_NSW06_2020)25)23,(Shanghai_SH0022_2020,Shanghai_SH0023_2020)26,(Taiwan_CGMH-CGU-04_2020,(Taiwan_CGMH-CGU-03_2020,Taiwan_CGMH-CGU-05_2020)28)27,Kuwait_KU17_2020,(Canada_BC_17397_2020,Canada_BC_13297_2020)31,(Australia_QLD09_2020,Australia_NSW07_2020)32,(USA_NY1-PV08001_2020,Canada_BC_37_0-2_2020,Canada_BC_69243_2020,(England_200990002_2020,Germany_BavPat2_2020)34)33)22,(France_IDF0373_2020,France_IDF0386-islP1_2020,France_IDF0372_2020)35,(Jiangsu_JS02_2020,Shanghai_SH0008_2020,USA_CA5_2020)36,(Wuhan_WIV02_2019,(USA_CA8_2020,Wuhan_HBCDC-HB-02_2019)38)37,(Australia_NSW03_2020,Australia_VIC03_2020)39,(Chongqing_IVDC-CQ-001_2020,(Japan_Hu_DP_Kng_19-027_2020,(Singapore_3_2020,Japan_Hu_DP_Kng_19-020_2020)42)41)40,(Japan_NA-20-05-1_2020,Taiwan_CGMH-CGU-01_2020)43,(Hangzhou_ZJU-09_2020,Australia_VIC01_2020)44,(Japan_OS-20-07-1_2020,Chongqing_ZX01_2020)45,(USA_MA1_2020,(Shanghai_SH0058_2020,((USA_CA3_2020,USA_CA4_2020)49,(Canada_ON-PHL2445_2020,Canada_ON-VIDO-01_2020)50)48)47)46,((France_B2334_2020,France_B2340_2020)52,((Georgia_Tb-468_2020,Georgia_Tb-537_2020,Georgia_Tb-54_2020)54,Italy_SPL1_2020)53)51,(Jiangsu_IVDC-JS-001_2020,Hangzhou_HZCDC0001_2020)57,(Hangzhou_ZJU-04_2020,Jiangsu_JS03_2020)58,(England_20102000106_2020,(England_09c_2020,(Brazil_ES-225_2020,England_20100001406_2020,(England_200940527_2020,(England_200990725_2020,England_200990724_2020)63)62)61)60,(England_200960515_2020,(Finland_FIN01032020_2020,(Finland_FIN-274_2020,Finland_FIN03032020B_2020)66)65)64,(Brazil_SPBR-10_2020,Switzerland_1000477102_2020,Brazil_SPBR-02_2020,England_200990006_2020,Netherlands_Utrecht_18_2020)67)59,(USA_CA6_2020,Taiwan_4_2020)68,(Netherlands_Utrecht_19_2020,Netherlands_Limburg_6_2020,Netherlands_Naarden_1364774_2020,(Netherlands_Dalen_1363624_2020,Netherlands_Loon_op_zand_1363512_2020)70,(Netherlands_Oss_1363500_2020,Netherlands_Tilburg_1363354_2020)71)69,(France_RA739_2020,England_200690300_2020)72,(Singapore_8_2020,(Singapore_5_2020,Singapore_9_2020,Singapore_10_2020)76)75,(Shanghai_SH0086_2020,(Finland_FIN-1'..b'1,(Switzerland_VD0503_2020,Switzerland_VD5615_2020)102,(Switzerland_1000477797_2020,Brazil_BA-312_2020,(Switzerland_GE8102_2020,(Brazil_SPBR-08_2020,Brazil_SPBR-13_2020)105)104)103,(Finland_FIN-313_2020,Netherlands_Utrecht_15_2020)106,(Mexico_CDMX-InDRE_01_2020,Vietnam_39607_2020,Netherlands_Overijssel_2_2020,(Switzerland_1000477796_2020,England_20099038206_2020)108,(Vietnam_CM296_2020,Vietnam_CM295_2020)109)107,(Switzerland_GE1422_2020,Netherlands_Diemen_1363454_2020,(Switzerland_GE1402_2020,(Switzerland_AG7120_2020,Netherlands_Helmond_1363548_2020)112)111)110,(Switzerland_BE6651_2020,Netherlands_NoordHolland_2_2020,(Switzerland_GE3895_2020,(Switzerland_GE0199_2020,Switzerland_BL0902_2020,Switzerland_GE9586_2020,Switzerland_1000477806_2020,Switzerland_BS0914_2020)115)114)113,Belgium_BC-03016_2020,(Switzerland_1000477757_2020,Brazil_SPBR-12_2020,Germany_Baden-Wuerttemberg-1_2020)117,(Netherlands_NoordHolland_1_2020,Netherlands_Utrecht_10_2020,Germany_NRW-011_2020,Netherlands_Utrecht_13_2020,Ne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| diff -r 000000000000 -r 524cb8f7a69a test-data/global_samples.vcf.gz |
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| Binary file test-data/global_samples.vcf.gz has changed |
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| diff -r 000000000000 -r 524cb8f7a69a test-data/mutation_annotation.pb |
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| Binary file test-data/mutation_annotation.pb has changed |
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| diff -r 000000000000 -r 524cb8f7a69a test-data/new_samples.vcf.gz |
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| Binary file test-data/new_samples.vcf.gz has changed |
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| diff -r 000000000000 -r 524cb8f7a69a test-data/rename_samples.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rename_samples.tabular Tue May 11 17:53:49 2021 +0000 |
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| @@ -0,0 +1,4 @@ +England/BRIS-1853249/2020|20-04-02 Spain/BRIS-1853249/2020|20-04-02 +Wales/PHWC-25B04/2020|20-03-24 Spain/BRIS-1853249/2020|20-04-02 +NPL/61-TW/2020|MT072688.1|20-01-13 Spain/BRIS-1853249/2020|20-04-02 +Wales/LIVE-A6831/2020|20-03-16 Spain/BRIS-1853249/2020|20-04-02 \ No newline at end of file |
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| diff -r 000000000000 -r 524cb8f7a69a test-data/sample_names.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_names.txt Tue May 11 17:53:49 2021 +0000 |
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(France_HF2174_2020:2,France_GE1977_2020:3,France_HF1684_2020:0,(node_39_condensed_2_leaves:0)80:1)79:2,Belgium_VAG-03013_2020:4,(Netherlands_Utrecht_1363564_2020:1,node_31_condensed_2_leaves:0)81:4,(England_20099107406_2020:1,Georgia_Tb_2020:0)83:1,(France_BFC2094_2020:1,France_BFC2147_2020:1,node_32_condensed_4_leaves:0)86:1,(Hungary_mbl1_2020:1,node_33_condensed_5_leaves:0)90:1,(Nigeria_Lagos01_2020:1,Netherlands_Delft_1363424_2020:1,Denmark_SSI-01_2020:1,England_200990723_2020:1,Switzerland_TI2045_2020:1,Switzerland_1000477377_2020:2,Denmark_SSI-05_2020:4,Chile_Santiago-2_2020:1,Brazil_SPBR-14_2020:1,Finland_FIN-318_2020:2,Netherlands_Limburg_5_2020:2,Belgium_DBA-03032_2020:2,Switzerland_SZ1417_2020:2,Belgium_GMH-03022_2020:2,Netherlands_Utrecht_14_2020:2,Netherlands_Utrecht_1_2020:2,Finland_FIN03032020C_2020:1,Netherlands_Berlicum_1363564_2020:1,(node_40_condensed_2_leaves:0)92:2,(node_41_condensed_2_leaves:0)93:1,(node_42_condensed_2_leaves:0)94:1,(Switzerland_1000477797_2020:1,Brazil_BA-312_2020:1,node_43_condensed_3_leaves:0)95:1,(Finland_FIN-313_2020:1,Netherlands_Utrecht_15_2020:0)98:2,(Switzerland_GE1422_2020:1,Netherlands_Diemen_1363454_2020:3,node_44_condensed_3_leaves:0)102:1,(Switzerland_BE6651_2020:1,Netherlands_NoordHolland_2_2020:1,node_45_condensed_6_leaves:0)105:1,Belgium_BC-03016_2020:2,(Switzerland_1000477757_2020:2,Brazil_SPBR-12_2020:1,Germany_Baden-Wuerttemberg-1_2020:0)108:1,(node_46_condensed_16_leaves:0)109:1,(Belgium_UMF-03025_2020:0,(node_47_condensed_2_leaves:0)114:1)113:1,node_34_condensed_7_leaves:0)91:3,(Netherlands_NoordHolland_3_2020:2,Netherlands_Flevoland_1_2020:0)115:1,(NetherlandsL_Houten_1363498_2020:1,Italy_UniSR1_2020:1,France_N1620_2020:1,node_35_condensed_3_leaves:0)116:1,(Georgia_Tb-673_2020:2,France_B2330_2020:1,France_PL1643_2020:2,France_HF1988_2020:1,France_B2348_2020:1,(France_B2351_2020:1,France_B2344_2020:1,France_B2349_2020:0)120:1,(France_IDF2256_2020:1,France_HF1871_2020:2)121:1,Netherlands_Haarlem_1363688_2020:1,node_36_condensed_6_leaves:0)119:2,node_25_condensed_15_leaves:0)73:1,node_11_condensed_3_leaves:0)70:3,node_1_condensed_27_leaves:0)1:0; |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_01_final_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_01_final_tree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((Wuhan_HBCDC-HB-06_2020:3,Wuhan_HBCDC-HB-02_2020:2,Wuhan_HBCDC-HB-04_2020:3,Shanghai_SH0075_2020:2,Shanghai_SH0010_2020:2,Tianmen_HBCDC-HB-07_2020:5,Shanghai_SH0041_2020:4,India_1-31_2020:4,Shanghai_SH0009_2020:1,Malaysia_MKAK-CL-2020-5096_2020:2,(France_GE1583_2020:1,Georgia_Tb-390_2020:1,Spain_Valencia6_2020:1,Spain_CastillayLeon201437_2020:1,node_12_condensed_6_leaves:0)129:5,(Sichuan_IVDC-SC-001_2020:1,USA_CA1_2020:1,USA_IL2_2020:2,Vietnam_CM99_2020:2,node_13_condensed_3_leaves:0)132:3,(Shanghai_SH0035_2020:2,Australia_QLD02_2020:2,Australia_QLD03_2020:1,Australia_VIC07_2020:1,(Netherlands_Utrecht_16_2020:1,Netherlands_Utrecht_17_2020:0)140:1,node_14_condensed_6_leaves:0)136:2,(Shandong_LY003_2020:2,Shandong_LY005_2020:2,node_15_condensed_3_leaves:0)142:1,(node_16_condensed_2_leaves:0)145:4,England_02_2020:3,(Chongqing_YC01_2020:2,((USA_CA-CDPH-UC7_2020:0,USA_CA-CDPH-UC9_2020:1)149:3,(node_37_condensed_2_leaves:0)150:2)148:2,Malaysia_MKAK-CL-2020-6430_2020:1,node_17_condensed_3_leaves:0)146:1,(Shanghai_SH0059_2020:3,USA_TX1_2020:4,(Japan_TY-WK-012_2020:1,node_26_condensed_2_leaves:0)157:1,Shanghai_SH0004_2020:1,Germany_BavPat3_2020:1,Shanghai_SH0005_2020:0)154:1,(Yunnan_IVDC-YN-003_2020:0,USA_AZ1_2020:1,Anhui_SZ005_2020:6)160:1,(Beijing_233_2020:1,node_18_condensed_3_leaves:0)161:2,node_2_condensed_10_leaves:0)128:2,Shanghai_SH0007_2020:3,Hangzhou_ZJU-07_2020:5,Wuhan_IPBCAMS-WH-03_2019:1,Wuhan_WH01_2019:2,Wuhan_WIV07_2019:1,Shanghai_SH0093_2020:2,Wuhan_HBCDC-HB-01_2019:1,Wuhan_IPBCAMS-WH-01_2019:3,Wuhan_IVDC-HB-04_2020:2,Wuhan_IVDC-HB-05_2019:2,Wuhan_WIV05_2019:2,Sweden_01_2020:7,Taiwan_2_2020:3,USA_CA2_2020:2,Shanghai_SH0040_2020:2,Singapore_7_2020:2,Australia_VIC02_2020:2,France_IDF0515_2020:3,Hangzhou_ZJU-01_2020:3,Shanghai_SH0037_2020:5,Nepal_61_2020:1,China_WH-09_2020:1,Jiangxi_IVDC-JX-002_2020:1,Zhejiang_WZ-01_2020:1,Japan_KY-V-029_2020:3,Hangzhou_ZJU-03_2020:1,Netherlands_Utrecht_12_2020:2,Singapore_1_2020:1,Taiwan_NTU02_2020:2,England_SHEF-BFD36_2020:3,France_IDF0626_2020:1,Malaysia_MKAK-CL-2020-7554_2020:2,Cambodia_0012_2020:1,(USA_CA-CDPH-UC2_2020:4,USA_CA-CDPH-UC3_2020:1,node_3_condensed_2_leaves:0)3:1,(node_4_condensed_2_leaves:0)6:1,(Germany_NRW-10_2020:1,Germany_NRW-09_2020:1,Poland_PL_P1_2020:1,(Germany_NRW-04_2020:0,Germany_NRW-07_2020:1,(node_27_condensed_3_leaves:0)9:2)8:2,node_5_condensed_5_leaves:0)7:2,(Malaysia_MKAK-CL-2020-5045_2020:2,node_6_condensed_3_leaves:0)12:1,(Jiangsu_JS01_2020:2,Shanghai_SH0031_2020:1)15:1,(Australia_NSW02_2020:1,(Hangzhou_ZJU-06_2020:1,(Shanghai_SH0085_2020:4,Shanghai_SH0094_2020:0)18:2)17:1)16:1,(India_1-27_2020:3,Shanghai_SH0011_2020:1,Fujian_13_2020:1,Singapore_11_2020:1,USA_WI1_2020:0)19:1,(Wuhan_HBCDC-HB-05_2020:1,Shandong_IVDC-SD-001_2020:3,England_200960041_2020:2,Australia_NSW05_2020:1,(Georgia_Tb-82_2020:2,Australia_NSW09_2020:3,(Canada_BC_25211_2020:4,Kuwait_KU09_2020:2)23:1,Kuwait_KU18_2020:1,Kuwait_KU12_2020:2,Australia_NSW06_2020:1)22:2,(node_19_condensed_2_leaves:0)25:2,(Taiwan_CGMH-CGU-04_2020:3,node_20_condensed_2_leaves:0)26:3,Kuwait_KU17_2020:1,(Canada_BC_17397_2020:2,Canada_BC_13297_2020:2)28:1,(Australia_QLD09_2020:1,Australia_NSW07_2020:0)29:1,(USA_NY1-PV08001_2020:3,Canada_BC_37_0-2_2020:0,Canada_BC_69243_2020:2,(England_200990002_2020:2,Germany_BavPat2_2020:1)31:2)30:1)21:4,(node_7_condensed_3_leaves:0)32:2,(Jiangsu_JS02_2020:4,Shanghai_SH0008_2020:3,USA_CA5_2020:1)33:1,(Wuhan_WIV02_2019:1,node_8_condensed_2_leaves:0)34:1,(node_9_condensed_2_leaves:0)36:1,(Japan_Hu_DP_Kng_19-027_2020:1,node_10_condensed_3_leaves:0)37:1,(Hangzhou_ZJU-09_2020:0,Australia_VIC01_2020:3)41:1,(USA_MA1_2020:3,(Shanghai_SH0058_2020:4,(node_28_condensed_2_leaves:0)46:1,node_21_condensed_2_leaves:0)44:1)43:1,((France_B2334_2020:1,France_B2340_2020:1)49:2,(Georgia_Tb-468_2020:1,Georgia_Tb-537_2020:1,Georgia_Tb-54_2020:0)51:1,Italy_SPL1_2020:0)48:2,(England_20102000106_2020:2,(England_09c_2020:0,Brazil_ES-225_2020:1,England_20100001406_2020:1,(node_29_condensed_3_leaves:0)57:1)55:2,(Brazil_SPBR-10_2020:1,Switzerland_1000477102_2020:2,Brazil_SPBR-02_2020:1,England_200990006_2020:0,Netherlands_Utrecht_18_2020:2)62:1,England_200960515_2020:1,(node_22_condensed_3_leaves:0)60:1)54:3,(Netherlands_Utrecht_19_2020:3,Netherlands_Limburg_6_2020:2,Netherlands_Naarden_1364774_2020:0,(node_23_condensed_2_leaves:0)65:1,(Netherlands_Oss_1363500_2020:0,Netherlands_Tilburg_1363354_2020:2)66:1)64:1,(Singapore_8_2020:1,(node_24_condensed_3_leaves:0)69:1)68:1,(Shanghai_SH0086_2020:3,(Finland_FIN-25_2020:6,Belgium_DB-03023_2020:4,Denmark_SSI-102_2020:3,Denmark_SSI-02_2020:1,Belgium_BM-03012_2020:3,England_20100022706_2020:2,Denmark_SSI-04_2020:3,Taiwan_NTU03_2020:2,Finland_FIN03032020A_2020:2,Switzerland_GE4984_2020:2,Switzerland_AG0361_2020:2,Finland_FIN-266_2020:1,Luxembourg_Lux1_2020:1,Japan_SMU-0311S3_2020:1,Denmark_SSI-03_2020:1,Netherlands_Gelderland_2_2020:1,Georgia_Tb-273_2020:1,Belgium_SH-03014_2020:1,((node_38_condensed_2_leaves:0)78:2,node_30_condensed_4_leaves:0)74:1,(France_HF2174_2020:2,France_GE1977_2020:3,France_HF1684_2020:0,(node_39_condensed_2_leaves:0)80:1)79:2,Belgium_VAG-03013_2020:4,(Netherlands_Utrecht_1363564_2020:1,node_31_condensed_2_leaves:0)81:4,(England_20099107406_2020:1,Georgia_Tb_2020:0)83:1,(France_BFC2094_2020:1,France_BFC2147_2020:1,node_32_condensed_4_leaves:0)86:1,(Hungary_mbl1_2020:1,node_33_condensed_5_leaves:0)90:1,(Nigeria_Lagos01_2020:1,Netherlands_Delft_1363424_2020:1,Denmark_SSI-01_2020:1,England_200990723_2020:1,Switzerland_TI2045_2020:1,Switzerland_1000477377_2020:2,Denmark_SSI-05_2020:4,Chile_Santiago-2_2020:1,Brazil_SPBR-14_2020:1,Finland_FIN-318_2020:2,Netherlands_Limburg_5_2020:2,Belgium_DBA-03032_2020:2,Switzerland_SZ1417_2020:2,Belgium_GMH-03022_2020:2,Netherlands_Utrecht_14_2020:2,Netherlands_Utrecht_1_2020:2,Finland_FIN03032020C_2020:1,Netherlands_Berlicum_1363564_2020:1,(node_40_condensed_2_leaves:0)92:2,(node_41_condensed_2_leaves:0)93:1,(node_42_condensed_2_leaves:0)94:1,(Switzerland_1000477797_2020:1,Brazil_BA-312_2020:1,node_43_condensed_3_leaves:0)95:1,(Finland_FIN-313_2020:1,Netherlands_Utrecht_15_2020:0)98:2,(Switzerland_GE1422_2020:1,Netherlands_Diemen_1363454_2020:3,node_44_condensed_3_leaves:0)102:1,(Switzerland_BE6651_2020:1,Netherlands_NoordHolland_2_2020:1,node_45_condensed_6_leaves:0)105:1,Belgium_BC-03016_2020:2,(Switzerland_1000477757_2020:2,Brazil_SPBR-12_2020:1,Germany_Baden-Wuerttemberg-1_2020:0)108:1,(node_46_condensed_16_leaves:0)109:1,(Belgium_UMF-03025_2020:0,(node_47_condensed_2_leaves:0)114:1)113:1,node_34_condensed_7_leaves:0)91:3,(Netherlands_NoordHolland_3_2020:2,Netherlands_Flevoland_1_2020:0)115:1,(NetherlandsL_Houten_1363498_2020:1,Italy_UniSR1_2020:1,France_N1620_2020:1,node_35_condensed_3_leaves:0)116:1,(Georgia_Tb-673_2020:2,France_B2330_2020:1,France_PL1643_2020:2,France_HF1988_2020:1,France_B2348_2020:1,(France_B2351_2020:1,France_B2344_2020:1,France_B2349_2020:0)120:1,(France_IDF2256_2020:1,France_HF1871_2020:2)121:1,Netherlands_Haarlem_1363688_2020:1,node_36_condensed_6_leaves:0)119:2,node_25_condensed_15_leaves:0)73:1,node_11_condensed_3_leaves:0)70:3,node_1_condensed_27_leaves:0)1:0; \ No newline at end of file |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_02_mutation_path.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02_mutation_path.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Sample1 19:G1440A,G2891A 86:A27669G +Sample2 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample3 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample4 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G +Sample5 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_02_uncondensed_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02_uncondensed_tree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_03_condensed_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03_condensed_tree.nh Tue May 11 17:53:49 2021 +0000 |
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| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_03_final_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03_final_tree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((Wuhan_HBCDC-HB-06_2020:3,Wuhan_HBCDC-HB-02_2020:2,Wuhan_HBCDC-HB-04_2020:3,Shanghai_SH0075_2020:2,Shanghai_SH0010_2020:2,Tianmen_HBCDC-HB-07_2020:5,Shanghai_SH0041_2020:4,India_1-31_2020:4,Shanghai_SH0009_2020:1,Malaysia_MKAK-CL-2020-5096_2020:2,(France_GE1583_2020:1,Georgia_Tb-390_2020:1,Spain_Valencia6_2020:1,Spain_CastillayLeon201437_2020:1,node_12_condensed_6_leaves:0)129:5,(Sichuan_IVDC-SC-001_2020:1,USA_CA1_2020:1,USA_IL2_2020:2,Vietnam_CM99_2020:2,node_13_condensed_3_leaves:0)132:3,(Shanghai_SH0035_2020:2,Australia_QLD02_2020:2,Australia_QLD03_2020:1,Australia_VIC07_2020:1,(Netherlands_Utrecht_16_2020:1,Netherlands_Utrecht_17_2020:0)140:1,node_14_condensed_6_leaves:0)136:2,(Shandong_LY003_2020:2,Shandong_LY005_2020:2,node_15_condensed_3_leaves:0)142:1,(node_16_condensed_2_leaves:0)145:4,England_02_2020:3,(Chongqing_YC01_2020:2,((USA_CA-CDPH-UC7_2020:0,USA_CA-CDPH-UC9_2020:1)149:3,(node_37_condensed_2_leaves:0)150:2)148:2,Malaysia_MKAK-CL-2020-6430_2020:1,node_17_condensed_3_leaves:0)146:1,(Shanghai_SH0059_2020:3,USA_TX1_2020:4,(Japan_TY-WK-012_2020:1,node_26_condensed_2_leaves:0)157:1,Shanghai_SH0004_2020:1,Germany_BavPat3_2020:1,Shanghai_SH0005_2020:0)154:1,(Yunnan_IVDC-YN-003_2020:0,USA_AZ1_2020:1,Anhui_SZ005_2020:6)160:1,(Beijing_233_2020:1,node_18_condensed_3_leaves:0)161:2,node_2_condensed_10_leaves:0)128:2,Shanghai_SH0007_2020:3,Hangzhou_ZJU-07_2020:5,Wuhan_IPBCAMS-WH-03_2019:1,Wuhan_WH01_2019:2,Wuhan_WIV07_2019:1,Shanghai_SH0093_2020:2,Wuhan_HBCDC-HB-01_2019:1,Wuhan_IPBCAMS-WH-01_2019:3,Wuhan_IVDC-HB-04_2020:2,Wuhan_IVDC-HB-05_2019:2,Wuhan_WIV05_2019:2,Sweden_01_2020:7,Taiwan_2_2020:3,USA_CA2_2020:2,Shanghai_SH0040_2020:2,Singapore_7_2020:2,Australia_VIC02_2020:2,France_IDF0515_2020:3,Hangzhou_ZJU-01_2020:3,Shanghai_SH0037_2020:5,Nepal_61_2020:1,China_WH-09_2020:1,Jiangxi_IVDC-JX-002_2020:1,Zhejiang_WZ-01_2020:1,Japan_KY-V-029_2020:3,Hangzhou_ZJU-03_2020:1,Netherlands_Utrecht_12_2020:2,Singapore_1_2020:1,Taiwan_NTU02_2020:2,England_SHEF-BFD36_2020:3,France_IDF0626_2020:1,Malaysia_MKAK-CL-2020-7554_2020:2,Cambodia_0012_2020:1,(USA_CA-CDPH-UC2_2020:4,USA_CA-CDPH-UC3_2020:1,node_3_condensed_2_leaves:0)3:1,(node_4_condensed_2_leaves:0)6:1,(Germany_NRW-10_2020:1,Germany_NRW-09_2020:1,Poland_PL_P1_2020:1,(Germany_NRW-04_2020:0,Germany_NRW-07_2020:1,(node_27_condensed_3_leaves:0)9:2)8:2,node_5_condensed_5_leaves:0)7:2,(Malaysia_MKAK-CL-2020-5045_2020:2,node_6_condensed_3_leaves:0)12:1,(Jiangsu_JS01_2020:2,Shanghai_SH0031_2020:1)15:1,(Australia_NSW02_2020:1,(Hangzhou_ZJU-06_2020:1,(Shanghai_SH0085_2020:4,Shanghai_SH0094_2020:0)18:2)17:1)16:1,(India_1-27_2020:3,Shanghai_SH0011_2020:1,Fujian_13_2020:1,Singapore_11_2020:1,USA_WI1_2020:0)19:1,(Wuhan_HBCDC-HB-05_2020:1,Shandong_IVDC-SD-001_2020:3,England_200960041_2020:2,Australia_NSW05_2020:1,(Georgia_Tb-82_2020:2,Australia_NSW09_2020:3,(Canada_BC_25211_2020:4,Kuwait_KU09_2020:2)23:1,Kuwait_KU18_2020:1,Kuwait_KU12_2020:2,Australia_NSW06_2020:1)22:2,(node_19_condensed_2_leaves:0)25:2,(Taiwan_CGMH-CGU-04_2020:3,node_20_condensed_2_leaves:0)26:3,Kuwait_KU17_2020:1,(Canada_BC_17397_2020:2,Canada_BC_13297_2020:2)28:1,(Australia_QLD09_2020:1,Australia_NSW07_2020:0)29:1,(USA_NY1-PV08001_2020:3,Canada_BC_37_0-2_2020:0,Canada_BC_69243_2020:2,(England_200990002_2020:2,Germany_BavPat2_2020:1)31:2)30:1)21:4,(node_7_condensed_3_leaves:0)32:2,(Jiangsu_JS02_2020:4,Shanghai_SH0008_2020:3,USA_CA5_2020:1)33:1,(Wuhan_WIV02_2019:1,node_8_condensed_2_leaves:0)34:1,(node_9_condensed_2_leaves:0)36:1,(Japan_Hu_DP_Kng_19-027_2020:1,node_10_condensed_3_leaves:0)37:1,(Hangzhou_ZJU-09_2020:0,Australia_VIC01_2020:3)41:1,(USA_MA1_2020:3,(Shanghai_SH0058_2020:4,(node_28_condensed_2_leaves:0)46:1,node_21_condensed_2_leaves:0)44:1)43:1,((France_B2334_2020:1,France_B2340_2020:1)49:2,(Georgia_Tb-468_2020:1,Georgia_Tb-537_2020:1,Georgia_Tb-54_2020:0)51:1,Italy_SPL1_2020:0)48:2,(England_20102000106_2020:2,(England_09c_2020:0,Brazil_ES-225_2020:1,England_20100001406_2020:1,(node_29_condensed_3_leaves:0)57:1)55:2,(Brazil_SPBR-10_2020:1,Switzerland_1000477102_2020:2,Brazil_SPBR-02_2020:1,England_200990006_2020:0,Netherlands_Utrecht_18_2020:2)62:1,England_200960515_2020:1,(node_22_condensed_3_leaves:0)60:1)54:3,(Netherlands_Utrecht_19_2020:3,Netherlands_Limburg_6_2020:2,Netherlands_Naarden_1364774_2020:0,(node_23_condensed_2_leaves:0)65:1,(Netherlands_Oss_1363500_2020:0,Netherlands_Tilburg_1363354_2020:2)66:1)64:1,(Singapore_8_2020:1,(node_24_condensed_3_leaves:0)69:1)68:1,(Shanghai_SH0086_2020:3,(Finland_FIN-25_2020:6,Belgium_DB-03023_2020:4,Denmark_SSI-102_2020:3,Denmark_SSI-02_2020:1,Belgium_BM-03012_2020:3,England_20100022706_2020:2,Denmark_SSI-04_2020:3,Taiwan_NTU03_2020:2,Finland_FIN03032020A_2020:2,Switzerland_GE4984_2020:2,Switzerland_AG0361_2020:2,Finland_FIN-266_2020:1,Luxembourg_Lux1_2020:1,Japan_SMU-0311S3_2020:1,Denmark_SSI-03_2020:1,Netherlands_Gelderland_2_2020:1,Georgia_Tb-273_2020:1,Belgium_SH-03014_2020:1,((node_38_condensed_2_leaves:0)78:2,node_30_condensed_4_leaves:0)74:1,(France_HF2174_2020:2,France_GE1977_2020:3,France_HF1684_2020:0,(node_39_condensed_2_leaves:0)80:1)79:2,Belgium_VAG-03013_2020:4,(Netherlands_Utrecht_1363564_2020:1,node_31_condensed_2_leaves:0)81:4,(England_20099107406_2020:1,Georgia_Tb_2020:0)83:1,(France_BFC2094_2020:1,France_BFC2147_2020:1,node_32_condensed_4_leaves:0)86:1,(Hungary_mbl1_2020:1,node_33_condensed_5_leaves:0)90:1,(Nigeria_Lagos01_2020:1,Netherlands_Delft_1363424_2020:1,Denmark_SSI-01_2020:1,England_200990723_2020:1,Switzerland_TI2045_2020:1,Switzerland_1000477377_2020:2,Denmark_SSI-05_2020:4,Chile_Santiago-2_2020:1,Brazil_SPBR-14_2020:1,Finland_FIN-318_2020:2,Netherlands_Limburg_5_2020:2,Belgium_DBA-03032_2020:2,Switzerland_SZ1417_2020:2,Belgium_GMH-03022_2020:2,Netherlands_Utrecht_14_2020:2,Netherlands_Utrecht_1_2020:2,Finland_FIN03032020C_2020:1,Netherlands_Berlicum_1363564_2020:1,(node_40_condensed_2_leaves:0)92:2,(node_41_condensed_2_leaves:0)93:1,(node_42_condensed_2_leaves:0)94:1,(Switzerland_1000477797_2020:1,Brazil_BA-312_2020:1,node_43_condensed_3_leaves:0)95:1,(Finland_FIN-313_2020:1,Netherlands_Utrecht_15_2020:0)98:2,(Switzerland_GE1422_2020:1,Netherlands_Diemen_1363454_2020:3,node_44_condensed_3_leaves:0)102:1,(Switzerland_BE6651_2020:1,Netherlands_NoordHolland_2_2020:1,node_45_condensed_6_leaves:0)105:1,Belgium_BC-03016_2020:2,(Switzerland_1000477757_2020:2,Brazil_SPBR-12_2020:1,Germany_Baden-Wuerttemberg-1_2020:0)108:1,(node_46_condensed_16_leaves:0)109:1,(Belgium_UMF-03025_2020:0,(node_47_condensed_2_leaves:0)114:1)113:1,node_34_condensed_7_leaves:0)91:3,(Netherlands_NoordHolland_3_2020:2,Netherlands_Flevoland_1_2020:0)115:1,(NetherlandsL_Houten_1363498_2020:1,Italy_UniSR1_2020:1,France_N1620_2020:1,node_35_condensed_3_leaves:0)116:1,(Georgia_Tb-673_2020:2,France_B2330_2020:1,France_PL1643_2020:2,France_HF1988_2020:1,France_B2348_2020:1,(France_B2351_2020:1,France_B2344_2020:1,France_B2349_2020:0)120:1,(France_IDF2256_2020:1,France_HF1871_2020:2)121:1,Netherlands_Haarlem_1363688_2020:1,node_36_condensed_6_leaves:0)119:2,node_25_condensed_15_leaves:0)73:1,node_11_condensed_3_leaves:0)70:3,node_1_condensed_27_leaves:0)1:0; \ No newline at end of file |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_04_mutation_paths.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04_mutation_paths.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Sample1 19:G1440A,G2891A 86:A27669G +Sample2 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample3 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample4 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G +Sample5 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_04_subtree_1.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04_subtree_1.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((Wuhan_HBCDC-HB-06_2020:3,Wuhan_HBCDC-HB-02_2020:2,Wuhan_HBCDC-HB-04_2020:3,Shanghai_SH0075_2020:2,Shanghai_SH0010_2020:2,Tianmen_HBCDC-HB-07_2020:5,Shanghai_SH0041_2020:4,India_1-31_2020:4)2:2,(Germany_NRW-10_2020:1,Germany_NRW-09_2020:1,Poland_PL_P1_2020:1,(Germany_NRW-04_2020:0,Germany_NRW-07_2020:1,node_27_condensed_3_leaves:2)20:2,node_5_condensed_5_leaves:0,(Sample1:0,(Sample3:0,Sample2:0,(Sample5:0,Sample4:0)88:1)87:1)86:1)19:2)1:0; \ No newline at end of file |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_04_subtree_1_expanded.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04_subtree_1_expanded.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +node_5_condensed_5_leaves: Germany_NRW-05_2020 Germany_NRW-03_2020 Germany_NRW-02-1_2020 Germany_NRW-06_2020 Brazil_SPBR-11_2020 +node_27_condensed_3_leaves: Germany_NRW-08_2020 Germany_NRW-01_2020 Netherlands_Limburg_4_2020 |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_04_subtree_1_mutations.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04_subtree_1_mutations.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,27 @@ +1: +2: C8782T,T28144C +Wuhan_HBCDC-HB-06_2020: G5657A,A23403G,A25725G +Wuhan_HBCDC-HB-02_2020: C12141A,C23816T +Wuhan_HBCDC-HB-04_2020: T18996C,C24370T,T29029C +Shanghai_SH0075_2020: T27618C,C28706T +Shanghai_SH0010_2020: C3176T,C21855T +Tianmen_HBCDC-HB-07_2020: A3175G,G3179A,C14422T,C14585T,C28315T +Shanghai_SH0041_2020: C207T,T946C,C6363T,A11430G +India_1-31_2020: A1691G,C6501T,C16877T,C24351T +19: G1440A,G2891A +Germany_NRW-10_2020: G7798T +Germany_NRW-09_2020: C27849T +Poland_PL_P1_2020: G198A +20: C4655T,C22323T +Germany_NRW-04_2020: +Germany_NRW-07_2020: T13494C +node_27_condensed_3_leaves: G8422A,C29546A +node_5_condensed_5_leaves: +86: A27669G +Sample1: +87: G14948A +Sample3: +Sample2: +88: A23013G +Sample5: +Sample4: |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_04_uncondensed_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04_uncondensed_tree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1 @@\n+((Wuhan_HBCDC-HB-06_2020:3,Wuhan_HBCDC-HB-02_2020:2,Wuhan_HBCDC-HB-04_2020:3,Shanghai_SH0075_2020:2,Shanghai_SH0010_2020:2,Tianmen_HBCDC-HB-07_2020:5,Shanghai_SH0041_2020:4,India_1-31_2020:4,Shanghai_SH0009_2020:1,Malaysia_MKAK-CL-2020-5096_2020:2,(France_GE1583_2020:1,Georgia_Tb-390_2020:1,Spain_Valencia6_2020:1,Spain_CastillayLeon201437_2020:1,Spain_Valencia4_2020,Chile_Santiago_op2d1_2020,Spain_Valencia5_2020,Chile_Santiago-1_2020,Chile_Santiago_op3d1_2020,Chile_Santiago_op4d1_2020:0)3:5,(Sichuan_IVDC-SC-001_2020:1,USA_CA1_2020:1,USA_IL2_2020:2,Vietnam_CM99_2020:2,Shanghai_SH0032_2020,Vietnam_VR03-38142_2020,Vietnam_38142_2020:0)4:3,(Shanghai_SH0035_2020:2,Australia_QLD02_2020:2,Australia_QLD03_2020:1,Australia_VIC07_2020:1,(Netherlands_Utrecht_16_2020:1,Netherlands_Utrecht_17_2020:0)6:1,Australia_QLD01_2020,Shanghai_SH0002_2020,Shanghai_SH0003_2020,USA_CA7_2020,Australia_QLD04_2020,Singapore_4_2020:0)5:2,(Shandong_LY003_2020:2,Shandong_LY005_2020:2,Shandong_LY006_2020,Shandong_LY004_2020,Shandong_LY008_2020:0)7:1,(Chile_Talca-1_2020,Chile_Talca-2_2020:0)8:4,England_02_2020:3,(Chongqing_YC01_2020:2,((USA_CA-CDPH-UC7_2020:0,USA_CA-CDPH-UC9_2020:1)11:3,(USA_CA-CDPH-UC5_2020,USA_CA-CDPH-UC6_2020:0)12:2)10:2,Malaysia_MKAK-CL-2020-6430_2020:1,USA_WA1_2020,Fujian_8_2020,Hangzhou_ZJU-08_2020:0)9:1,(Shanghai_SH0059_2020:3,USA_TX1_2020:4,(Japan_TY-WK-012_2020:1,Japan_TY-WK-501_2020,Japan_TY-WK-521_2020:0)14:1,Shanghai_SH0004_2020:1,Germany_BavPat3_2020:1,Shanghai_SH0005_2020:0)13:1,(Yunnan_IVDC-YN-003_2020:0,USA_AZ1_2020:1,Anhui_SZ005_2020:6)15:1,(Beijing_233_2020:1,Beijing_235_2020,Beijing_231_2020,Beijing_105_2020:0)16:2,Wuhan_WH04_2020,Wuhan_HBCDC-HB-03_2020,Hangzhou_ZJU-02_2020,Shanghai_SH0024_2020,Australia_NSW01_2020,Taiwan_3_2020,Taiwan_NTU01_2020,Belgium_GHB-03021_2020,Shanghai_SH0043_2020,Shanghai_SH0013_2020:0)2:2,Shanghai_SH0007_2020:3,Hangzhou_ZJU-07_2020:5,Wuhan_IPBCAMS-WH-03_2019:1,Wuhan_WH01_2019:2,Wuhan_WIV07_2019:1,Shanghai_SH0093_2020:2,Wuhan_HBCDC-HB-01_2019:1,Wuhan_IPBCAMS-WH-01_2019:3,Wuhan_IVDC-HB-04_2020:2,Wuhan_IVDC-HB-05_2019:2,Wuhan_WIV05_2019:2,Sweden_01_2020:7,Taiwan_2_2020:3,USA_CA2_2020:2,Shanghai_SH0040_2020:2,Singapore_7_2020:2,Australia_VIC02_2020:2,France_IDF0515_2020:3,Hangzhou_ZJU-01_2020:3,Shanghai_SH0037_2020:5,Nepal_61_2020:1,China_WH-09_2020:1,Jiangxi_IVDC-JX-002_2020:1,Zhejiang_WZ-01_2020:1,Japan_KY-V-029_2020:3,Hangzhou_ZJU-03_2020:1,Netherlands_Utrecht_12_2020:2,Singapore_1_2020:1,Taiwan_NTU02_2020:2,England_SHEF-BFD36_2020:3,France_IDF0626_2020:1,Malaysia_MKAK-CL-2020-7554_2020:2,Cambodia_0012_2020:1,(USA_CA-CDPH-UC2_2020:4,USA_CA-CDPH-UC3_2020:1,USA_CA9_2020,USA_CA-CDPH-UC4_2020:0)17:1,(Australia_NSW08_2020,Australia_NSW10_2020:0)18:1,(Germany_NRW-10_2020:1,Germany_NRW-09_2020:1,Poland_PL_P1_2020:1,(Germany_NRW-04_2020:0,Germany_NRW-07_2020:1,(Germany_NRW-08_2020,Germany_NRW-01_2020,Netherlands_Limburg_4_2020:0)21:2)20:2,Germany_NRW-05_2020,Germany_NRW-03_2020,Germany_NRW-02-1_2020,Germany_NRW-06_2020,Brazil_SPBR-11_2020:0,(Sample1:0,(Sample3:0,Sample2:0,(Sample5:0,Sample4:0)88:1)87:1)86:1)19:2,(Malaysia_MKAK-CL-2020-5045_2020:2,Singapore_2_2020,Singapore_6_2020,Malaysia_MKAK-CL-2020-5047_2020:0)22:1,(Jiangsu_JS01_2020:2,Shanghai_SH0031_2020:1)23:1,(Australia_NSW02_2020:1,(Hangzhou_ZJU-06_2020:1,(Shanghai_SH0085_2020:4,Shanghai_SH0094_2020:0)26:2)25:1)24:1,(India_1-27_2020:3,Shanghai_SH0011_2020:1,Fujian_13_2020:1,Singapore_11_2020:1,USA_WI1_2020:0)27:1,(Wuhan_HBCDC-HB-05_2020:1,Shandong_IVDC-SD-001_2020:3,England_200960041_2020:2,Australia_NSW05_2020:1,(Georgia_Tb-82_2020:2,Australia_NSW09_2020:3,(Canada_BC_25211_2020:4,Kuwait_KU09_2020:2)30:1,Kuwait_KU18_2020:1,Kuwait_KU12_2020:2,Australia_NSW06_2020:1)29:2,(Shanghai_SH0022_2020,Shanghai_SH0023_2020:0)31:2,(Taiwan_CGMH-CGU-04_2020:3,Taiwan_CGMH-CGU-03_2020,Taiwan_CGMH-CGU-05_2020:0)32:3,Kuwait_KU17_2020:1,(Canada_BC_17397_2020:2,Canada_BC_13297_2020:2)33:1,(Australia_QLD09_2020:1,Australia_NSW07_2020:0)34:1,(USA_NY1-PV'..b'lands_Utrecht_6_2020,Netherlands_Utrecht_1363628_2020:0)65:4,(England_20099107406_2020:1,Georgia_Tb_2020:0)66:1,(France_BFC2094_2020:1,France_BFC2147_2020:1,France_HF2196_2020,Switzerland_GE6679_2020,Switzerland_BE2536_2020,Switzerland_GE4135_2020:0)67:1,(Hungary_mbl1_2020:1,Switzerland_GE5373_2020,Switzerland_GE3121_2020,Panama_328677_2020,Georgia_Tb-712_2020,Spain_Galicia201663_2020:0)68:1,(Nigeria_Lagos01_2020:1,Netherlands_Delft_1363424_2020:1,Denmark_SSI-01_2020:1,England_200990723_2020:1,Switzerland_TI2045_2020:1,Switzerland_1000477377_2020:2,Denmark_SSI-05_2020:4,Chile_Santiago-2_2020:1,Brazil_SPBR-14_2020:1,Finland_FIN-318_2020:2,Netherlands_Limburg_5_2020:2,Belgium_DBA-03032_2020:2,Switzerland_SZ1417_2020:2,Belgium_GMH-03022_2020:2,Netherlands_Utrecht_14_2020:2,Netherlands_Utrecht_1_2020:2,Finland_FIN03032020C_2020:1,Netherlands_Berlicum_1363564_2020:1,(Netherlands_Limburg_3_2020,Netherlands_Utrecht_2_2020:0)70:2,(Switzerland_GR2988_2020,Switzerland_GR3043_2020:0)71:1,(Switzerland_VD0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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_05_current_tree.nw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_05_current_tree.nw Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((Wuhan_HBCDC-HB-06_2020:3,Wuhan_HBCDC-HB-02_2020:2,Wuhan_HBCDC-HB-04_2020:3,Shanghai_SH0075_2020:2,Shanghai_SH0010_2020:2,Tianmen_HBCDC-HB-07_2020:5,Shanghai_SH0041_2020:4,India_1-31_2020:4,Shanghai_SH0009_2020:1,Malaysia_MKAK-CL-2020-5096_2020:2,(France_GE1583_2020:1,Georgia_Tb-390_2020:1,Spain_Valencia6_2020:1,Spain_CastillayLeon201437_2020:1,node_12_condensed_6_leaves:0)3:5,(Sichuan_IVDC-SC-001_2020:1,USA_CA1_2020:1,USA_IL2_2020:2,Vietnam_CM99_2020:2,node_13_condensed_3_leaves:0)4:3,(Shanghai_SH0035_2020:2,Australia_QLD02_2020:2,Australia_QLD03_2020:1,Australia_VIC07_2020:1,(Netherlands_Utrecht_16_2020:1,Netherlands_Utrecht_17_2020:0)6:1,node_14_condensed_6_leaves:0)5:2,(Shandong_LY003_2020:2,Shandong_LY005_2020:2,node_15_condensed_3_leaves:0)7:1,(node_16_condensed_2_leaves:0)8:4,England_02_2020:3,(Chongqing_YC01_2020:2,((USA_CA-CDPH-UC7_2020:0,USA_CA-CDPH-UC9_2020:1)11:3,(node_37_condensed_2_leaves:0)12:2)10:2,Malaysia_MKAK-CL-2020-6430_2020:1,node_17_condensed_3_leaves:0)9:1,(Shanghai_SH0059_2020:3,USA_TX1_2020:4,(Japan_TY-WK-012_2020:1,node_26_condensed_2_leaves:0)14:1,Shanghai_SH0004_2020:1,Germany_BavPat3_2020:1,Shanghai_SH0005_2020:0)13:1,(Yunnan_IVDC-YN-003_2020:0,USA_AZ1_2020:1,Anhui_SZ005_2020:6)15:1,(Beijing_233_2020:1,node_18_condensed_3_leaves:0)16:2,node_2_condensed_10_leaves:0)2:2,Shanghai_SH0007_2020:3,Hangzhou_ZJU-07_2020:5,Wuhan_IPBCAMS-WH-03_2019:1,Wuhan_WH01_2019:2,Wuhan_WIV07_2019:1,Shanghai_SH0093_2020:2,Wuhan_HBCDC-HB-01_2019:1,Wuhan_IPBCAMS-WH-01_2019:3,Wuhan_IVDC-HB-04_2020:2,Wuhan_IVDC-HB-05_2019:2,Wuhan_WIV05_2019:2,Sweden_01_2020:7,Taiwan_2_2020:3,USA_CA2_2020:2,Shanghai_SH0040_2020:2,Singapore_7_2020:2,Australia_VIC02_2020:2,France_IDF0515_2020:3,Hangzhou_ZJU-01_2020:3,Shanghai_SH0037_2020:5,Nepal_61_2020:1,China_WH-09_2020:1,Jiangxi_IVDC-JX-002_2020:1,Zhejiang_WZ-01_2020:1,Japan_KY-V-029_2020:3,Hangzhou_ZJU-03_2020:1,Netherlands_Utrecht_12_2020:2,Singapore_1_2020:1,Taiwan_NTU02_2020:2,England_SHEF-BFD36_2020:3,France_IDF0626_2020:1,Malaysia_MKAK-CL-2020-7554_2020:2,Cambodia_0012_2020:1,(USA_CA-CDPH-UC2_2020:4,USA_CA-CDPH-UC3_2020:1,node_3_condensed_2_leaves:0)17:1,(node_4_condensed_2_leaves:0)18:1,(Germany_NRW-10_2020:1,Germany_NRW-09_2020:1,Poland_PL_P1_2020:1,(Germany_NRW-04_2020:0,Germany_NRW-07_2020:1,(node_27_condensed_3_leaves:0)21:2)20:2,node_5_condensed_5_leaves:0)19:2,(Malaysia_MKAK-CL-2020-5045_2020:2,node_6_condensed_3_leaves:0)22:1,(Jiangsu_JS01_2020:2,Shanghai_SH0031_2020:1)23:1,(Australia_NSW02_2020:1,(Hangzhou_ZJU-06_2020:1,(Shanghai_SH0085_2020:4,Shanghai_SH0094_2020:0)26:2)25:1)24:1,(India_1-27_2020:3,Shanghai_SH0011_2020:1,Fujian_13_2020:1,Singapore_11_2020:1,USA_WI1_2020:0)27:1,(Wuhan_HBCDC-HB-05_2020:1,Shandong_IVDC-SD-001_2020:3,England_200960041_2020:2,Australia_NSW05_2020:1,(Georgia_Tb-82_2020:2,Australia_NSW09_2020:3,(Canada_BC_25211_2020:4,Kuwait_KU09_2020:2)30:1,Kuwait_KU18_2020:1,Kuwait_KU12_2020:2,Australia_NSW06_2020:1)29:2,(node_19_condensed_2_leaves:0)31:2,(Taiwan_CGMH-CGU-04_2020:3,node_20_condensed_2_leaves:0)32:3,Kuwait_KU17_2020:1,(Canada_BC_17397_2020:2,Canada_BC_13297_2020:2)33:1,(Australia_QLD09_2020:1,Australia_NSW07_2020:0)34:1,(USA_NY1-PV08001_2020:3,Canada_BC_37_0-2_2020:0,Canada_BC_69243_2020:2,(England_200990002_2020:2,Germany_BavPat2_2020:1)36:2)35:1)28:4,(node_7_condensed_3_leaves:0)37:2,(Jiangsu_JS02_2020:4,Shanghai_SH0008_2020:3,USA_CA5_2020:1)38:1,(Wuhan_WIV02_2019:1,node_8_condensed_2_leaves:0)39:1,(node_9_condensed_2_leaves:0)40:1,(Japan_Hu_DP_Kng_19-027_2020:1,node_10_condensed_3_leaves:0)41:1,(Hangzhou_ZJU-09_2020:0,Australia_VIC01_2020:3)42:1,(USA_MA1_2020:3,(Shanghai_SH0058_2020:4,(node_28_condensed_2_leaves:0)45:1,node_21_condensed_2_leaves:0)44:1)43:1,((France_B2334_2020:1,France_B2340_2020:1)47:2,(Georgia_Tb-468_2020:1,Georgia_Tb-537_2020:1,Georgia_Tb-54_2020:0)48:1,Italy_SPL1_2020:0)46:2,(England_20102000106_2020:2,(England_09c_2020:0,Brazil_ES-225_2020:1,England_20100001406_2020:1,(node_29_condensed_3_leaves:0)51:1)50:2,(Brazil_SPBR-10_2020:1,Switzerland_1000477102_2020:2,Brazil_SPBR-02_2020:1,England_200990006_2020:0,Netherlands_Utrecht_18_2020:2)52:1,England_200960515_2020:1,(node_22_condensed_3_leaves:0)53:1)49:3,(Netherlands_Utrecht_19_2020:3,Netherlands_Limburg_6_2020:2,Netherlands_Naarden_1364774_2020:0,(node_23_condensed_2_leaves:0)55:1,(Netherlands_Oss_1363500_2020:0,Netherlands_Tilburg_1363354_2020:2)56:1)54:1,(Singapore_8_2020:1,(node_24_condensed_3_leaves:0)58:1)57:1,(Shanghai_SH0086_2020:3,(Finland_FIN-25_2020:6,Belgium_DB-03023_2020:4,Denmark_SSI-102_2020:3,Denmark_SSI-02_2020:1,Belgium_BM-03012_2020:3,England_20100022706_2020:2,Denmark_SSI-04_2020:3,Taiwan_NTU03_2020:2,Finland_FIN03032020A_2020:2,Switzerland_GE4984_2020:2,Switzerland_AG0361_2020:2,Finland_FIN-266_2020:1,Luxembourg_Lux1_2020:1,Japan_SMU-0311S3_2020:1,Denmark_SSI-03_2020:1,Netherlands_Gelderland_2_2020:1,Georgia_Tb-273_2020:1,Belgium_SH-03014_2020:1,((node_38_condensed_2_leaves:0)62:2,node_30_condensed_4_leaves:0)61:1,(France_HF2174_202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|
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_05_parsimony_scores.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_05_parsimony_scores.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1771 @@\n+#Sample\tTree node\tParsimony score\tOptimal (y/n)\tParsimony-increasing mutations (for optimal nodes)\n+Sample1\t1\t3\t\tn\tN/A\n+Sample1\t2\t4\t\tn\tN/A\n+Sample1\tWuhan_HBCDC-HB-06_2020\t6\t\tn\tN/A\n+Sample1\tWuhan_HBCDC-HB-02_2020\t6\t\tn\tN/A\n+Sample1\tWuhan_HBCDC-HB-04_2020\t6\t\tn\tN/A\n+Sample1\tShanghai_SH0075_2020\t6\t\tn\tN/A\n+Sample1\tShanghai_SH0010_2020\t6\t\tn\tN/A\n+Sample1\tTianmen_HBCDC-HB-07_2020\t6\t\tn\tN/A\n+Sample1\tShanghai_SH0041_2020\t6\t\tn\tN/A\n+Sample1\tIndia_1-31_2020\t6\t\tn\tN/A\n+Sample1\tShanghai_SH0009_2020\t6\t\tn\tN/A\n+Sample1\tMalaysia_MKAK-CL-2020-5096_2020\t6\t\tn\tN/A\n+Sample1\t3\t6\t\tn\tN/A\n+Sample1\tFrance_GE1583_2020\t11\t\tn\tN/A\n+Sample1\tGeorgia_Tb-390_2020\t11\t\tn\tN/A\n+Sample1\tSpain_Valencia6_2020\t11\t\tn\tN/A\n+Sample1\tSpain_CastillayLeon201437_2020\t11\t\tn\tN/A\n+Sample1\tnode_12_condensed_6_leaves\t11\t\tn\tN/A\n+Sample1\t4\t6\t\tn\tN/A\n+Sample1\tSichuan_IVDC-SC-001_2020\t9\t\tn\tN/A\n+Sample1\tUSA_CA1_2020\t9\t\tn\tN/A\n+Sample1\tUSA_IL2_2020\t9\t\tn\tN/A\n+Sample1\tVietnam_CM99_2020\t9\t\tn\tN/A\n+Sample1\tnode_13_condensed_3_leaves\t9\t\tn\tN/A\n+Sample1\t5\t6\t\tn\tN/A\n+Sample1\tShanghai_SH0035_2020\t8\t\tn\tN/A\n+Sample1\tAustralia_QLD02_2020\t8\t\tn\tN/A\n+Sample1\tAustralia_QLD03_2020\t8\t\tn\tN/A\n+Sample1\tAustralia_VIC07_2020\t8\t\tn\tN/A\n+Sample1\t6\t8\t\tn\tN/A\n+Sample1\tNetherlands_Utrecht_16_2020\t9\t\tn\tN/A\n+Sample1\tNetherlands_Utrecht_17_2020\t9\t\tn\tN/A\n+Sample1\tnode_14_condensed_6_leaves\t8\t\tn\tN/A\n+Sample1\t7\t6\t\tn\tN/A\n+Sample1\tShandong_LY003_2020\t7\t\tn\tN/A\n+Sample1\tShandong_LY005_2020\t7\t\tn\tN/A\n+Sample1\tnode_15_condensed_3_leaves\t7\t\tn\tN/A\n+Sample1\t8\t6\t\tn\tN/A\n+Sample1\tnode_16_condensed_2_leaves\t10\t\tn\tN/A\n+Sample1\tEngland_02_2020\t6\t\tn\tN/A\n+Sample1\t9\t6\t\tn\tN/A\n+Sample1\tChongqing_YC01_2020\t7\t\tn\tN/A\n+Sample1\t10\t7\t\tn\tN/A\n+Sample1\t11\t9\t\tn\tN/A\n+Sample1\tUSA_CA-CDPH-UC7_2020\t12\t\tn\tN/A\n+Sample1\tUSA_CA-CDPH-UC9_2020\t12\t\tn\tN/A\n+Sample1\t12\t9\t\tn\tN/A\n+Sample1\tnode_37_condensed_2_leaves\t11\t\tn\tN/A\n+Sample1\tMalaysia_MKAK-CL-2020-6430_2020\t7\t\tn\tN/A\n+Sample1\tnode_17_condensed_3_leaves\t7\t\tn\tN/A\n+Sample1\t13\t6\t\tn\tN/A\n+Sample1\tShanghai_SH0059_2020\t7\t\tn\tN/A\n+Sample1\tUSA_TX1_2020\t7\t\tn\tN/A\n+Sample1\t14\t7\t\tn\tN/A\n+Sample1\tJapan_TY-WK-012_2020\t8\t\tn\tN/A\n+Sample1\tnode_26_condensed_2_leaves\t8\t\tn\tN/A\n+Sample1\tShanghai_SH0004_2020\t7\t\tn\tN/A\n+Sample1\tGermany_BavPat3_2020\t7\t\tn\tN/A\n+Sample1\tShanghai_SH0005_2020\t7\t\tn\tN/A\n+Sample1\t15\t6\t\tn\tN/A\n+Sample1\tYunnan_IVDC-YN-003_2020\t7\t\tn\tN/A\n+Sample1\tUSA_AZ1_2020\t7\t\tn\tN/A\n+Sample1\tAnhui_SZ005_2020\t5\t\tn\tN/A\n+Sample1\t16\t6\t\tn\tN/A\n+Sample1\tBeijing_233_2020\t8\t\tn\tN/A\n+Sample1\tnode_18_condensed_3_leaves\t8\t\tn\tN/A\n+Sample1\tnode_2_condensed_10_leaves\t6\t\tn\tN/A\n+Sample1\tShanghai_SH0007_2020\t4\t\tn\tN/A\n+Sample1\tHangzhou_ZJU-07_2020\t4\t\tn\tN/A\n+Sample1\tWuhan_IPBCAMS-WH-03_2019\t4\t\tn\tN/A\n+Sample1\tWuhan_WH01_2019\t4\t\tn\tN/A\n+Sample1\tWuhan_WIV07_2019\t4\t\tn\tN/A\n+Sample1\tShanghai_SH0093_2020\t4\t\tn\tN/A\n+Sample1\tWuhan_HBCDC-HB-01_2019\t4\t\tn\tN/A\n+Sample1\tWuhan_IPBCAMS-WH-01_2019\t4\t\tn\tN/A\n+Sample1\tWuhan_IVDC-HB-04_2020\t4\t\tn\tN/A\n+Sample1\tWuhan_IVDC-HB-05_2019\t4\t\tn\tN/A\n+Sample1\tWuhan_WIV05_2019\t4\t\tn\tN/A\n+Sample1\tSweden_01_2020\t4\t\tn\tN/A\n+Sample1\tTaiwan_2_2020\t4\t\tn\tN/A\n+Sample1\tUSA_CA2_2020\t4\t\tn\tN/A\n+Sample1\tShanghai_SH0040_2020\t4\t\tn\tN/A\n+Sample1\tSingapore_7_2020\t4\t\tn\tN/A\n+Sample1\tAustralia_VIC02_2020\t4\t\tn\tN/A\n+Sample1\tFrance_IDF0515_2020\t4\t\tn\tN/A\n+Sample1\tHangzhou_ZJU-01_2020\t4\t\tn\tN/A\n+Sample1\tShanghai_SH0037_2020\t4\t\tn\tN/A\n+Sample1\tNepal_61_2020\t4\t\tn\tN/A\n+Sample1\tChina_WH-09_2020\t4\t\tn\tN/A\n+Sample1\tJiangxi_IVDC-JX-002_2020\t4\t\tn\tN/A\n+Sample1\tZhejiang_WZ-01_2020\t4\t\tn\tN/A\n+Sample1\tJapan_KY-V-029_2020\t4\t\tn\tN/A\n+Sample1\tHangzhou_ZJU-03_2020\t4\t\tn\tN/A\n+Sample1\tNetherlands_Utrecht_12_2020\t4\t\tn\tN/A\n+Sample1\tSingapore_1_2020\t4\t\tn\tN/A\n+Sample1\tTaiwan_NTU02_2020\t4\t\tn\tN/A\n+Sample1\tEngland_SHEF-BFD36_2020\t4\t\tn\tN/A\n+Sample1\tFrance_IDF0626_2020\t4\t\tn\tN/A\n+Sample1\tMalaysia_MKAK-CL-2020-7554_2020\t4\t\tn\tN/A\n+Sample1\tCambodia_0012_2020\t4\t\tn\tN/A\n+Sample1\t17\t4\t\tn\tN/A\n+Sample1\tUSA_CA-CDPH-UC2_2020\t5\t\tn\tN/A\n+Sample1\tUSA_CA-CDPH-UC3_2020\t5\t\tn\tN/A\n+Sample1\tnode_3_condensed_2_leaves\t5\t\tn\tN/A\n+Sample1\t18\t4\t\tn\tN/A\n+Sample1\tnode_4_condensed_2_leaves\t5\t\tn\tN/A\n+Sample1\t19\t1\t\ty\tA276'..b'elderland_2_2020\t10\t\tn\tN/A\n+Sample5\tGeorgia_Tb-273_2020\t10\t\tn\tN/A\n+Sample5\tBelgium_SH-03014_2020\t10\t\tn\tN/A\n+Sample5\t61\t10\t\tn\tN/A\n+Sample5\t62\t11\t\tn\tN/A\n+Sample5\tnode_38_condensed_2_leaves\t13\t\tn\tN/A\n+Sample5\tnode_30_condensed_4_leaves\t11\t\tn\tN/A\n+Sample5\t63\t10\t\tn\tN/A\n+Sample5\tFrance_HF2174_2020\t12\t\tn\tN/A\n+Sample5\tFrance_GE1977_2020\t12\t\tn\tN/A\n+Sample5\tFrance_HF1684_2020\t12\t\tn\tN/A\n+Sample5\t64\t12\t\tn\tN/A\n+Sample5\tnode_39_condensed_2_leaves\t13\t\tn\tN/A\n+Sample5\tBelgium_VAG-03013_2020\t10\t\tn\tN/A\n+Sample5\t65\t10\t\tn\tN/A\n+Sample5\tNetherlands_Utrecht_1363564_2020\t14\t\tn\tN/A\n+Sample5\tnode_31_condensed_2_leaves\t14\t\tn\tN/A\n+Sample5\t66\t10\t\tn\tN/A\n+Sample5\tEngland_20099107406_2020\t11\t\tn\tN/A\n+Sample5\tGeorgia_Tb_2020\t11\t\tn\tN/A\n+Sample5\t67\t10\t\tn\tN/A\n+Sample5\tFrance_BFC2094_2020\t11\t\tn\tN/A\n+Sample5\tFrance_BFC2147_2020\t11\t\tn\tN/A\n+Sample5\tnode_32_condensed_4_leaves\t11\t\tn\tN/A\n+Sample5\t68\t10\t\tn\tN/A\n+Sample5\tHungary_mbl1_2020\t11\t\tn\tN/A\n+Sample5\tnode_33_condensed_5_leaves\t11\t\tn\tN/A\n+Sample5\t69\t10\t\tn\tN/A\n+Sample5\tNigeria_Lagos01_2020\t13\t\tn\tN/A\n+Sample5\tNetherlands_Delft_1363424_2020\t13\t\tn\tN/A\n+Sample5\tDenmark_SSI-01_2020\t13\t\tn\tN/A\n+Sample5\tEngland_200990723_2020\t13\t\tn\tN/A\n+Sample5\tSwitzerland_TI2045_2020\t13\t\tn\tN/A\n+Sample5\tSwitzerland_1000477377_2020\t13\t\tn\tN/A\n+Sample5\tDenmark_SSI-05_2020\t13\t\tn\tN/A\n+Sample5\tChile_Santiago-2_2020\t13\t\tn\tN/A\n+Sample5\tBrazil_SPBR-14_2020\t13\t\tn\tN/A\n+Sample5\tFinland_FIN-318_2020\t13\t\tn\tN/A\n+Sample5\tNetherlands_Limburg_5_2020\t13\t\tn\tN/A\n+Sample5\tBelgium_DBA-03032_2020\t13\t\tn\tN/A\n+Sample5\tSwitzerland_SZ1417_2020\t13\t\tn\tN/A\n+Sample5\tBelgium_GMH-03022_2020\t13\t\tn\tN/A\n+Sample5\tNetherlands_Utrecht_14_2020\t13\t\tn\tN/A\n+Sample5\tNetherlands_Utrecht_1_2020\t13\t\tn\tN/A\n+Sample5\tFinland_FIN03032020C_2020\t13\t\tn\tN/A\n+Sample5\tNetherlands_Berlicum_1363564_2020\t13\t\tn\tN/A\n+Sample5\t70\t13\t\tn\tN/A\n+Sample5\tnode_40_condensed_2_leaves\t15\t\tn\tN/A\n+Sample5\t71\t13\t\tn\tN/A\n+Sample5\tnode_41_condensed_2_leaves\t14\t\tn\tN/A\n+Sample5\t72\t13\t\tn\tN/A\n+Sample5\tnode_42_condensed_2_leaves\t14\t\tn\tN/A\n+Sample5\t73\t13\t\tn\tN/A\n+Sample5\tSwitzerland_1000477797_2020\t14\t\tn\tN/A\n+Sample5\tBrazil_BA-312_2020\t14\t\tn\tN/A\n+Sample5\tnode_43_condensed_3_leaves\t14\t\tn\tN/A\n+Sample5\t74\t13\t\tn\tN/A\n+Sample5\tFinland_FIN-313_2020\t15\t\tn\tN/A\n+Sample5\tNetherlands_Utrecht_15_2020\t15\t\tn\tN/A\n+Sample5\t75\t13\t\tn\tN/A\n+Sample5\tSwitzerland_GE1422_2020\t14\t\tn\tN/A\n+Sample5\tNetherlands_Diemen_1363454_2020\t14\t\tn\tN/A\n+Sample5\tnode_44_condensed_3_leaves\t14\t\tn\tN/A\n+Sample5\t76\t13\t\tn\tN/A\n+Sample5\tSwitzerland_BE6651_2020\t14\t\tn\tN/A\n+Sample5\tNetherlands_NoordHolland_2_2020\t14\t\tn\tN/A\n+Sample5\tnode_45_condensed_6_leaves\t14\t\tn\tN/A\n+Sample5\tBelgium_BC-03016_2020\t13\t\tn\tN/A\n+Sample5\t77\t13\t\tn\tN/A\n+Sample5\tSwitzerland_1000477757_2020\t14\t\tn\tN/A\n+Sample5\tBrazil_SPBR-12_2020\t14\t\tn\tN/A\n+Sample5\tGermany_Baden-Wuerttemberg-1_2020\t14\t\tn\tN/A\n+Sample5\t78\t13\t\tn\tN/A\n+Sample5\tnode_46_condensed_16_leaves\t14\t\tn\tN/A\n+Sample5\t79\t13\t\tn\tN/A\n+Sample5\tBelgium_UMF-03025_2020\t14\t\tn\tN/A\n+Sample5\t80\t14\t\tn\tN/A\n+Sample5\tnode_47_condensed_2_leaves\t15\t\tn\tN/A\n+Sample5\tnode_34_condensed_7_leaves\t13\t\tn\tN/A\n+Sample5\t81\t10\t\tn\tN/A\n+Sample5\tNetherlands_NoordHolland_3_2020\t11\t\tn\tN/A\n+Sample5\tNetherlands_Flevoland_1_2020\t11\t\tn\tN/A\n+Sample5\t82\t10\t\tn\tN/A\n+Sample5\tNetherlandsL_Houten_1363498_2020\t11\t\tn\tN/A\n+Sample5\tItaly_UniSR1_2020\t11\t\tn\tN/A\n+Sample5\tFrance_N1620_2020\t11\t\tn\tN/A\n+Sample5\tnode_35_condensed_3_leaves\t11\t\tn\tN/A\n+Sample5\t83\t10\t\tn\tN/A\n+Sample5\tGeorgia_Tb-673_2020\t12\t\tn\tN/A\n+Sample5\tFrance_B2330_2020\t12\t\tn\tN/A\n+Sample5\tFrance_PL1643_2020\t12\t\tn\tN/A\n+Sample5\tFrance_HF1988_2020\t12\t\tn\tN/A\n+Sample5\tFrance_B2348_2020\t12\t\tn\tN/A\n+Sample5\t84\t12\t\tn\tN/A\n+Sample5\tFrance_B2351_2020\t13\t\tn\tN/A\n+Sample5\tFrance_B2344_2020\t13\t\tn\tN/A\n+Sample5\tFrance_B2349_2020\t13\t\tn\tN/A\n+Sample5\t85\t12\t\tn\tN/A\n+Sample5\tFrance_IDF2256_2020\t13\t\tn\tN/A\n+Sample5\tFrance_HF1871_2020\t13\t\tn\tN/A\n+Sample5\tNetherlands_Haarlem_1363688_2020\t12\t\tn\tN/A\n+Sample5\tnode_36_condensed_6_leaves\t12\t\tn\tN/A\n+Sample5\tnode_25_condensed_15_leaves\t10\t\tn\tN/A\n+Sample5\tnode_11_condensed_3_leaves\t9\t\tn\tN/A\n+Sample5\tnode_1_condensed_27_leaves\t6\t\tn\tN/A\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_06_final_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_06_final_tree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((Wuhan_HBCDC-HB-06_2020:3,Wuhan_HBCDC-HB-02_2020:2,Wuhan_HBCDC-HB-04_2020:3,Shanghai_SH0075_2020:2,Shanghai_SH0010_2020:2,Tianmen_HBCDC-HB-07_2020:5,Shanghai_SH0041_2020:4,India_1-31_2020:4,Shanghai_SH0009_2020:1,Malaysia_MKAK-CL-2020-5096_2020:2,(France_GE1583_2020:1,Georgia_Tb-390_2020:1,Spain_Valencia6_2020:1,Spain_CastillayLeon201437_2020:1,node_12_condensed_6_leaves:0)3:5,(Sichuan_IVDC-SC-001_2020:1,USA_CA1_2020:1,USA_IL2_2020:2,Vietnam_CM99_2020:2,node_13_condensed_3_leaves:0)4:3,(Shanghai_SH0035_2020:2,Australia_QLD02_2020:2,Australia_QLD03_2020:1,Australia_VIC07_2020:1,(Netherlands_Utrecht_16_2020:1,Netherlands_Utrecht_17_2020:0)6:1,node_14_condensed_6_leaves:0)5:2,(Shandong_LY003_2020:2,Shandong_LY005_2020:2,node_15_condensed_3_leaves:0)7:1,(node_16_condensed_2_leaves:0)8:4,England_02_2020:3,(Chongqing_YC01_2020:2,((USA_CA-CDPH-UC7_2020:0,USA_CA-CDPH-UC9_2020:1)11:3,(node_37_condensed_2_leaves:0)12:2)10:2,Malaysia_MKAK-CL-2020-6430_2020:1,node_17_condensed_3_leaves:0)9:1,(Shanghai_SH0059_2020:3,USA_TX1_2020:4,(Japan_TY-WK-012_2020:1,node_26_condensed_2_leaves:0)14:1,Shanghai_SH0004_2020:1,Germany_BavPat3_2020:1,Shanghai_SH0005_2020:0)13:1,(Yunnan_IVDC-YN-003_2020:0,USA_AZ1_2020:1,Anhui_SZ005_2020:6)15:1,(Beijing_233_2020:1,node_18_condensed_3_leaves:0)16:2,node_2_condensed_10_leaves:0)2:2,Shanghai_SH0007_2020:3,Hangzhou_ZJU-07_2020:5,Wuhan_IPBCAMS-WH-03_2019:1,Wuhan_WH01_2019:2,Wuhan_WIV07_2019:1,Shanghai_SH0093_2020:2,Wuhan_HBCDC-HB-01_2019:1,Wuhan_IPBCAMS-WH-01_2019:3,Wuhan_IVDC-HB-04_2020:2,Wuhan_IVDC-HB-05_2019:2,Wuhan_WIV05_2019:2,Sweden_01_2020:7,Taiwan_2_2020:3,USA_CA2_2020:2,Shanghai_SH0040_2020:2,Singapore_7_2020:2,Australia_VIC02_2020:2,France_IDF0515_2020:3,Hangzhou_ZJU-01_2020:3,Shanghai_SH0037_2020:5,Nepal_61_2020:1,China_WH-09_2020:1,Jiangxi_IVDC-JX-002_2020:1,Zhejiang_WZ-01_2020:1,Japan_KY-V-029_2020:3,Hangzhou_ZJU-03_2020:1,Netherlands_Utrecht_12_2020:2,Singapore_1_2020:1,Taiwan_NTU02_2020:2,England_SHEF-BFD36_2020:3,France_IDF0626_2020:1,Malaysia_MKAK-CL-2020-7554_2020:2,Cambodia_0012_2020:1,(USA_CA-CDPH-UC2_2020:4,USA_CA-CDPH-UC3_2020:1,node_3_condensed_2_leaves:0)17:1,(node_4_condensed_2_leaves:0)18:1,(Germany_NRW-10_2020:1,Germany_NRW-09_2020:1,Poland_PL_P1_2020:1,(Germany_NRW-04_2020:0,Germany_NRW-07_2020:1,(node_27_condensed_3_leaves:0)21:2)20:2,node_5_condensed_5_leaves:0,(Sample1:0,(Sample3:0,Sample2:0,(Sample5:0,Sample4:0)88:1)87:1)86:1)19:2,(Malaysia_MKAK-CL-2020-5045_2020:2,node_6_condensed_3_leaves:0)22:1,(Jiangsu_JS01_2020:2,Shanghai_SH0031_2020:1)23:1,(Australia_NSW02_2020:1,(Hangzhou_ZJU-06_2020:1,(Shanghai_SH0085_2020:4,Shanghai_SH0094_2020:0)26:2)25:1)24:1,(India_1-27_2020:3,Shanghai_SH0011_2020:1,Fujian_13_2020:1,Singapore_11_2020:1,USA_WI1_2020:0)27:1,(Wuhan_HBCDC-HB-05_2020:1,Shandong_IVDC-SD-001_2020:3,England_200960041_2020:2,Australia_NSW05_2020:1,(Georgia_Tb-82_2020:2,Australia_NSW09_2020:3,(Canada_BC_25211_2020:4,Kuwait_KU09_2020:2)30:1,Kuwait_KU18_2020:1,Kuwait_KU12_2020:2,Australia_NSW06_2020:1)29:2,(node_19_condensed_2_leaves:0)31:2,(Taiwan_CGMH-CGU-04_2020:3,node_20_condensed_2_leaves:0)32:3,Kuwait_KU17_2020:1,(Canada_BC_17397_2020:2,Canada_BC_13297_2020:2)33:1,(Australia_QLD09_2020:1,Australia_NSW07_2020:0)34:1,(USA_NY1-PV08001_2020:3,Canada_BC_37_0-2_2020:0,Canada_BC_69243_2020:2,(England_200990002_2020:2,Germany_BavPat2_2020:1)36:2)35:1)28:4,(node_7_condensed_3_leaves:0)37:2,(Jiangsu_JS02_2020:4,Shanghai_SH0008_2020:3,USA_CA5_2020:1)38:1,(Wuhan_WIV02_2019:1,node_8_condensed_2_leaves:0)39:1,(node_9_condensed_2_leaves:0)40:1,(Japan_Hu_DP_Kng_19-027_2020:1,node_10_condensed_3_leaves:0)41:1,(Hangzhou_ZJU-09_2020:0,Australia_VIC01_2020:3)42:1,(USA_MA1_2020:3,(Shanghai_SH0058_2020:4,(node_28_condensed_2_leaves:0)45:1,node_21_condensed_2_leaves:0)44:1)43:1,((France_B2334_2020:1,France_B2340_2020:1)47:2,(Georgia_Tb-468_2020:1,Georgia_Tb-537_2020:1,Georgia_Tb-54_2020:0)48:1,Italy_SPL1_2020:0)46:2,(England_20102000106_2020:2,(England_09c_2020:0,Brazil_ES-225_2020:1,England_20100001406_2020:1,(node_29_condensed_3_leaves:0)51:1)50:2,(Brazil_SPBR-10_2020:1,Switzerland_1000477102_2020:2,Brazil_SPBR-02_2020:1,England_200990006_2020:0,Netherlands_Utrecht_18_2020:2)52:1,England_200960515_2020:1,(node_22_condensed_3_leaves:0)53:1)49:3,(Netherlands_Utrecht_19_2020:3,Netherlands_Limburg_6_2020:2,Netherlands_Naarden_1364774_2020:0,(node_23_condensed_2_leaves:0)55:1,(Netherlands_Oss_1363500_2020:0,Netherlands_Tilburg_1363354_2020:2)56:1)54:1,(Singapore_8_2020:1,(node_24_condensed_3_leaves:0)58:1)57:1,(Shanghai_SH0086_2020:3,(Finland_FIN-25_2020:6,Belgium_DB-03023_2020:4,Denmark_SSI-102_2020:3,Denmark_SSI-02_2020:1,Belgium_BM-03012_2020:3,England_20100022706_2020:2,Denmark_SSI-04_2020:3,Taiwan_NTU03_2020:2,Finland_FIN03032020A_2020:2,Switzerland_GE4984_2020:2,Switzerland_AG0361_2020:2,Finland_FIN-266_2020:1,Luxembourg_Lux1_2020:1,Japan_SMU-0311S3_2020:1,Denmark_SSI-03_2020:1,Netherlands_Gelderland_2_2020:1,Georgia_Tb-273_2020:1,Belgium_SH-03014_2020:1,((node_38_condensed_2_leaves:0)62:2,node_30_condensed_4_leaves:0)61:1,(France_HF2174_2020:2,France_GE1977_2020:3,France_HF1684_2020:0,(node_39_condensed_2_leaves:0)64:1)63:2,Belgium_VAG-03013_2020:4,(Netherlands_Utrecht_1363564_2020:1,node_31_condensed_2_leaves:0)65:4,(England_20099107406_2020:1,Georgia_Tb_2020:0)66:1,(France_BFC2094_2020:1,France_BFC2147_2020:1,node_32_condensed_4_leaves:0)67:1,(Hungary_mbl1_2020:1,node_33_condensed_5_leaves:0)68:1,(Nigeria_Lagos01_2020:1,Netherlands_Delft_1363424_2020:1,Denmark_SSI-01_2020:1,England_200990723_2020:1,Switzerland_TI2045_2020:1,Switzerland_1000477377_2020:2,Denmark_SSI-05_2020:4,Chile_Santiago-2_2020:1,Brazil_SPBR-14_2020:1,Finland_FIN-318_2020:2,Netherlands_Limburg_5_2020:2,Belgium_DBA-03032_2020:2,Switzerland_SZ1417_2020:2,Belgium_GMH-03022_2020:2,Netherlands_Utrecht_14_2020:2,Netherlands_Utrecht_1_2020:2,Finland_FIN03032020C_2020:1,Netherlands_Berlicum_1363564_2020:1,(node_40_condensed_2_leaves:0)70:2,(node_41_condensed_2_leaves:0)71:1,(node_42_condensed_2_leaves:0)72:1,(Switzerland_1000477797_2020:1,Brazil_BA-312_2020:1,node_43_condensed_3_leaves:0)73:1,(Finland_FIN-313_2020:1,Netherlands_Utrecht_15_2020:0)74:2,(Switzerland_GE1422_2020:1,Netherlands_Diemen_1363454_2020:3,node_44_condensed_3_leaves:0)75:1,(Switzerland_BE6651_2020:1,Netherlands_NoordHolland_2_2020:1,node_45_condensed_6_leaves:0)76:1,Belgium_BC-03016_2020:2,(Switzerland_1000477757_2020:2,Brazil_SPBR-12_2020:1,Germany_Baden-Wuerttemberg-1_2020:0)77:1,(node_46_condensed_16_leaves:0)78:1,(Belgium_UMF-03025_2020:0,(node_47_condensed_2_leaves:0)80:1)79:1,node_34_condensed_7_leaves:0)69:3,(Netherlands_NoordHolland_3_2020:2,Netherlands_Flevoland_1_2020:0)81:1,(NetherlandsL_Houten_1363498_2020:1,Italy_UniSR1_2020:1,France_N1620_2020:1,node_35_condensed_3_leaves:0)82:1,(Georgia_Tb-673_2020:2,France_B2330_2020:1,France_PL1643_2020:2,France_HF1988_2020:1,France_B2348_2020:1,(France_B2351_2020:1,France_B2344_2020:1,France_B2349_2020:0)84:1,(France_IDF2256_2020:1,France_HF1871_2020:2)85:1,Netherlands_Haarlem_1363688_2020:1,node_36_condensed_6_leaves:0)83:2,node_25_condensed_15_leaves:0)60:1,node_11_condensed_3_leaves:0)59:3,node_1_condensed_27_leaves:0)1:0; \ No newline at end of file |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_06_mutation_paths.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_06_mutation_paths.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Sample1 19:G1440A,G2891A 86:A27669G +Sample2 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample3 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample4 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G +Sample5 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_07_single_subtree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_07_single_subtree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((Sample1:0,(Sample3:0,Sample2:0,(Sample5:0,Sample4:0)88:1)87:1)86:3,(Japan_SMU-0311S3_2020:1,France_BFC2147_2020:2)60:4)1:0; \ No newline at end of file |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_07_single_subtree_mutations.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_07_single_subtree_mutations.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +1: +86: G1440A,G2891A,A27669G +Sample1: +87: G14948A +Sample3: +Sample2: +88: A23013G +Sample5: +Sample4: +60: C241T,C3037T,C14408T,A23403G +Japan_SMU-0311S3_2020: C29743T +France_BFC2147_2020: C13051T,C15324T |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_08_final_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_08_final_tree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((Wuhan_HBCDC-HB-06_2020:3,Wuhan_HBCDC-HB-02_2020:2,Wuhan_HBCDC-HB-04_2020:3,Shanghai_SH0075_2020:2,Shanghai_SH0010_2020:2,Tianmen_HBCDC-HB-07_2020:5,Shanghai_SH0041_2020:4,India_1-31_2020:4,Shanghai_SH0009_2020:1,Malaysia_MKAK-CL-2020-5096_2020:2,(France_GE1583_2020:1,Georgia_Tb-390_2020:1,Spain_Valencia6_2020:1,Spain_CastillayLeon201437_2020:1,node_12_condensed_6_leaves:0)3:5,(Sichuan_IVDC-SC-001_2020:1,USA_CA1_2020:1,USA_IL2_2020:2,Vietnam_CM99_2020:2,node_13_condensed_3_leaves:0)4:3,(Shanghai_SH0035_2020:2,Australia_QLD02_2020:2,Australia_QLD03_2020:1,Australia_VIC07_2020:1,(Netherlands_Utrecht_16_2020:1,Netherlands_Utrecht_17_2020:0)6:1,node_14_condensed_6_leaves:0)5:2,(Shandong_LY003_2020:2,Shandong_LY005_2020:2,node_15_condensed_3_leaves:0)7:1,(node_16_condensed_2_leaves:0)8:4,England_02_2020:3,(Chongqing_YC01_2020:2,((USA_CA-CDPH-UC7_2020:0,USA_CA-CDPH-UC9_2020:1)11:3,(node_37_condensed_2_leaves:0)12:2)10:2,Malaysia_MKAK-CL-2020-6430_2020:1,node_17_condensed_3_leaves:0)9:1,(Shanghai_SH0059_2020:3,USA_TX1_2020:4,(Japan_TY-WK-012_2020:1,node_26_condensed_2_leaves:0)14:1,Shanghai_SH0004_2020:1,Germany_BavPat3_2020:1,Shanghai_SH0005_2020:0)13:1,(Yunnan_IVDC-YN-003_2020:0,USA_AZ1_2020:1,Anhui_SZ005_2020:6)15:1,(Beijing_233_2020:1,node_18_condensed_3_leaves:0)16:2,node_2_condensed_10_leaves:0)2:2,Shanghai_SH0007_2020:3,Hangzhou_ZJU-07_2020:5,Wuhan_IPBCAMS-WH-03_2019:1,Wuhan_WH01_2019:2,Wuhan_WIV07_2019:1,Shanghai_SH0093_2020:2,Wuhan_HBCDC-HB-01_2019:1,Wuhan_IPBCAMS-WH-01_2019:3,Wuhan_IVDC-HB-04_2020:2,Wuhan_IVDC-HB-05_2019:2,Wuhan_WIV05_2019:2,Sweden_01_2020:7,Taiwan_2_2020:3,USA_CA2_2020:2,Shanghai_SH0040_2020:2,Singapore_7_2020:2,Australia_VIC02_2020:2,France_IDF0515_2020:3,Hangzhou_ZJU-01_2020:3,Shanghai_SH0037_2020:5,Nepal_61_2020:1,China_WH-09_2020:1,Jiangxi_IVDC-JX-002_2020:1,Zhejiang_WZ-01_2020:1,Japan_KY-V-029_2020:3,Hangzhou_ZJU-03_2020:1,Netherlands_Utrecht_12_2020:2,Singapore_1_2020:1,Taiwan_NTU02_2020:2,England_SHEF-BFD36_2020:3,France_IDF0626_2020:1,Malaysia_MKAK-CL-2020-7554_2020:2,Cambodia_0012_2020:1,(USA_CA-CDPH-UC2_2020:4,USA_CA-CDPH-UC3_2020:1,node_3_condensed_2_leaves:0)17:1,(node_4_condensed_2_leaves:0)18:1,(Germany_NRW-10_2020:1,Germany_NRW-09_2020:1,Poland_PL_P1_2020:1,(Germany_NRW-04_2020:0,Germany_NRW-07_2020:1,(node_27_condensed_3_leaves:0)21:2)20:2,node_5_condensed_5_leaves:0,(Sample1:0,(Sample3:0,Sample2:0,(Sample5:0,Sample4:0)88:1)87:1)86:1)19:2,(Malaysia_MKAK-CL-2020-5045_2020:2,node_6_condensed_3_leaves:0)22:1,(Jiangsu_JS01_2020:2,Shanghai_SH0031_2020:1)23:1,(Australia_NSW02_2020:1,(Hangzhou_ZJU-06_2020:1,(Shanghai_SH0085_2020:4,Shanghai_SH0094_2020:0)26:2)25:1)24:1,(India_1-27_2020:3,Shanghai_SH0011_2020:1,Fujian_13_2020:1,Singapore_11_2020:1,USA_WI1_2020:0)27:1,(Wuhan_HBCDC-HB-05_2020:1,Shandong_IVDC-SD-001_2020:3,England_200960041_2020:2,Australia_NSW05_2020:1,(Georgia_Tb-82_2020:2,Australia_NSW09_2020:3,(Canada_BC_25211_2020:4,Kuwait_KU09_2020:2)30:1,Kuwait_KU18_2020:1,Kuwait_KU12_2020:2,Australia_NSW06_2020:1)29:2,(node_19_condensed_2_leaves:0)31:2,(Taiwan_CGMH-CGU-04_2020:3,node_20_condensed_2_leaves:0)32:3,Kuwait_KU17_2020:1,(Canada_BC_17397_2020:2,Canada_BC_13297_2020:2)33:1,(Australia_QLD09_2020:1,Australia_NSW07_2020:0)34:1,(USA_NY1-PV08001_2020:3,Canada_BC_37_0-2_2020:0,Canada_BC_69243_2020:2,(England_200990002_2020:2,Germany_BavPat2_2020:1)36:2)35:1)28:4,(node_7_condensed_3_leaves:0)37:2,(Jiangsu_JS02_2020:4,Shanghai_SH0008_2020:3,USA_CA5_2020:1)38:1,(Wuhan_WIV02_2019:1,node_8_condensed_2_leaves:0)39:1,(node_9_condensed_2_leaves:0)40:1,(Japan_Hu_DP_Kng_19-027_2020:1,node_10_condensed_3_leaves:0)41:1,(Hangzhou_ZJU-09_2020:0,Australia_VIC01_2020:3)42:1,(USA_MA1_2020:3,(Shanghai_SH0058_2020:4,(node_28_condensed_2_leaves:0)45:1,node_21_condensed_2_leaves:0)44:1)43:1,((France_B2334_2020:1,France_B2340_2020:1)47:2,(Georgia_Tb-468_2020:1,Georgia_Tb-537_2020:1,Georgia_Tb-54_2020:0)48:1,Italy_SPL1_2020:0)46:2,(England_20102000106_2020:2,(England_09c_2020:0,Brazil_ES-225_2020:1,England_20100001406_2020:1,(node_29_condensed_3_leaves:0)51:1)50:2,(Brazil_SPBR-10_2020:1,Switzerland_1000477102_2020:2,Brazil_SPBR-02_2020:1,England_200990006_2020:0,Netherlands_Utrecht_18_2020:2)52:1,England_200960515_2020:1,(node_22_condensed_3_leaves:0)53:1)49:3,(Netherlands_Utrecht_19_2020:3,Netherlands_Limburg_6_2020:2,Netherlands_Naarden_1364774_2020:0,(node_23_condensed_2_leaves:0)55:1,(Netherlands_Oss_1363500_2020:0,Netherlands_Tilburg_1363354_2020:2)56:1)54:1,(Singapore_8_2020:1,(node_24_condensed_3_leaves:0)58:1)57:1,(Shanghai_SH0086_2020:3,(Finland_FIN-25_2020:6,Belgium_DB-03023_2020:4,Denmark_SSI-102_2020:3,Denmark_SSI-02_2020:1,Belgium_BM-03012_2020:3,England_20100022706_2020:2,Denmark_SSI-04_2020:3,Taiwan_NTU03_2020:2,Finland_FIN03032020A_2020:2,Switzerland_GE4984_2020:2,Switzerland_AG0361_2020:2,Finland_FIN-266_2020:1,Luxembourg_Lux1_2020:1,Japan_SMU-0311S3_2020:1,Denmark_SSI-03_2020:1,Netherlands_Gelderland_2_2020:1,Georgia_Tb-273_2020:1,Belgium_SH-03014_2020:1,((node_38_condensed_2_leaves:0)62:2,node_30_condensed_4_leaves:0)61:1,(France_HF2174_2020:2,France_GE1977_2020:3,France_HF1684_2020:0,(node_39_condensed_2_leaves:0)64:1)63:2,Belgium_VAG-03013_2020:4,(Netherlands_Utrecht_1363564_2020:1,node_31_condensed_2_leaves:0)65:4,(England_20099107406_2020:1,Georgia_Tb_2020:0)66:1,(France_BFC2094_2020:1,France_BFC2147_2020:1,node_32_condensed_4_leaves:0)67:1,(Hungary_mbl1_2020:1,node_33_condensed_5_leaves:0)68:1,(Nigeria_Lagos01_2020:1,Netherlands_Delft_1363424_2020:1,Denmark_SSI-01_2020:1,England_200990723_2020:1,Switzerland_TI2045_2020:1,Switzerland_1000477377_2020:2,Denmark_SSI-05_2020:4,Chile_Santiago-2_2020:1,Brazil_SPBR-14_2020:1,Finland_FIN-318_2020:2,Netherlands_Limburg_5_2020:2,Belgium_DBA-03032_2020:2,Switzerland_SZ1417_2020:2,Belgium_GMH-03022_2020:2,Netherlands_Utrecht_14_2020:2,Netherlands_Utrecht_1_2020:2,Finland_FIN03032020C_2020:1,Netherlands_Berlicum_1363564_2020:1,(node_40_condensed_2_leaves:0)70:2,(node_41_condensed_2_leaves:0)71:1,(node_42_condensed_2_leaves:0)72:1,(Switzerland_1000477797_2020:1,Brazil_BA-312_2020:1,node_43_condensed_3_leaves:0)73:1,(Finland_FIN-313_2020:1,Netherlands_Utrecht_15_2020:0)74:2,(Switzerland_GE1422_2020:1,Netherlands_Diemen_1363454_2020:3,node_44_condensed_3_leaves:0)75:1,(Switzerland_BE6651_2020:1,Netherlands_NoordHolland_2_2020:1,node_45_condensed_6_leaves:0)76:1,Belgium_BC-03016_2020:2,(Switzerland_1000477757_2020:2,Brazil_SPBR-12_2020:1,Germany_Baden-Wuerttemberg-1_2020:0)77:1,(node_46_condensed_16_leaves:0)78:1,(Belgium_UMF-03025_2020:0,(node_47_condensed_2_leaves:0)80:1)79:1,node_34_condensed_7_leaves:0)69:3,(Netherlands_NoordHolland_3_2020:2,Netherlands_Flevoland_1_2020:0)81:1,(NetherlandsL_Houten_1363498_2020:1,Italy_UniSR1_2020:1,France_N1620_2020:1,node_35_condensed_3_leaves:0)82:1,(Georgia_Tb-673_2020:2,France_B2330_2020:1,France_PL1643_2020:2,France_HF1988_2020:1,France_B2348_2020:1,(France_B2351_2020:1,France_B2344_2020:1,France_B2349_2020:0)84:1,(France_IDF2256_2020:1,France_HF1871_2020:2)85:1,Netherlands_Haarlem_1363688_2020:1,node_36_condensed_6_leaves:0)83:2,node_25_condensed_15_leaves:0)60:1,node_11_condensed_3_leaves:0)59:3,node_1_condensed_27_leaves:0)1:0; \ No newline at end of file |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_08_mutation_path.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_08_mutation_path.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Sample1 19:G1440A,G2891A 86:A27669G +Sample2 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample3 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample4 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G +Sample5 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_09_final_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_09_final_tree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((Wuhan_HBCDC-HB-06_2020:3,Wuhan_HBCDC-HB-02_2020:2,Wuhan_HBCDC-HB-04_2020:3,Shanghai_SH0075_2020:2,Shanghai_SH0010_2020:2,Tianmen_HBCDC-HB-07_2020:5,Shanghai_SH0041_2020:4,India_1-31_2020:4,Shanghai_SH0009_2020:1,Malaysia_MKAK-CL-2020-5096_2020:2,(France_GE1583_2020:1,Georgia_Tb-390_2020:1,Spain_Valencia6_2020:1,Spain_CastillayLeon201437_2020:1,node_12_condensed_6_leaves:0)3:5,(Sichuan_IVDC-SC-001_2020:1,USA_CA1_2020:1,USA_IL2_2020:2,Vietnam_CM99_2020:2,node_13_condensed_3_leaves:0)4:3,(Shanghai_SH0035_2020:2,Australia_QLD02_2020:2,Australia_QLD03_2020:1,Australia_VIC07_2020:1,(Netherlands_Utrecht_16_2020:1,Netherlands_Utrecht_17_2020:0)6:1,node_14_condensed_6_leaves:0)5:2,(Shandong_LY003_2020:2,Shandong_LY005_2020:2,node_15_condensed_3_leaves:0)7:1,(node_16_condensed_2_leaves:0)8:4,England_02_2020:3,(Chongqing_YC01_2020:2,((USA_CA-CDPH-UC7_2020:0,USA_CA-CDPH-UC9_2020:1)11:3,(node_37_condensed_2_leaves:0)12:2)10:2,Malaysia_MKAK-CL-2020-6430_2020:1,node_17_condensed_3_leaves:0)9:1,(Shanghai_SH0059_2020:3,USA_TX1_2020:4,(Japan_TY-WK-012_2020:1,node_26_condensed_2_leaves:0)14:1,Shanghai_SH0004_2020:1,Germany_BavPat3_2020:1,Shanghai_SH0005_2020:0)13:1,(Yunnan_IVDC-YN-003_2020:0,USA_AZ1_2020:1,Anhui_SZ005_2020:6)15:1,(Beijing_233_2020:1,node_18_condensed_3_leaves:0)16:2,node_2_condensed_10_leaves:0)2:2,Shanghai_SH0007_2020:3,Hangzhou_ZJU-07_2020:5,Wuhan_IPBCAMS-WH-03_2019:1,Wuhan_WH01_2019:2,Wuhan_WIV07_2019:1,Shanghai_SH0093_2020:2,Wuhan_HBCDC-HB-01_2019:1,Wuhan_IPBCAMS-WH-01_2019:3,Wuhan_IVDC-HB-04_2020:2,Wuhan_IVDC-HB-05_2019:2,Wuhan_WIV05_2019:2,Sweden_01_2020:7,Taiwan_2_2020:3,USA_CA2_2020:2,Shanghai_SH0040_2020:2,Singapore_7_2020:2,Australia_VIC02_2020:2,France_IDF0515_2020:3,Hangzhou_ZJU-01_2020:3,Shanghai_SH0037_2020:5,Nepal_61_2020:1,China_WH-09_2020:1,Jiangxi_IVDC-JX-002_2020:1,Zhejiang_WZ-01_2020:1,Japan_KY-V-029_2020:3,Hangzhou_ZJU-03_2020:1,Netherlands_Utrecht_12_2020:2,Singapore_1_2020:1,Taiwan_NTU02_2020:2,England_SHEF-BFD36_2020:3,France_IDF0626_2020:1,Malaysia_MKAK-CL-2020-7554_2020:2,Cambodia_0012_2020:1,(USA_CA-CDPH-UC2_2020:4,USA_CA-CDPH-UC3_2020:1,node_3_condensed_2_leaves:0)17:1,(node_4_condensed_2_leaves:0)18:1,(Germany_NRW-10_2020:1,Germany_NRW-09_2020:1,Poland_PL_P1_2020:1,(Germany_NRW-04_2020:0,Germany_NRW-07_2020:1,(node_27_condensed_3_leaves:0)21:2)20:2,node_5_condensed_5_leaves:0,(Sample1:0,(Sample3:0,Sample2:0,(Sample5:0,Sample4:0)88:1)87:1)86:1)19:2,(Malaysia_MKAK-CL-2020-5045_2020:2,node_6_condensed_3_leaves:0)22:1,(Jiangsu_JS01_2020:2,Shanghai_SH0031_2020:1)23:1,(Australia_NSW02_2020:1,(Hangzhou_ZJU-06_2020:1,(Shanghai_SH0085_2020:4,Shanghai_SH0094_2020:0)26:2)25:1)24:1,(India_1-27_2020:3,Shanghai_SH0011_2020:1,Fujian_13_2020:1,Singapore_11_2020:1,USA_WI1_2020:0)27:1,(Wuhan_HBCDC-HB-05_2020:1,Shandong_IVDC-SD-001_2020:3,England_200960041_2020:2,Australia_NSW05_2020:1,(Georgia_Tb-82_2020:2,Australia_NSW09_2020:3,(Canada_BC_25211_2020:4,Kuwait_KU09_2020:2)30:1,Kuwait_KU18_2020:1,Kuwait_KU12_2020:2,Australia_NSW06_2020:1)29:2,(node_19_condensed_2_leaves:0)31:2,(Taiwan_CGMH-CGU-04_2020:3,node_20_condensed_2_leaves:0)32:3,Kuwait_KU17_2020:1,(Canada_BC_17397_2020:2,Canada_BC_13297_2020:2)33:1,(Australia_QLD09_2020:1,Australia_NSW07_2020:0)34:1,(USA_NY1-PV08001_2020:3,Canada_BC_37_0-2_2020:0,Canada_BC_69243_2020:2,(England_200990002_2020:2,Germany_BavPat2_2020:1)36:2)35:1)28:4,(node_7_condensed_3_leaves:0)37:2,(Jiangsu_JS02_2020:4,Shanghai_SH0008_2020:3,USA_CA5_2020:1)38:1,(Wuhan_WIV02_2019:1,node_8_condensed_2_leaves:0)39:1,(node_9_condensed_2_leaves:0)40:1,(Japan_Hu_DP_Kng_19-027_2020:1,node_10_condensed_3_leaves:0)41:1,(Hangzhou_ZJU-09_2020:0,Australia_VIC01_2020:3)42:1,(USA_MA1_2020:3,(Shanghai_SH0058_2020:4,(node_28_condensed_2_leaves:0)45:1,node_21_condensed_2_leaves:0)44:1)43:1,((France_B2334_2020:1,France_B2340_2020:1)47:2,(Georgia_Tb-468_2020:1,Georgia_Tb-537_2020:1,Georgia_Tb-54_2020:0)48:1,Italy_SPL1_2020:0)46:2,(England_20102000106_2020:2,(England_09c_2020:0,Brazil_ES-225_2020:1,England_20100001406_2020:1,(node_29_condensed_3_leaves:0)51:1)50:2,(Brazil_SPBR-10_2020:1,Switzerland_1000477102_2020:2,Brazil_SPBR-02_2020:1,England_200990006_2020:0,Netherlands_Utrecht_18_2020:2)52:1,England_200960515_2020:1,(node_22_condensed_3_leaves:0)53:1)49:3,(Netherlands_Utrecht_19_2020:3,Netherlands_Limburg_6_2020:2,Netherlands_Naarden_1364774_2020:0,(node_23_condensed_2_leaves:0)55:1,(Netherlands_Oss_1363500_2020:0,Netherlands_Tilburg_1363354_2020:2)56:1)54:1,(Singapore_8_2020:1,(node_24_condensed_3_leaves:0)58:1)57:1,(Shanghai_SH0086_2020:3,(Finland_FIN-25_2020:6,Belgium_DB-03023_2020:4,Denmark_SSI-102_2020:3,Denmark_SSI-02_2020:1,Belgium_BM-03012_2020:3,England_20100022706_2020:2,Denmark_SSI-04_2020:3,Taiwan_NTU03_2020:2,Finland_FIN03032020A_2020:2,Switzerland_GE4984_2020:2,Switzerland_AG0361_2020:2,Finland_FIN-266_2020:1,Luxembourg_Lux1_2020:1,Japan_SMU-0311S3_2020:1,Denmark_SSI-03_2020:1,Netherlands_Gelderland_2_2020:1,Georgia_Tb-273_2020:1,Belgium_SH-03014_2020:1,((node_38_condensed_2_leaves:0)62:2,node_30_condensed_4_leaves:0)61:1,(France_HF2174_2020:2,France_GE1977_2020:3,France_HF1684_2020:0,(node_39_condensed_2_leaves:0)64:1)63:2,Belgium_VAG-03013_2020:4,(Netherlands_Utrecht_1363564_2020:1,node_31_condensed_2_leaves:0)65:4,(England_20099107406_2020:1,Georgia_Tb_2020:0)66:1,(France_BFC2094_2020:1,France_BFC2147_2020:1,node_32_condensed_4_leaves:0)67:1,(Hungary_mbl1_2020:1,node_33_condensed_5_leaves:0)68:1,(Nigeria_Lagos01_2020:1,Netherlands_Delft_1363424_2020:1,Denmark_SSI-01_2020:1,England_200990723_2020:1,Switzerland_TI2045_2020:1,Switzerland_1000477377_2020:2,Denmark_SSI-05_2020:4,Chile_Santiago-2_2020:1,Brazil_SPBR-14_2020:1,Finland_FIN-318_2020:2,Netherlands_Limburg_5_2020:2,Belgium_DBA-03032_2020:2,Switzerland_SZ1417_2020:2,Belgium_GMH-03022_2020:2,Netherlands_Utrecht_14_2020:2,Netherlands_Utrecht_1_2020:2,Finland_FIN03032020C_2020:1,Netherlands_Berlicum_1363564_2020:1,(node_40_condensed_2_leaves:0)70:2,(node_41_condensed_2_leaves:0)71:1,(node_42_condensed_2_leaves:0)72:1,(Switzerland_1000477797_2020:1,Brazil_BA-312_2020:1,node_43_condensed_3_leaves:0)73:1,(Finland_FIN-313_2020:1,Netherlands_Utrecht_15_2020:0)74:2,(Switzerland_GE1422_2020:1,Netherlands_Diemen_1363454_2020:3,node_44_condensed_3_leaves:0)75:1,(Switzerland_BE6651_2020:1,Netherlands_NoordHolland_2_2020:1,node_45_condensed_6_leaves:0)76:1,Belgium_BC-03016_2020:2,(Switzerland_1000477757_2020:2,Brazil_SPBR-12_2020:1,Germany_Baden-Wuerttemberg-1_2020:0)77:1,(node_46_condensed_16_leaves:0)78:1,(Belgium_UMF-03025_2020:0,(node_47_condensed_2_leaves:0)80:1)79:1,node_34_condensed_7_leaves:0)69:3,(Netherlands_NoordHolland_3_2020:2,Netherlands_Flevoland_1_2020:0)81:1,(NetherlandsL_Houten_1363498_2020:1,Italy_UniSR1_2020:1,France_N1620_2020:1,node_35_condensed_3_leaves:0)82:1,(Georgia_Tb-673_2020:2,France_B2330_2020:1,France_PL1643_2020:2,France_HF1988_2020:1,France_B2348_2020:1,(France_B2351_2020:1,France_B2344_2020:1,France_B2349_2020:0)84:1,(France_IDF2256_2020:1,France_HF1871_2020:2)85:1,Netherlands_Haarlem_1363688_2020:1,node_36_condensed_6_leaves:0)83:2,node_25_condensed_15_leaves:0)60:1,node_11_condensed_3_leaves:0)59:3,node_1_condensed_27_leaves:0)1:0; \ No newline at end of file |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_09_mutation_path.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_09_mutation_path.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Sample1 19:G1440A,G2891A 86:A27669G +Sample2 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample3 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample4 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G +Sample5 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_10_final_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_10_final_tree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((Wuhan_HBCDC-HB-06_2020:3,Wuhan_HBCDC-HB-02_2020:2,Wuhan_HBCDC-HB-04_2020:3,Shanghai_SH0075_2020:2,Shanghai_SH0010_2020:2,Tianmen_HBCDC-HB-07_2020:5,Shanghai_SH0041_2020:4,India_1-31_2020:4,Shanghai_SH0009_2020:1,Malaysia_MKAK-CL-2020-5096_2020:2,(France_GE1583_2020:1,Georgia_Tb-390_2020:1,Spain_Valencia6_2020:1,Spain_CastillayLeon201437_2020:1,node_12_condensed_6_leaves:0)3:5,(Sichuan_IVDC-SC-001_2020:1,USA_CA1_2020:1,USA_IL2_2020:2,Vietnam_CM99_2020:2,node_13_condensed_3_leaves:0)4:3,(Shanghai_SH0035_2020:2,Australia_QLD02_2020:2,Australia_QLD03_2020:1,Australia_VIC07_2020:1,(Netherlands_Utrecht_16_2020:1,Netherlands_Utrecht_17_2020:0)6:1,node_14_condensed_6_leaves:0)5:2,(Shandong_LY003_2020:2,Shandong_LY005_2020:2,node_15_condensed_3_leaves:0)7:1,(node_16_condensed_2_leaves:0)8:4,England_02_2020:3,(Chongqing_YC01_2020:2,((USA_CA-CDPH-UC7_2020:0,USA_CA-CDPH-UC9_2020:1)11:3,(node_37_condensed_2_leaves:0)12:2)10:2,Malaysia_MKAK-CL-2020-6430_2020:1,node_17_condensed_3_leaves:0)9:1,(Shanghai_SH0059_2020:3,USA_TX1_2020:4,(Japan_TY-WK-012_2020:1,node_26_condensed_2_leaves:0)14:1,Shanghai_SH0004_2020:1,Germany_BavPat3_2020:1,Shanghai_SH0005_2020:0)13:1,(Yunnan_IVDC-YN-003_2020:0,USA_AZ1_2020:1,Anhui_SZ005_2020:6)15:1,(Beijing_233_2020:1,node_18_condensed_3_leaves:0)16:2,node_2_condensed_10_leaves:0)2:2,Shanghai_SH0007_2020:3,Hangzhou_ZJU-07_2020:5,Wuhan_IPBCAMS-WH-03_2019:1,Wuhan_WH01_2019:2,Wuhan_WIV07_2019:1,Shanghai_SH0093_2020:2,Wuhan_HBCDC-HB-01_2019:1,Wuhan_IPBCAMS-WH-01_2019:3,Wuhan_IVDC-HB-04_2020:2,Wuhan_IVDC-HB-05_2019:2,Wuhan_WIV05_2019:2,Sweden_01_2020:7,Taiwan_2_2020:3,USA_CA2_2020:2,Shanghai_SH0040_2020:2,Singapore_7_2020:2,Australia_VIC02_2020:2,France_IDF0515_2020:3,Hangzhou_ZJU-01_2020:3,Shanghai_SH0037_2020:5,Nepal_61_2020:1,China_WH-09_2020:1,Jiangxi_IVDC-JX-002_2020:1,Zhejiang_WZ-01_2020:1,Japan_KY-V-029_2020:3,Hangzhou_ZJU-03_2020:1,Netherlands_Utrecht_12_2020:2,Singapore_1_2020:1,Taiwan_NTU02_2020:2,England_SHEF-BFD36_2020:3,France_IDF0626_2020:1,Malaysia_MKAK-CL-2020-7554_2020:2,Cambodia_0012_2020:1,(USA_CA-CDPH-UC2_2020:4,USA_CA-CDPH-UC3_2020:1,node_3_condensed_2_leaves:0)17:1,(node_4_condensed_2_leaves:0)18:1,(Germany_NRW-10_2020:1,Germany_NRW-09_2020:1,Poland_PL_P1_2020:1,(Germany_NRW-04_2020:0,Germany_NRW-07_2020:1,(node_27_condensed_3_leaves:0)21:2)20:2,node_5_condensed_5_leaves:0,(Sample1:0,(Sample3:0,(Sample4:0,Sample5:0)86:1,Sample2:0)87:1)88:1)19:2,(Malaysia_MKAK-CL-2020-5045_2020:2,node_6_condensed_3_leaves:0)22:1,(Jiangsu_JS01_2020:2,Shanghai_SH0031_2020:1)23:1,(Australia_NSW02_2020:1,(Hangzhou_ZJU-06_2020:1,(Shanghai_SH0085_2020:4,Shanghai_SH0094_2020:0)26:2)25:1)24:1,(India_1-27_2020:3,Shanghai_SH0011_2020:1,Fujian_13_2020:1,Singapore_11_2020:1,USA_WI1_2020:0)27:1,(Wuhan_HBCDC-HB-05_2020:1,Shandong_IVDC-SD-001_2020:3,England_200960041_2020:2,Australia_NSW05_2020:1,(Georgia_Tb-82_2020:2,Australia_NSW09_2020:3,(Canada_BC_25211_2020:4,Kuwait_KU09_2020:2)30:1,Kuwait_KU18_2020:1,Kuwait_KU12_2020:2,Australia_NSW06_2020:1)29:2,(node_19_condensed_2_leaves:0)31:2,(Taiwan_CGMH-CGU-04_2020:3,node_20_condensed_2_leaves:0)32:3,Kuwait_KU17_2020:1,(Canada_BC_17397_2020:2,Canada_BC_13297_2020:2)33:1,(Australia_QLD09_2020:1,Australia_NSW07_2020:0)34:1,(USA_NY1-PV08001_2020:3,Canada_BC_37_0-2_2020:0,Canada_BC_69243_2020:2,(England_200990002_2020:2,Germany_BavPat2_2020:1)36:2)35:1)28:4,(node_7_condensed_3_leaves:0)37:2,(Jiangsu_JS02_2020:4,Shanghai_SH0008_2020:3,USA_CA5_2020:1)38:1,(Wuhan_WIV02_2019:1,node_8_condensed_2_leaves:0)39:1,(node_9_condensed_2_leaves:0)40:1,(Japan_Hu_DP_Kng_19-027_2020:1,node_10_condensed_3_leaves:0)41:1,(Hangzhou_ZJU-09_2020:0,Australia_VIC01_2020:3)42:1,(USA_MA1_2020:3,(Shanghai_SH0058_2020:4,(node_28_condensed_2_leaves:0)45:1,node_21_condensed_2_leaves:0)44:1)43:1,((France_B2334_2020:1,France_B2340_2020:1)47:2,(Georgia_Tb-468_2020:1,Georgia_Tb-537_2020:1,Georgia_Tb-54_2020:0)48:1,Italy_SPL1_2020:0)46:2,(England_20102000106_2020:2,(England_09c_2020:0,Brazil_ES-225_2020:1,England_20100001406_2020:1,(node_29_condensed_3_leaves:0)51:1)50:2,(Brazil_SPBR-10_2020:1,Switzerland_1000477102_2020:2,Brazil_SPBR-02_2020:1,England_200990006_2020:0,Netherlands_Utrecht_18_2020:2)52:1,England_200960515_2020:1,(node_22_condensed_3_leaves:0)53:1)49:3,(Netherlands_Utrecht_19_2020:3,Netherlands_Limburg_6_2020:2,Netherlands_Naarden_1364774_2020:0,(node_23_condensed_2_leaves:0)55:1,(Netherlands_Oss_1363500_2020:0,Netherlands_Tilburg_1363354_2020:2)56:1)54:1,(Singapore_8_2020:1,(node_24_condensed_3_leaves:0)58:1)57:1,(Shanghai_SH0086_2020:3,(Finland_FIN-25_2020:6,Belgium_DB-03023_2020:4,Denmark_SSI-102_2020:3,Denmark_SSI-02_2020:1,Belgium_BM-03012_2020:3,England_20100022706_2020:2,Denmark_SSI-04_2020:3,Taiwan_NTU03_2020:2,Finland_FIN03032020A_2020:2,Switzerland_GE4984_2020:2,Switzerland_AG0361_2020:2,Finland_FIN-266_2020:1,Luxembourg_Lux1_2020:1,Japan_SMU-0311S3_2020:1,Denmark_SSI-03_2020:1,Netherlands_Gelderland_2_2020:1,Georgia_Tb-273_2020:1,Belgium_SH-03014_2020:1,((node_38_condensed_2_leaves:0)62:2,node_30_condensed_4_leaves:0)61:1,(France_HF2174_2020:2,France_GE1977_2020:3,France_HF1684_2020:0,(node_39_condensed_2_leaves:0)64:1)63:2,Belgium_VAG-03013_2020:4,(Netherlands_Utrecht_1363564_2020:1,node_31_condensed_2_leaves:0)65:4,(England_20099107406_2020:1,Georgia_Tb_2020:0)66:1,(France_BFC2094_2020:1,France_BFC2147_2020:1,node_32_condensed_4_leaves:0)67:1,(Hungary_mbl1_2020:1,node_33_condensed_5_leaves:0)68:1,(Nigeria_Lagos01_2020:1,Netherlands_Delft_1363424_2020:1,Denmark_SSI-01_2020:1,England_200990723_2020:1,Switzerland_TI2045_2020:1,Switzerland_1000477377_2020:2,Denmark_SSI-05_2020:4,Chile_Santiago-2_2020:1,Brazil_SPBR-14_2020:1,Finland_FIN-318_2020:2,Netherlands_Limburg_5_2020:2,Belgium_DBA-03032_2020:2,Switzerland_SZ1417_2020:2,Belgium_GMH-03022_2020:2,Netherlands_Utrecht_14_2020:2,Netherlands_Utrecht_1_2020:2,Finland_FIN03032020C_2020:1,Netherlands_Berlicum_1363564_2020:1,(node_40_condensed_2_leaves:0)70:2,(node_41_condensed_2_leaves:0)71:1,(node_42_condensed_2_leaves:0)72:1,(Switzerland_1000477797_2020:1,Brazil_BA-312_2020:1,node_43_condensed_3_leaves:0)73:1,(Finland_FIN-313_2020:1,Netherlands_Utrecht_15_2020:0)74:2,(Switzerland_GE1422_2020:1,Netherlands_Diemen_1363454_2020:3,node_44_condensed_3_leaves:0)75:1,(Switzerland_BE6651_2020:1,Netherlands_NoordHolland_2_2020:1,node_45_condensed_6_leaves:0)76:1,Belgium_BC-03016_2020:2,(Switzerland_1000477757_2020:2,Brazil_SPBR-12_2020:1,Germany_Baden-Wuerttemberg-1_2020:0)77:1,(node_46_condensed_16_leaves:0)78:1,(Belgium_UMF-03025_2020:0,(node_47_condensed_2_leaves:0)80:1)79:1,node_34_condensed_7_leaves:0)69:3,(Netherlands_NoordHolland_3_2020:2,Netherlands_Flevoland_1_2020:0)81:1,(NetherlandsL_Houten_1363498_2020:1,Italy_UniSR1_2020:1,France_N1620_2020:1,node_35_condensed_3_leaves:0)82:1,(Georgia_Tb-673_2020:2,France_B2330_2020:1,France_PL1643_2020:2,France_HF1988_2020:1,France_B2348_2020:1,(France_B2351_2020:1,France_B2344_2020:1,France_B2349_2020:0)84:1,(France_IDF2256_2020:1,France_HF1871_2020:2)85:1,Netherlands_Haarlem_1363688_2020:1,node_36_condensed_6_leaves:0)83:2,node_25_condensed_15_leaves:0)60:1,node_11_condensed_3_leaves:0)59:3,node_1_condensed_27_leaves:0)1:0; \ No newline at end of file |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_10_mutation_path.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_10_mutation_path.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Sample1 19:G1440A,G2891A 88:A27669G +Sample2 19:G1440A,G2891A 88:A27669G 87:G14948A +Sample3 19:G1440A,G2891A 88:A27669G 87:G14948A +Sample4 19:G1440A,G2891A 88:A27669G 87:G14948A 86:A23013G +Sample5 19:G1440A,G2891A 88:A27669G 87:G14948A 86:A23013G |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_11_final_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_11_final_tree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((Wuhan_HBCDC-HB-06_2020:3,Wuhan_HBCDC-HB-02_2020:2,Wuhan_HBCDC-HB-04_2020:3,Shanghai_SH0075_2020:2,Shanghai_SH0010_2020:2,Tianmen_HBCDC-HB-07_2020:5,Shanghai_SH0041_2020:4,India_1-31_2020:4,Shanghai_SH0009_2020:1,Malaysia_MKAK-CL-2020-5096_2020:2,(France_GE1583_2020:1,Georgia_Tb-390_2020:1,Spain_Valencia6_2020:1,Spain_CastillayLeon201437_2020:1,node_12_condensed_6_leaves:0)3:5,(Sichuan_IVDC-SC-001_2020:1,USA_CA1_2020:1,USA_IL2_2020:2,Vietnam_CM99_2020:2,node_13_condensed_3_leaves:0)4:3,(Shanghai_SH0035_2020:2,Australia_QLD02_2020:2,Australia_QLD03_2020:1,Australia_VIC07_2020:1,(Netherlands_Utrecht_16_2020:1,Netherlands_Utrecht_17_2020:0)6:1,node_14_condensed_6_leaves:0)5:2,(Shandong_LY003_2020:2,Shandong_LY005_2020:2,node_15_condensed_3_leaves:0)7:1,(node_16_condensed_2_leaves:0)8:4,England_02_2020:3,(Chongqing_YC01_2020:2,((USA_CA-CDPH-UC7_2020:0,USA_CA-CDPH-UC9_2020:1)11:3,(node_37_condensed_2_leaves:0)12:2)10:2,Malaysia_MKAK-CL-2020-6430_2020:1,node_17_condensed_3_leaves:0)9:1,(Shanghai_SH0059_2020:3,USA_TX1_2020:4,(Japan_TY-WK-012_2020:1,node_26_condensed_2_leaves:0)14:1,Shanghai_SH0004_2020:1,Germany_BavPat3_2020:1,Shanghai_SH0005_2020:0)13:1,(Yunnan_IVDC-YN-003_2020:0,USA_AZ1_2020:1,Anhui_SZ005_2020:6)15:1,(Beijing_233_2020:1,node_18_condensed_3_leaves:0)16:2,node_2_condensed_10_leaves:0)2:2,Shanghai_SH0007_2020:3,Hangzhou_ZJU-07_2020:5,Wuhan_IPBCAMS-WH-03_2019:1,Wuhan_WH01_2019:2,Wuhan_WIV07_2019:1,Shanghai_SH0093_2020:2,Wuhan_HBCDC-HB-01_2019:1,Wuhan_IPBCAMS-WH-01_2019:3,Wuhan_IVDC-HB-04_2020:2,Wuhan_IVDC-HB-05_2019:2,Wuhan_WIV05_2019:2,Sweden_01_2020:7,Taiwan_2_2020:3,USA_CA2_2020:2,Shanghai_SH0040_2020:2,Singapore_7_2020:2,Australia_VIC02_2020:2,France_IDF0515_2020:3,Hangzhou_ZJU-01_2020:3,Shanghai_SH0037_2020:5,Nepal_61_2020:1,China_WH-09_2020:1,Jiangxi_IVDC-JX-002_2020:1,Zhejiang_WZ-01_2020:1,Japan_KY-V-029_2020:3,Hangzhou_ZJU-03_2020:1,Netherlands_Utrecht_12_2020:2,Singapore_1_2020:1,Taiwan_NTU02_2020:2,England_SHEF-BFD36_2020:3,France_IDF0626_2020:1,Malaysia_MKAK-CL-2020-7554_2020:2,Cambodia_0012_2020:1,(USA_CA-CDPH-UC2_2020:4,USA_CA-CDPH-UC3_2020:1,node_3_condensed_2_leaves:0)17:1,(node_4_condensed_2_leaves:0)18:1,(Germany_NRW-10_2020:1,Germany_NRW-09_2020:1,Poland_PL_P1_2020:1,(Germany_NRW-04_2020:0,Germany_NRW-07_2020:1,(node_27_condensed_3_leaves:0)21:2)20:2,node_5_condensed_5_leaves:0,(Sample1:0,(Sample3:0,(Sample4:0,Sample5:0)86:1,Sample2:0)87:1)88:1)19:2,(Malaysia_MKAK-CL-2020-5045_2020:2,node_6_condensed_3_leaves:0)22:1,(Jiangsu_JS01_2020:2,Shanghai_SH0031_2020:1)23:1,(Australia_NSW02_2020:1,(Hangzhou_ZJU-06_2020:1,(Shanghai_SH0085_2020:4,Shanghai_SH0094_2020:0)26:2)25:1)24:1,(India_1-27_2020:3,Shanghai_SH0011_2020:1,Fujian_13_2020:1,Singapore_11_2020:1,USA_WI1_2020:0)27:1,(Wuhan_HBCDC-HB-05_2020:1,Shandong_IVDC-SD-001_2020:3,England_200960041_2020:2,Australia_NSW05_2020:1,(Georgia_Tb-82_2020:2,Australia_NSW09_2020:3,(Canada_BC_25211_2020:4,Kuwait_KU09_2020:2)30:1,Kuwait_KU18_2020:1,Kuwait_KU12_2020:2,Australia_NSW06_2020:1)29:2,(node_19_condensed_2_leaves:0)31:2,(Taiwan_CGMH-CGU-04_2020:3,node_20_condensed_2_leaves:0)32:3,Kuwait_KU17_2020:1,(Canada_BC_17397_2020:2,Canada_BC_13297_2020:2)33:1,(Australia_QLD09_2020:1,Australia_NSW07_2020:0)34:1,(USA_NY1-PV08001_2020:3,Canada_BC_37_0-2_2020:0,Canada_BC_69243_2020:2,(England_200990002_2020:2,Germany_BavPat2_2020:1)36:2)35:1)28:4,(node_7_condensed_3_leaves:0)37:2,(Jiangsu_JS02_2020:4,Shanghai_SH0008_2020:3,USA_CA5_2020:1)38:1,(Wuhan_WIV02_2019:1,node_8_condensed_2_leaves:0)39:1,(node_9_condensed_2_leaves:0)40:1,(Japan_Hu_DP_Kng_19-027_2020:1,node_10_condensed_3_leaves:0)41:1,(Hangzhou_ZJU-09_2020:0,Australia_VIC01_2020:3)42:1,(USA_MA1_2020:3,(Shanghai_SH0058_2020:4,(node_28_condensed_2_leaves:0)45:1,node_21_condensed_2_leaves:0)44:1)43:1,((France_B2334_2020:1,France_B2340_2020:1)47:2,(Georgia_Tb-468_2020:1,Georgia_Tb-537_2020:1,Georgia_Tb-54_2020:0)48:1,Italy_SPL1_2020:0)46:2,(England_20102000106_2020:2,(England_09c_2020:0,Brazil_ES-225_2020:1,England_20100001406_2020:1,(node_29_condensed_3_leaves:0)51:1)50:2,(Brazil_SPBR-10_2020:1,Switzerland_1000477102_2020:2,Brazil_SPBR-02_2020:1,England_200990006_2020:0,Netherlands_Utrecht_18_2020:2)52:1,England_200960515_2020:1,(node_22_condensed_3_leaves:0)53:1)49:3,(Netherlands_Utrecht_19_2020:3,Netherlands_Limburg_6_2020:2,Netherlands_Naarden_1364774_2020:0,(node_23_condensed_2_leaves:0)55:1,(Netherlands_Oss_1363500_2020:0,Netherlands_Tilburg_1363354_2020:2)56:1)54:1,(Singapore_8_2020:1,(node_24_condensed_3_leaves:0)58:1)57:1,(Shanghai_SH0086_2020:3,(Finland_FIN-25_2020:6,Belgium_DB-03023_2020:4,Denmark_SSI-102_2020:3,Denmark_SSI-02_2020:1,Belgium_BM-03012_2020:3,England_20100022706_2020:2,Denmark_SSI-04_2020:3,Taiwan_NTU03_2020:2,Finland_FIN03032020A_2020:2,Switzerland_GE4984_2020:2,Switzerland_AG0361_2020:2,Finland_FIN-266_2020:1,Luxembourg_Lux1_2020:1,Japan_SMU-0311S3_2020:1,Denmark_SSI-03_2020:1,Netherlands_Gelderland_2_2020:1,Georgia_Tb-273_2020:1,Belgium_SH-03014_2020:1,((node_38_condensed_2_leaves:0)62:2,node_30_condensed_4_leaves:0)61:1,(France_HF2174_2020:2,France_GE1977_2020:3,France_HF1684_2020:0,(node_39_condensed_2_leaves:0)64:1)63:2,Belgium_VAG-03013_2020:4,(Netherlands_Utrecht_1363564_2020:1,node_31_condensed_2_leaves:0)65:4,(England_20099107406_2020:1,Georgia_Tb_2020:0)66:1,(France_BFC2094_2020:1,France_BFC2147_2020:1,node_32_condensed_4_leaves:0)67:1,(Hungary_mbl1_2020:1,node_33_condensed_5_leaves:0)68:1,(Nigeria_Lagos01_2020:1,Netherlands_Delft_1363424_2020:1,Denmark_SSI-01_2020:1,England_200990723_2020:1,Switzerland_TI2045_2020:1,Switzerland_1000477377_2020:2,Denmark_SSI-05_2020:4,Chile_Santiago-2_2020:1,Brazil_SPBR-14_2020:1,Finland_FIN-318_2020:2,Netherlands_Limburg_5_2020:2,Belgium_DBA-03032_2020:2,Switzerland_SZ1417_2020:2,Belgium_GMH-03022_2020:2,Netherlands_Utrecht_14_2020:2,Netherlands_Utrecht_1_2020:2,Finland_FIN03032020C_2020:1,Netherlands_Berlicum_1363564_2020:1,(node_40_condensed_2_leaves:0)70:2,(node_41_condensed_2_leaves:0)71:1,(node_42_condensed_2_leaves:0)72:1,(Switzerland_1000477797_2020:1,Brazil_BA-312_2020:1,node_43_condensed_3_leaves:0)73:1,(Finland_FIN-313_2020:1,Netherlands_Utrecht_15_2020:0)74:2,(Switzerland_GE1422_2020:1,Netherlands_Diemen_1363454_2020:3,node_44_condensed_3_leaves:0)75:1,(Switzerland_BE6651_2020:1,Netherlands_NoordHolland_2_2020:1,node_45_condensed_6_leaves:0)76:1,Belgium_BC-03016_2020:2,(Switzerland_1000477757_2020:2,Brazil_SPBR-12_2020:1,Germany_Baden-Wuerttemberg-1_2020:0)77:1,(node_46_condensed_16_leaves:0)78:1,(Belgium_UMF-03025_2020:0,(node_47_condensed_2_leaves:0)80:1)79:1,node_34_condensed_7_leaves:0)69:3,(Netherlands_NoordHolland_3_2020:2,Netherlands_Flevoland_1_2020:0)81:1,(NetherlandsL_Houten_1363498_2020:1,Italy_UniSR1_2020:1,France_N1620_2020:1,node_35_condensed_3_leaves:0)82:1,(Georgia_Tb-673_2020:2,France_B2330_2020:1,France_PL1643_2020:2,France_HF1988_2020:1,France_B2348_2020:1,(France_B2351_2020:1,France_B2344_2020:1,France_B2349_2020:0)84:1,(France_IDF2256_2020:1,France_HF1871_2020:2)85:1,Netherlands_Haarlem_1363688_2020:1,node_36_condensed_6_leaves:0)83:2,node_25_condensed_15_leaves:0)60:1,node_11_condensed_3_leaves:0)59:3,node_1_condensed_27_leaves:0)1:0; \ No newline at end of file |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_11_mutation_path.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_11_mutation_path.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Sample1 19:G1440A,G2891A 88:A27669G +Sample2 19:G1440A,G2891A 88:A27669G 87:G14948A +Sample3 19:G1440A,G2891A 88:A27669G 87:G14948A +Sample4 19:G1440A,G2891A 88:A27669G 87:G14948A 86:A23013G +Sample5 19:G1440A,G2891A 88:A27669G 87:G14948A 86:A23013G |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_12_final_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_12_final_tree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((Wuhan_HBCDC-HB-06_2020,Wuhan_HBCDC-HB-02_2020,Wuhan_HBCDC-HB-04_2020,Shanghai_SH0075_2020,Shanghai_SH0010_2020,Tianmen_HBCDC-HB-07_2020,Shanghai_SH0041_2020,India_1-31_2020,Shanghai_SH0009_2020,Malaysia_MKAK-CL-2020-5096_2020,(France_GE1583_2020,Georgia_Tb-390_2020,Spain_Valencia6_2020,Spain_CastillayLeon201437_2020,node_12_condensed_6_leaves)3,(Sichuan_IVDC-SC-001_2020,USA_CA1_2020,USA_IL2_2020,Vietnam_CM99_2020,node_13_condensed_3_leaves)4,(Shanghai_SH0035_2020,Australia_QLD02_2020,Australia_QLD03_2020,Australia_VIC07_2020,(Netherlands_Utrecht_16_2020,Netherlands_Utrecht_17_2020)6,node_14_condensed_6_leaves)5,(Shandong_LY003_2020,Shandong_LY005_2020,node_15_condensed_3_leaves)7,(node_16_condensed_2_leaves)8,England_02_2020,(Chongqing_YC01_2020,((USA_CA-CDPH-UC7_2020,USA_CA-CDPH-UC9_2020)11,(node_37_condensed_2_leaves)12)10,Malaysia_MKAK-CL-2020-6430_2020,node_17_condensed_3_leaves)9,(Shanghai_SH0059_2020,USA_TX1_2020,(Japan_TY-WK-012_2020,node_26_condensed_2_leaves)14,Shanghai_SH0004_2020,Germany_BavPat3_2020,Shanghai_SH0005_2020)13,(Yunnan_IVDC-YN-003_2020,USA_AZ1_2020,Anhui_SZ005_2020)15,(Beijing_233_2020,node_18_condensed_3_leaves)16,node_2_condensed_10_leaves)2,Shanghai_SH0007_2020,Hangzhou_ZJU-07_2020,Wuhan_IPBCAMS-WH-03_2019,Wuhan_WH01_2019,Wuhan_WIV07_2019,Shanghai_SH0093_2020,Wuhan_HBCDC-HB-01_2019,Wuhan_IPBCAMS-WH-01_2019,Wuhan_IVDC-HB-04_2020,Wuhan_IVDC-HB-05_2019,Wuhan_WIV05_2019,Sweden_01_2020,Taiwan_2_2020,USA_CA2_2020,Shanghai_SH0040_2020,Singapore_7_2020,Australia_VIC02_2020,France_IDF0515_2020,Hangzhou_ZJU-01_2020,Shanghai_SH0037_2020,Nepal_61_2020,China_WH-09_2020,Jiangxi_IVDC-JX-002_2020,Zhejiang_WZ-01_2020,Japan_KY-V-029_2020,Hangzhou_ZJU-03_2020,Netherlands_Utrecht_12_2020,Singapore_1_2020,Taiwan_NTU02_2020,England_SHEF-BFD36_2020,France_IDF0626_2020,Malaysia_MKAK-CL-2020-7554_2020,Cambodia_0012_2020,(USA_CA-CDPH-UC2_2020,USA_CA-CDPH-UC3_2020,node_3_condensed_2_leaves)17,(node_4_condensed_2_leaves)18,(Germany_NRW-10_2020,Germany_NRW-09_2020,Poland_PL_P1_2020,(Germany_NRW-04_2020,Germany_NRW-07_2020,(node_27_condensed_3_leaves)21)20,node_5_condensed_5_leaves,(Sample1,(Sample3,Sample2,(Sample5,Sample4)88)87)86)19,(Malaysia_MKAK-CL-2020-5045_2020,node_6_condensed_3_leaves)22,(Jiangsu_JS01_2020,Shanghai_SH0031_2020)23,(Australia_NSW02_2020,(Hangzhou_ZJU-06_2020,(Shanghai_SH0085_2020,Shanghai_SH0094_2020)26)25)24,(India_1-27_2020,Shanghai_SH0011_2020,Fujian_13_2020,Singapore_11_2020,USA_WI1_2020)27,(Wuhan_HBCDC-HB-05_2020,Shandong_IVDC-SD-001_2020,England_200960041_2020,Australia_NSW05_2020,(Georgia_Tb-82_2020,Australia_NSW09_2020,(Canada_BC_25211_2020,Kuwait_KU09_2020)30,Kuwait_KU18_2020,Kuwait_KU12_2020,Australia_NSW06_2020)29,(node_19_condensed_2_leaves)31,(Taiwan_CGMH-CGU-04_2020,node_20_condensed_2_leaves)32,Kuwait_KU17_2020,(Canada_BC_17397_2020,Canada_BC_13297_2020)33,(Australia_QLD09_2020,Australia_NSW07_2020)34,(USA_NY1-PV08001_2020,Canada_BC_37_0-2_2020,Canada_BC_69243_2020,(England_200990002_2020,Germany_BavPat2_2020)36)35)28,(node_7_condensed_3_leaves)37,(Jiangsu_JS02_2020,Shanghai_SH0008_2020,USA_CA5_2020)38,(Wuhan_WIV02_2019,node_8_condensed_2_leaves)39,(node_9_condensed_2_leaves)40,(Japan_Hu_DP_Kng_19-027_2020,node_10_condensed_3_leaves)41,(Hangzhou_ZJU-09_2020,Australia_VIC01_2020)42,(USA_MA1_2020,(Shanghai_SH0058_2020,(node_28_condensed_2_leaves)45,node_21_condensed_2_leaves)44)43,((France_B2334_2020,France_B2340_2020)47,(Georgia_Tb-468_2020,Georgia_Tb-537_2020,Georgia_Tb-54_2020)48,Italy_SPL1_2020)46,(England_20102000106_2020,(England_09c_2020,Brazil_ES-225_2020,England_20100001406_2020,(node_29_condensed_3_leaves)51)50,(Brazil_SPBR-10_2020,Switzerland_1000477102_2020,Brazil_SPBR-02_2020,England_200990006_2020,Netherlands_Utrecht_18_2020)52,England_200960515_2020,(node_22_condensed_3_leaves)53)49,(Netherlands_Utrecht_19_2020,Netherlands_Limburg_6_2020,Netherlands_Naarden_1364774_2020,(node_23_condensed_2_leaves)55,(Netherlands_Oss_1363500_2020,Netherlands_Tilburg_1363354_2020)56)54,(Singapore_8_2020,(node_24_condensed_3_leaves)58)57,(Shanghai_SH0086_2020,(Finland_FIN-25_2020,Belgium_DB-03023_2020,Denmark_SSI-102_2020,Denmark_SSI-02_2020,Belgium_BM-03012_2020,England_20100022706_2020,Denmark_SSI-04_2020,Taiwan_NTU03_2020,Finland_FIN03032020A_2020,Switzerland_GE4984_2020,Switzerland_AG0361_2020,Finland_FIN-266_2020,Luxembourg_Lux1_2020,Japan_SMU-0311S3_2020,Denmark_SSI-03_2020,Netherlands_Gelderland_2_2020,Georgia_Tb-273_2020,Belgium_SH-03014_2020,((node_38_condensed_2_leaves)62,node_30_condensed_4_leaves)61,(France_HF2174_2020,France_GE1977_2020,France_HF1684_2020,(node_39_condensed_2_leaves)64)63,Belgium_VAG-03013_2020,(Netherlands_Utrecht_1363564_2020,node_31_condensed_2_leaves)65,(England_20099107406_2020,Georgia_Tb_2020)66,(France_BFC2094_2020,France_BFC2147_2020,node_32_condensed_4_leaves)67,(Hungary_mbl1_2020,node_33_condensed_5_leaves)68,(Nigeria_Lagos01_2020,Netherlands_Delft_1363424_2020,Denmark_SSI-01_2020,England_200990723_2020,Switzerland_TI2045_2020,Switzerland_1000477377_2020,Denmark_SSI-05_2020,Chile_Santiago-2_2020,Brazil_SPBR-14_2020,Finland_FIN-318_2020,Netherlands_Limburg_5_2020,Belgium_DBA-03032_2020,Switzerland_SZ1417_2020,Belgium_GMH-03022_2020,Netherlands_Utrecht_14_2020,Netherlands_Utrecht_1_2020,Finland_FIN03032020C_2020,Netherlands_Berlicum_1363564_2020,(node_40_condensed_2_leaves)70,(node_41_condensed_2_leaves)71,(node_42_condensed_2_leaves)72,(Switzerland_1000477797_2020,Brazil_BA-312_2020,node_43_condensed_3_leaves)73,(Finland_FIN-313_2020,Netherlands_Utrecht_15_2020)74,(Switzerland_GE1422_2020,Netherlands_Diemen_1363454_2020,node_44_condensed_3_leaves)75,(Switzerland_BE6651_2020,Netherlands_NoordHolland_2_2020,node_45_condensed_6_leaves)76,Belgium_BC-03016_2020,(Switzerland_1000477757_2020,Brazil_SPBR-12_2020,Germany_Baden-Wuerttemberg-1_2020)77,(node_46_condensed_16_leaves)78,(Belgium_UMF-03025_2020,(node_47_condensed_2_leaves)80)79,node_34_condensed_7_leaves)69,(Netherlands_NoordHolland_3_2020,Netherlands_Flevoland_1_2020)81,(NetherlandsL_Houten_1363498_2020,Italy_UniSR1_2020,France_N1620_2020,node_35_condensed_3_leaves)82,(Georgia_Tb-673_2020,France_B2330_2020,France_PL1643_2020,France_HF1988_2020,France_B2348_2020,(France_B2351_2020,France_B2344_2020,France_B2349_2020)84,(France_IDF2256_2020,France_HF1871_2020)85,Netherlands_Haarlem_1363688_2020,node_36_condensed_6_leaves)83,node_25_condensed_15_leaves)60,node_11_condensed_3_leaves)59,node_1_condensed_27_leaves)1; \ No newline at end of file |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_12_mutation_path.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_12_mutation_path.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Sample1 19:G1440A,G2891A 86:A27669G +Sample2 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample3 19:G1440A,G2891A 86:A27669G 87:G14948A +Sample4 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G +Sample5 19:G1440A,G2891A 86:A27669G 87:G14948A 88:A23013G |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_13_path_clades.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_13_path_clades.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,90 @@\n+clade\troot_id\tfrom_tree_root\n+20A\t28\tC241T,C3037T,C14408T,A23403G\n+B.1.108\t28\tC241T,C3037T,C14408T,A23403G\n+B.1.350\t53\tC241T,C3037T,C14408T,A23403G > G25563T\n+20C\t61\tC241T,C3037T,C14408T,A23403G > G25563T > C1059T\n+B.1.371\t61\tC241T,C3037T,C14408T,A23403G > G25563T > C1059T\n+B.1.440\t212\tC241T,C3037T,C14408T,A23403G > G25563T > C18877T,C26735T\n+B.1.221\t268\tC241T,C3037T,C14408T,A23403G > > C3602T,C6941T,C15324T,C21855T,A25505G,G25906C,G25996T,C28651T,C28869T\n+B.1.505\t99\tC241T,C3037T,C14408T,A23403G > G25563T > C1059T > C66A,C4455T,C7768T,A8773G,C11916T,C17304T,C18998T,T24805C,C26270T,G29540A\n+B.1.465\t216\tC241T,C3037T,C14408T,A23403G > G25563T > C18877T,C26735T > T241C,A8821G,C15752T,G24197T,T26066C\n+B.1.182\t318\tC241T,C3037T,C14408T,A23403G > > > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C\n+B.1.221.1\t269\tC241T,C3037T,C14408T,A23403G > > C3602T,C6941T,C15324T,C21855T,A25505G,G25906C,G25996T,C28651T,C28869T > G4442T,C6525T,A16044T\n+B.1.221.2\t271\tC241T,C3037T,C14408T,A23403G > > C3602T,C6941T,C15324T,C21855T,A25505G,G25906C,G25996T,C28651T,C28869T > G4504T,T8983G,G11761T,T12655C,C26461T,A28133T\n+20G\t109\tC241T,C3037T,C14408T,A23403G > G25563T > C1059T > > C10319T,A18424G,C21304T,G25907T,C27964T,C28472T,C28869T\n+B.1.2\t109\tC241T,C3037T,C14408T,A23403G > G25563T > C1059T > > C10319T,A18424G,C21304T,G25907T,C27964T,C28472T,C28869T\n+B.1.523\t217\tC241T,C3037T,C14408T,A23403G > G25563T > C18877T,C26735T > > G1659T,C3884T,C20199T,C26139T,T27634C,G28975T\n+20E.EU1\t361\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T\n+B.1.177.14\t361\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T\n+B.1.258\t319\tC241T,C3037T,C14408T,A23403G > > > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C > C27800A\n+B.1.427\t136\tC241T,C3037T,C14408T,A23403G > G25563T > C1059T > > G17014T,G21600T,G22018T,T22917G,C26681T,A28272T,C28887T,C29362T > G9738C,G13713A,C16394T\n+B.1.429\t138\tC241T,C3037T,C14408T,A23403G > G25563T > C1059T > > G17014T,G21600T,G22018T,T22917G,C26681T,A28272T,C28887T,C29362T > C2395T,T2597C,C8947T,C12100T,A12878G,T24349C,G27890T\n+B.1.36\t223\tC241T,C3037T,C14408T,A23403G > G25563T > C18877T,C26735T > > > C22444T,C28854T\n+B.1.160\t238\tC241T,C3037T,C14408T,A23403G > G25563T > C18877T,C26735T > > > C4543T,G9526T,C11497T,G15766T,A16889G,G17019T,G22992A,C25710T,T26876C,G28975C,G29399A\n+20B\t427\tC241T,C3037T,C14408T,A23403G > > > > > G28881A,G28882A,G28883C\n+B.1.1.119\t427\tC241T,C3037T,C14408T,A23403G > > > > > G28881A,G28882A,G28883C\n+B.1.1.77\t655\tC241T,C3037T,C14408T,A23403G > > > > > T19839C,G28881A,G28882A,G28883C\n+B.1.177.11\t365\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > T4195A,C10977T,G25049T,G25062T,C26151T,C28657T,C29366T\n+B.1.258.16\t321\tC241T,C3037T,C14408T,A23403G > > > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C > C27800A > C4893T,C7844T,T24925C,C27920T,C29762T\n+B.1.258.2\t336\tC241T,C3037T,C14408T,A23403G > > > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C > G1464A,A10978T,T20799C > G5572T,G28375T\n+B.1.258.3\t338\tC241T,C3037T,C14408T,A23403G > > > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C > G1464A,A10978T,T20799C > G18803T\n+B.1.1.4\t429\tC241T,C3037T,C14408T,A23403G > > > > > G28881A,G28882A,G28883C > T19839C\n+B.1.177\t366\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T\n+G.1\t337\tC241T,C3037T,C14408T,A23403G > > > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C > G1464A,A10978T,T20799C > G5572T,G28375T > G2072A,C27294T\n+B.1.36.1\t225\tC241T,C3037T,C14408T,A23403G > G25563T > C18877T,C26735T > > > C22444T,C28854T > T1947C > G2659T,G5008T,G19549T,G22918T,C25349A,G25947C,G26062T\n+20A.EU2\t240\tC241T,C3037T,C14408T,A23403G > G25563T > C18877T,C26735T > > > C4543T,G9526T,C11497T,G15766T,A16889G,G17019T,G22992A,C25710T,T26876C,G28975C,G29399A > G13993T > G5629T\n+B.1.316\t438\tC241T,C3037T,C14408T,A23403G > > > > '..b'10507T,C11152T,C11824T,A18840G,G23309C,G26918T,G27589A,G28436T\n+B.1.177.21\t368\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T > > > G204T > T16242A\n+B.1.177.22\t369\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T > > > G204T > C21614T\n+B.1.1.198\t563\tC241T,C3037T,C14408T,A23403G > > > > > G28881A,G28882A,G28883C > > > > > > T505C,G872T,C3261T,T7783C,A15984T,C20946T,C22075T,G25552T,C27945T,G28221T,C29750T\n+B.1.177.15\t393\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > > > > > > C5170T,C10078T,G11132T,G11417T,G22051T,G29179T\n+B.1.177.19\t387\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > > > > > G23311C > T29185A\n+B.1.177.25\t380\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T > > > > > A1866G,A6889C,C12923T,C18029T,C19269T,A27137G\n+B.1.146\t573\tC241T,C3037T,C14408T,A23403G > > > > > G28881A,G28882A,G28883C > > > > > > > C7843T,G15438T,C25207T,G26918T,C28453T,T29464C\n+B.1.177.10\t391\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > > > > > > G22346T > G28321A\n+B.1.177.9\t392\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > > > > > > G22346T > G21800T,A22053C\n+B.1.177.20\t388\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > > > > > G23311C > > C10626T\n+B.1.177.18\t389\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > > > > > G23311C > > G25440T,C27752T\n+B.1.177.2\t377\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T > > > > > A1987G > T14721C,T25519G\n+B.1.177.6\t370\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T > > > G204T > C21614T > > C6317T\n+20I/501Y.V1\t618\tC241T,C3037T,C14408T,A23403G > > > > > G28881A,G28882A,G28883C > > > > > > > > C913T,C3267T,C5388A,C5986T,T6954C,C14676T,C15279T,T16176C,A23063T,C23271A,C23604A,C23709T,T24506G,G24914C,C27972T,G28048T,A28111G,G28280C,A28281T,T28282A,C28977T\n+B.1.1.7\t618\tC241T,C3037T,C14408T,A23403G > > > > > G28881A,G28882A,G28883C > > > > > > > > C913T,C3267T,C5388A,C5986T,T6954C,C14676T,C15279T,T16176C,A23063T,C23271A,C23604A,C23709T,T24506G,G24914C,C27972T,G28048T,A28111G,G28280C,A28281T,T28282A,C28977T\n+B.1.177.3\t378\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T > > > > > A1987G > > G6344T\n+B.1.177.4\t379\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T > > > > > A1987G > > C66T,G10870T,A11781G,C25614T\n+B.1.177.12\t371\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T > > > G204T > C21614T > > > G17944T,C24334T,T24814C,C27769T\n+B.1.1.219\t626\tC241T,C3037T,C14408T,A23403G > > > > > G28881A,G28882A,G28883C > > > > > > > > > G5572A,A6366T,G11410A,C19488T,G25776T\n+B.1.1.315\t631\tC241T,C3037T,C14408T,A23403G > > > > > G28881A,G28882A,G28883C > > > > > > > > > A1163T,T3256C,C5622T,G14202T,G19542T,C19718T,C22388T,C26060T,G29227T,C29466T,A29771G\n+B.1.177.5\t372\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T > > > G204T > C21614T > > > > T24769C,C25460T\n+B.1.177.7\t373\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T > > > G204T > C21614T > > > > > C15480T\n+B.1.177.8\t374\tC241T,C3037T,C14408T,A23403G > > > > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > > C27944T > > > G204T > C21614T > > > > > G8179T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_13_path_mutations.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_13_path_mutations.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,139 @@\n+sample_id\tpath_from_root\n+England/MILK-9A8AB8/2020|20-08-31\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > C3602T,C6941T,C15324T,C21855T,A25505G,G25906C,G25996T,C28651T,C28869T (268) > G4442T,C6525T,A16044T (269) > C222T\n+England/CAMC-106415F/2021|21-01-15\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > C3602T,C6941T,C15324T,C21855T,A25505G,G25906C,G25996T,C28651T,C28869T (268) > G4504T,T8983G,G11761T,T12655C,C26461T,A28133T (271) > C12116T,C12459T,A23503T,A23989T,C24023T,G28899A\n+England/CAMC-C470F2/2020|20-12-10\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > C3602T,C6941T,C15324T,C21855T,A25505G,G25906C,G25996T,C28651T,C28869T (268) > G4504T,T8983G,G11761T,T12655C,C26461T,A28133T (271) > C6794T,C8814T,C13452T\n+Spain/R60/2020|LR884131.1|20-04-17\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > (28_polytomy_2) > (28_polytomy_3) > T19839C,G28881A,G28882A,G28883C (655) > G3849A,G27506T,C29203T\n+USA/CA-CZB-5682/2020|MW276261.1|20-07-23\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > (28_polytomy_2) > (28_polytomy_3) > T19839C,G28881A,G28882A,G28883C (655) > (655_polytomy_0) > A14424G,G18880T,C28057T,C29774T\n+England/QEUH-9C7EA8/2020|20-09-11\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > C3602T,C6941T,C15324T,C21855T,A25505G,G25906C,G25996T,C28651T,C28869T (268) > G4442T,C6525T,A16044T (269) > G2407T,T2924C,G11761T\n+Scotland/QEUH-9D11C0/2020|20-09-16\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > (28_polytomy_2) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > T4195A,C10977T,G25049T,G25062T,C26151T,C28657T,C29366T (365) > C24334T\n+England/QEUH-A0077A/2020|20-10-02\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > (28_polytomy_2) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > T4195A,C10977T,G25049T,G25062T,C26151T,C28657T,C29366T (365) > C6027T,T10977C,A25327G\n+England/ALDP-AA0ED1/2020|20-10-22\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > (28_polytomy_2) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > (361_polytomy_0) > C27944T (366) > C445T,G28079T\n+England/QEUH-A4CF6B/2020|20-10-05\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > (28_polytomy_2) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > (361_polytomy_0) > C27944T (366) > (366_polytomy_0) > C4534T,C5544T\n+Switzerland/270068/2020|LR882987.1|20-09-02\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > (28_polytomy_2) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > (361_polytomy_0) > (361_polytomy_1) > C13671T,C14805T,G17278T,A20284T,T20285C,A27755T (381) > G17058T\n+Switzerland/332169/2020|LR898966.1|20-10-22\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > (28_polytomy_2) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > (361_polytomy_0) > (361_polytomy_1) > C13671T,C14805T,G17278T,A20284T,T20285C,A27755T (381) > G21830T,C27881T\n+England/MILK-ABB8D5/2020|20-10-21\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > (28_polytomy_2) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > (361_polytomy_0) > (361_polytomy_1) > (361_polytomy_2) > (361_polytomy_3) > C28310A (385) > C9857A,A28304T\n+England/NORT-2884A8/2020|20-11-22\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > (28_polytomy_2) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > (361_polytomy_0) > (361_polytomy_1) > (361_polytomy_2) > (361_polytomy_3) > C28310A (385) > C6525T,C10376T,G17032A,C23557T,C24106T\n+England/QEUH-AD0DDB/2020|20-10-26\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > (28_polytomy_2) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > (361_polytomy_0) > (361_polytomy_1) > (361_polytomy_2) > (361_polytomy_3) > (361_polytomy_4) '..b'T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > G25494T (323) > C25386T (324) > C21302T,C21304A,C26256T,C27119T,C28453T\n+Wales/PHWC-47F3A5/2020|20-10-07\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > G25494T (323) > G28817T (325) > T9655C,G28198T\n+England/ALDP-A85BCC/2020|20-10-17\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > G25494T (323) > G28817T (325) > T209C,T11857C\n+England/ALDP-A2FCA3/2020|20-10-05\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > (322_polytomy_0) > C20451T,G21770A (326) > T7919G (327) > C24734T\n+Scotland/MILK-A69E6B/2020|20-10-09\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > (322_polytomy_0) > C20451T,G21770A (326) > T7919G (327) > A28483G,A28877G\n+England/MILK-A7D1A7/2020|20-10-13\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > (322_polytomy_0) > C20451T,G21770A (326) > G18583A (328) > T4579A,T27835C\n+England/MILK-A91486/2020|20-10-16\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > (322_polytomy_0) > C20451T,G21770A (326) > G18583A (328) > G2272T,G20679T,G24586T\n+AUT/2021006354/2021|MW672357.1|21-02\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > (322_polytomy_0) > C16394T,C22127T,G23876A,G25947T (329) > C829T,C14697T,C18176T,G19398T,G28083T,G28975T (333) > C878T,C12374T,C20384T,C21639T,C29367T\n+England/MILK-E7F4C6/2021|21-01-02\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > (322_polytomy_0) > C16394T,C22127T,G23876A,G25947T (329) > C829T,C14697T,C18176T,G19398T,G28083T,G28975T (333) > T9070C,C10296T\n+England/ALDP-AA169C/2020|20-10-22\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > (322_polytomy_0) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > G25218T (331) > C23191T,G23909A\n+England/MILK-A474DA/2020|20-10-06\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > (322_polytomy_0) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > G25218T (331) > A6659G\n+England/ALDP-B483EA/2020|20-11-07\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > (322_polytomy_0) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > T8110C (332) > C10039A,T18402C,C29738T\n+England/QEUH-AA0035/2020|20-10-20\tC241T,C3037T,C14408T,A23403G (28) > (28_polytomy_0) > (28_polytomy_1) > T7767C,C8047T,C17104T,A20268G,C22879A,G29734C (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > (322_polytomy_0) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > T8110C (332) > G11417T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_13_sample_names.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_13_sample_names.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,138 @@ +England/MILK-9A8AB8/2020|20-08-31 +England/CAMC-106415F/2021|21-01-15 +England/CAMC-C470F2/2020|20-12-10 +Spain/R60/2020|LR884131.1|20-04-17 +USA/CA-CZB-5682/2020|MW276261.1|20-07-23 +England/QEUH-9C7EA8/2020|20-09-11 +Scotland/QEUH-9D11C0/2020|20-09-16 +England/QEUH-A0077A/2020|20-10-02 +England/ALDP-AA0ED1/2020|20-10-22 +England/QEUH-A4CF6B/2020|20-10-05 +Switzerland/270068/2020|LR882987.1|20-09-02 +Switzerland/332169/2020|LR898966.1|20-10-22 +England/MILK-ABB8D5/2020|20-10-21 +England/NORT-2884A8/2020|20-11-22 +England/QEUH-AD0DDB/2020|20-10-26 +Wales/MILK-9E3240/2020|20-09-21 +England/CAMC-949688/2020|20-07-27 +England/SHEF-C3AED/2020|20-07-30 +England/MILK-99D755/2020|20-08-31 +England/MILK-99D764/2020|20-08-31 +Wales/PHWC-48212D/2020|20-10-20 +England/QEUH-9C80B0/2020|20-09-10 +England/MILK-A06194/2020|20-10-01 +England/CAMC-B32AA2/2020|20-11-05 +USA/AK-PHL660/2020|MW173157.1|20-06-27 +England/LOND-DC4E3/2020|20-11-04 +England/MILK-99D3AC/2020|20-08-31 +England/PHEC-1491AD/2020|20-10-17 +England/QEUH-9B3A8D/2020|20-09-04 +England/NORW-F1F9C/2020|20-10-24 +England/PHEC-14E15D/2020|20-12-09 +England/PHEC-149635/2020|20-10-28 +England/ALDP-A95DE1/2020|20-10-20 +England/ALDP-9E75E9/2020|20-09-25 +England/MILK-AC7B0A/2020|20-10-21 +England/NOTT-11336A/2020|20-09-16 +England/MILK-A799FE/2020|20-10-15 +England/CAMC-A417F5/2020|20-10-06 +England/QEUH-AE2A48/2020|20-10-26 +England/ALDP-A68CF9/2020|20-10-12 +England/CAMB-1B6439/2020|20-09-22 +England/MILK-9F1898/2020|20-09-25 +England/MILK-A7CDC2/2020|20-10-13 +England/CAMC-A5845E/2020|20-10-08 +England/ALDP-AA10DA/2020|20-10-22 +Wales/PHWC-4815AA/2020|20-10-13 +England/QEUH-962E81/2020|20-08-10 +England/QEUH-96E605/2020|20-08-17 +Japan/TKYE622411_2020/2020|LC593808.1|20-07 +England/CAMC-B36516/2020|20-11-05 +England/CAMC-B362D3/2020|20-11-05 +England/MILK-B3A284/2020|20-11-01 +England/CAMC-B365AD/2020|20-11-05 +covid_hub_pl_ibch_0157|LR991987.1|20-05-19 +Poland/1/2020|LR899030.1|20-05-20 +England/MILK-6166F0/2020|20-07-05 +England/ALDP-9BCA93/2020|20-09-09 +USA/WI-UW-1194/2020|MT981478.1|20-08-11 +USA/CA-CZB-3284/2020|MW134086.1|20-07-17 +USA/CA-QDX-2817/2020|MW460624.1|20-12-26 +USA/CA-QDX-2803/2020|MW460610.1|20-12-26 +England/SHEF-CDD62/2020|20-05-27 +England/SHEF-10B22B9/2020|20-04-20 +England/QEUH-9B703C/2020|20-09-09 +England/MILK-970CE0/2020|20-08-18 +England/SHEF-10C9BD2/2020|20-12-20 +England/SHEF-10CC3AA/2020|20-12-17 +England/MILK-A1BC04/2020|20-10-03 +England/ALDP-9BE8B5/2020|20-09-09 +Scotland/EDB10724/2020|20-12-04 +Scotland/CVR4309/2020|20-09-14 +England/QEUH-AE4EA4/2020|20-10-27 +England/ALDP-9BECB9/2020|20-09-10 +Wales/PHWC-16E6A3/2020|20-10-02 +England/MILK-9A9D09/2020|20-09-01 +England/QEUH-B6C0E9/2020|20-11-11 +England/CAMC-AEA62E/2020|20-10-25 +England/MILK-11A5634/2021|21-01-29 +GHA/nmimr-SARS-CoV-2-TRA-182/2021|MW598412.1|21-01-12 +USA/MA-Broad_CRSP-00367/2021|MW599505.1|21-01-08 +USA/MA-MGH-03951/2021|MW617773.1|21-01-22 +USA/CO-CDC-STM-000008403/2021|MW617544.1|21-01-31 +England/LOND-12F65DC/2021|21-01-19 +Switzerland/310500/2020|LR898805.1|20-10-08 +Switzerland/300433/2020|LR898634.1|20-09-29 +England/MILK-9A699F/2020|20-09-01 +England/CAMC-947392/2020|20-07-18 +England/MILK-977469/2020|20-07-24 +USA/CA-LACPHL-AF00169/2021|MW485829.1|21-01-08 +USA/CA-LACPHL-AF00029/2020|MW424876.1|20-12-20 +England/CAMC-A65DDB/2020|20-10-11 +England/CAMC-AAF5A0/2020|20-10-22 +England/MILK-ABBF2B/2020|20-10-22 +England/QEUH-96A85E/2020|20-08-14 +HongKong/Homo-sapiens/HKG/Case5132/2020|MW181761.1|20-10-06 +HongKong/Homo-sapiens/HKG/Case5126/2020|MW181753.1|20-10-06 +England/PHEC-149F0D/2020|20-11-19 +England/MILK-BE717A/2020|20-11-29 +CAN/COVID_CRCHUM_Pre_Freeze_6/2020|MW309430.1|20-09-04 +Scotland/QEUH-BEAF22/2020|20-12-04 +England/MILK-A230C1/2020|20-10-03 +Northern_Ireland/QEUH-969C53/2020|20-08-14 +England/ALDP-9E79B0/2020|20-09-24 +England/MILK-B561FE/2020|20-11-06 +England/CAMC-9DFBC4/2020|20-09-21 +England/QEUH-AD1165/2020|20-10-25 +England/ALDP-FB5E3E/2021|21-01-11 +England/ALDP-E8756E/2021|21-01-04 +England/ALDP-A2EAE6/2020|20-10-05 +Scotland/QEUH-A636C3/2020|20-10-10 +England/QEUH-A76C07/2020|20-10-12 +England/MILK-AC7997/2020|20-10-21 +Scotland/QEUH-9DC927/2020|20-09-22 +Scotland/QEUH-9B75D3/2020|20-09-04 +England/CAMC-AEACFF/2020|20-10-25 +England/MILK-97356A/2020|20-08-14 +England/MILK-9A9F7C/2020|20-08-31 +England/OXON-F42364/2020|20-12-18 +England/MILK-9C2766/2020|20-09-10 +England/ALDP-A95A9F/2020|20-10-19 +England/PHEC-149FA3/2020|20-11-20 +England/QEUH-C9332B/2020|20-12-17 +England/CAMC-A649C9/2020|20-10-10 +England/MILK-B04890/2020|20-10-24 +England/CAMC-A57F03/2020|20-10-09 +England/MILK-A7D15C/2020|20-10-13 +Wales/PHWC-47F3A5/2020|20-10-07 +England/ALDP-A85BCC/2020|20-10-17 +England/ALDP-A2FCA3/2020|20-10-05 +Scotland/MILK-A69E6B/2020|20-10-09 +England/MILK-A7D1A7/2020|20-10-13 +England/MILK-A91486/2020|20-10-16 +AUT/2021006354/2021|MW672357.1|21-02 +England/MILK-E7F4C6/2021|21-01-02 +England/ALDP-AA169C/2020|20-10-22 +England/MILK-A474DA/2020|20-10-06 +England/ALDP-B483EA/2020|20-11-07 +England/QEUH-AA0035/2020|20-10-20 |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_14_all_paths.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_14_all_paths.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1704 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4-02\tC593T\n+Scotland/EDB1824/2020|20-04-16\tC8240T,T8941C,C9438T,C19185T,G27358T\n+Spain/H12_46/2020|LR884009.1|20-04-08\tC7967T,C16694T\n+680\tC3037T,A20268G\n+Spain/R11/2020|LR884126.1|20-03-06\tT3037C\n+Spain/LP19_4952/2020|LR884066.1|20-03-07\t\n+HKG/HKU-904a/2020|MT365032.1|20-01-30\tC4158T,C18828T\n+681\tA17858G,C18060T\n+USA/MN-MDH-1475/2020|MT920008.1|20-03-23\tA7966G,A22422G\n+USA/CA-CZB-1615/2020|MT628267.1|20-04-14\tC4776T,C9491T,C17747T,G28086T\n+682\tT9477A,C14805T,G25979T\n+USA/FL-BPHL-0393/2020|MT757005.1|20-03-17\t\n+683\tC28863T\n+Spain/R10_33/2020|LR884127.1|20-03-02\tT25979G\n+684\tC28657T\n+685\tC4540T\n+686\tC25714T,C26029A\n+Scotland/CVR3062/2020|20-04-24\tG805A,C5673T,C11960T,C27567T\n+Scotland/CVR2435/2020|20-04-14\tC15274T\n+687\tC28311T\n+England/OXON-B0922/2020|20-03-28\tC147A,G6894T,C18928T,A21489C\n+AUS/VIC995/2020|MT451680.1|20-03-31\tG17632A\n+688\tC275T,C1567T,C4543T,A5234G,A5488G,C10029T,G10105T,C11005A,C12815T,C16466T,T16857C,T18417C,A22525G,T22917G,A23403G,G24697A,C25613T,C26681T,A28272T,G28975T,C29421T\n+USA/WA-S4100/2021|MW555971.1|21-01-18\tG5234A,C12890T,C19944T\n+USA/WA-S4074/2021|MW555949.1|21-01-19\tC3165T,T10105G,C11563T,G22525A,G25311T,C27630T\n+689\tG22468T,G28878A,G29742A\n+690\tT22468G\n+691\tC4573T,C10747T,G11230T,G11266T,G11521T,C16575T,C17745T,C22000T,C22033A,G23401T,C23604G,T24097C,G28167A,G28378C\n+England/ALDP-CB55B4/2020|20-12-20\tC4940T,G21867T,C29523T\n+England/CAMC-CF4B5D/2020|20-12-21\tG529A,A963G,G2246A,A5068G,C12525T,G21255C,T23698A,G28881A\n+692\tG16381A,T17877C,G25500T\n+USA/WI-UW-06/2020|MT772088.1|20-03-21\tC1929T,C20316T\n+USA/MI-MDHHS-SC20124/2020|MT439284.1|20-03-24\tC25854T\n+693\tC24370T\n+GHA/34927_S20/2020|MT890226.1|20-05-23\tC27641T,G29402T\n+GHA/35563_S37/2020|MT890230.1|20-05-24\tC2306T,C5672T,C5986T,C13515T,G24926T\n+694\tT1885A,C5907T,C10138T,G11417T,C11824T,C18129T,G18181A,T20100C,T21982C,G22132T,T22917G,G23402A,G25687T,G26062T,C29686T\n+GHA/WACCBIP_nCoV_GS115/2021|MW571124.1|21-01-07\tC1385T,A1395G,A9750G,A26069G\n+USA/GA-CDC-LC0010641/2021|MW640882.1|21-01-26\tA4984T,A7854G,A21062G,A28254C\n+695\tA481G,G521T,C2197T,G10850A,C12469T,C16391T,G17014T,A23064C,C23525T,C25904T,C27294T,A27489G,A28272T,C28377T\n+EGY/CUNCI-HGC9I036/2020|MW504609.1|20-12-25\tG16236A,C16694T,G21624A,A21625C,C22097T,G29773T\n+EGY/CUNCI-HGC12I049/2021|MW595907.1|21-01-03\tC6541T,C9988T,T25904C\n+696\tG9802A,G11230T,A16512G,C19951T,G26428T\n+England/CAMC-C91F38/2020|20-12-11\tC4438T,G6446T,C6638T,C10834T,C12469T,C16466T,C16726T,G17140T,G21210C,T22287C,G23402A,C26299T,T27134C,A28273T,G29227A\n+SLE/KGH-G-8626/2020|MT872492.1|20-04-10\tC10818T,T11230G,C25702T\n+697\tT490A,C3177T,C24034T,T26729C,G28077C\n+USA/COVID20-0008/2020|MT764174.1|20-03-10\tT18736C\n+USA/IL-CDC-IL2/2020|MT044257.1|20-01-28\t\n+698\tC6696T\n+England/LIVE-9E66F/2020|20-04-10\tC7765T,G10256T\n+Scotland/CVR705/2020|20-03-26\tC11001T,G17122T\n+699\tG1397A,T28688C,G29742T\n+England/PHEC-1A601/2020|20-03-04\tA19526G\n+England/PHEC-2275E/2020|20-06-22\tG2246A,C5512T,C20132T,A23586G,C26822T,T27384C,T27484C,G28975T,G29639T\n+700\tA1079C,C9319T,C19862T,T27384C\n+USA/CA-QDX-1421/2020|MW065371.1|20-03-18\tC7764T,C29625T\n+USA/CA-QDX-2080/2020|MW190832.1|20-03-19\tC6701T,T7225C\n+701\tC1076T\n+AUS/VIC1255/2020|MT451830.1|20-04-11\tT13857C,C25469T,C27964T\n+AUS/VIC1878/2020|MT745600.1|20-03-29\tA28955T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_14_path_clades.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_14_path_clades.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,554 @@\n+clade\troot_id\tfrom_tree_root\n+19A\t1\t\n+B\t1\t\n+B.26\t4\t > C7423T\n+B.48\t5\t > C20270T\n+B.15\t8\t > T4949C\n+B.5\t9\t > C29635T\n+B.54\t10\t > C14805T,G26144T\n+B.47\t24\t > A10982G\n+B.20\t660\t > A14940G\n+B.52\t661\t > A1904G,C8090T,C10789T\n+B.11\t662\t > T514C\n+B.46\t663\t > A12557G,C24904T,A27359G\n+B.1.14\t664\t > C25692T\n+B.27\t665\t > G29032A\n+B.19\t666\t > C10277T\n+B.6\t674\t > C6312A,C13730T,C23929T,C28311T\n+19B\t676\t > C8782T,T28144C\n+A\t676\t > C8782T,T28144C\n+B.10\t698\t > C6696T\n+B.4\t699\t > G1397A,T28688C,G29742T\n+B.23\t6\t > C20270T > A29683T\n+B.33\t11\t > C14805T,G26144T > T17247C\n+B.28\t18\t > C14805T,G26144T > G28842T\n+B.29\t19\t > C14805T,G26144T > C23707T\n+B.40\t20\t > C14805T,G26144T > A2480G,C2558T\n+B.30\t21\t > C14805T,G26144T > A4236G,T25655C\n+B.41\t22\t > C14805T,G26144T > G5572T\n+B.31\t23\t > C14805T,G26144T > G13627T,C15540T,A28338G\n+B.1\t26\t > C241T > C14408T\n+B.3\t658\t > C241T > T241C,G1440A,G2891A\n+B.18\t668\t > G29711T > C1218T,G27806T\n+B.13\t669\t > G29711T > A4838G,C7420T,C14937T,C20148T\n+B.51\t670\t > G29711T > T2116A\n+B.45\t672\t > C28854T > C12710T\n+B.12\t673\t > C28854T > C11752T,C25665T,A27700G,T28854C,T28912C\n+B.6.6\t675\t > C6312A,C13730T,C23929T,C28311T > C6310A,C19524T\n+A.1\t681\t > C8782T,T28144C > A17858G,C18060T\n+A.2\t682\t > C8782T,T28144C > T9477A,C14805T,G25979T\n+A.3\t697\t > C8782T,T28144C > T490A,C3177T,C24034T,T26729C,G28077C\n+B.4.4\t700\t > G1397A,T28688C,G29742T > A1079C,C9319T,C19862T,T27384C\n+B.4.5\t701\t > G1397A,T28688C,G29742T > C1076T\n+B.37\t13\t > C14805T,G26144T > T17247C > C8078T\n+B.35\t14\t > C14805T,G26144T > T17247C > A7479G,C25572T\n+B.32\t15\t > C14805T,G26144T > T17247C > A1587G\n+B.34\t16\t > C14805T,G26144T > T17247C > C988T\n+B.39\t17\t > C14805T,G26144T > T17247C > A1515G,C9223T\n+B.3.1\t659\t > C241T > T241C,G1440A,G2891A > G28851T\n+A.5\t678\t > C8782T,T28144C > A23403G,C26088T > G23403A\n+A.10\t680\t > C8782T,T28144C > A23403G,C26088T > C3037T,A20268G\n+A.28\t695\t > C8782T,T28144C > G22468T,G28878A,G29742A > A481G,G521T,C2197T,G10850A,C12469T,C16391T,G17014T,A23064C,C23525T,C25904T,C27294T,A27489G,A28272T,C28377T\n+A.12\t696\t > C8782T,T28144C > G22468T,G28878A,G29742A > G9802A,G11230T,A16512G,C19951T,G26428T\n+20A\t28\t > C241T > C14408T > A23403G > C3037T\n+B.1.108\t28\t > C241T > C14408T > A23403G > C3037T\n+A.23.1\t691\t > C8782T,T28144C > G22468T,G28878A,G29742A > T22468G > C4573T,C10747T,G11230T,G11266T,G11521T,C16575T,C17745T,C22000T,C22033A,G23401T,C23604G,T24097C,G28167A,G28378C\n+A.4\t692\t > C8782T,T28144C > G22468T,G28878A,G29742A > T22468G > G16381A,T17877C,G25500T\n+A.11\t693\t > C8782T,T28144C > G22468T,G28878A,G29742A > T22468G > C24370T\n+A.21\t694\t > C8782T,T28144C > G22468T,G28878A,G29742A > T22468G > T1885A,C5907T,C10138T,G11417T,C11824T,C18129T,G18181A,T20100C,T21982C,G22132T,T22917G,G23402A,G25687T,G26062T,C29686T\n+B.1.105\t45\t > C241T > C14408T > A23403G > C3037T > G28514T\n+B.1.152\t46\t > C241T > C14408T > A23403G > C3037T > G1914A,T16456C\n+B.1.103\t47\t > C241T > C14408T > A23403G > C3037T > C25665T,G28325T\n+B.1.188\t48\t > C241T > C14408T > A23403G > C3037T > C3487T,C11308T,T15264C,C16332T,C19170T,C25791T,C28854T,C29614T\n+B.1.378\t49\t > C241T > C14408T > A23403G > C3037T > G3871T\n+B.1.199\t50\t > C241T > C14408T > A23403G > C3037T > C2939T\n+B.1.139\t51\t > C241T > C14408T > A23403G > C3037T > A696C\n+B.1.91\t52\t > C241T > C14408T > A23403G > C3037T > G24077T\n+B.1.350\t53\t > C241T > C14408T > A23403G > C3037T > G25563T\n+B.1.216\t267\t > C241T > C14408T > A23403G > C3037T > T3011C,G22205T,T27869C,T28853G\n+B.1.221\t268\t > C241T > C14408T > A23403G > C3037T > C3602T,C6941T,C15324T,C21855T,A25505G,G25906C,G25996T,C28651T,C28869T\n+B.1.525\t272\t > C241T > C14408T > A23403G > C3037T > C1498T,G2659A,C6285T,T8593C,C14407T,C18171T,A20724G,A21717G,C21762T,G23012A,G23593C,T24224C,C24748T,C26305T,T26767C,C28308G,A28699G,C28887T,G29543T\n+B.1.222\t273\t > C241T > C14408T > A23403G > C3037T > C1545T,C22879A\n+B.1.379\t274\t > C241T > C14408T > A23403G > C3037T > A11782G,G22203T\n+B.1.182\t275\t > C241T > C14408T > A23403G > C3037T > A20268G\n+B.1.5\t341\t > C241T > C14408T > A2'..b'C2416T > G8371T > C22477T > C3811T,G22225A\n+B.1.36.20\t221\t > C241T > C14408T > A23403G > C3037T > G25563T > C18877T > C26735T > C22444T > C593T,T3118C,T10200C,A12547G,C21772T,C28854T\n+B.1.36.28\t226\t > C241T > C14408T > A23403G > C3037T > G25563T > C18877T > C26735T > C22444T,C28854T > T1947C,T7292C,T8410C,C10833T,C11572T,C16293T,T23986C\n+B.1.36.16\t233\t > C241T > C14408T > A23403G > C3037T > G25563T > C18877T > C26735T > C22444T,C28854T > G25494T\n+B.1.36.9\t234\t > C241T > C14408T > A23403G > C3037T > G25563T > C18877T > C26735T > C22444T,C28854T > C2523T,G3994A,C5730T,C9924T,C11109T,C24138A\n+B.1.36.12\t236\t > C241T > C14408T > A23403G > C3037T > G25563T > C18877T > C26735T > C22444T,C28854T > C11514T,C13168T,G24764T\n+B.1.36.10\t237\t > C241T > C14408T > A23403G > C3037T > G25563T > C18877T > C26735T > C22444T,C28854T > C2898T,C6681T,C7728T,G12191T,T16993C,G25311T\n+B.1.471\t246\t > C241T > C14408T > A23403G > C3037T > G25563T > C18877T > C26735T > C16915T,T24202C,G28899T > G21204T,G29692T\n+B.1.472\t247\t > C241T > C14408T > A23403G > C3037T > G25563T > C18877T > C26735T > C16915T,T24202C,G28899T > C26534T\n+B.1.258.14\t334\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A,C27800A > G18186T,C28854T\n+B.1.1.289\t433\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > T19839C > G25552T > G11801A\n+B.1.1.2\t434\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > T19839C > G25552T > A26332G,A28877T,G28878C\n+20J/501Y.V3\t478\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > G25088T > A6319G,T26149C > T733C,C2749T,C3828T,A5648C,A6613G,C12778T,C13860T,G17259T,C21614T,C21621A,C21638T,G21974T,G22132T,G23012A,A23063T,C23525T,C24642T,G28167A,C28512G,A28877T,G28878C\n+P.2\t480\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > G25088T > C12053T > C100T,T10667G,C11824T,G23012A,G28628T,G28975T,C29754T\n+B.1.1.143\t481\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > G25088T > C12053T > T22020C,G23628T,C25728T,G26063T\n+C.3\t502\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > G2447T,G22199T\n+C.14\t503\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > G29179T\n+C.13\t504\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > A21131G\n+C.1\t505\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > C18747T\n+C.2\t508\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > T8323C,C10369T,T14345C,T15437C,G18292T,C25624T\n+C.4\t509\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > G24794T\n+B.1.1.293\t518\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > C3373A,C15960T > T15960C > C643T,C4897T,C4898T,C9561T,G22349T,C25904T,C27920T\n+B.1.1.50\t523\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > C313T > G4510A > G15438T,G25785T\n+B.1.1.209\t524\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > C313T > G4510A > G19480A\n+B.1.1.47\t526\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > C313T > C9286T > C19763T\n+B.1.1.284\t527\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > C313T > C9286T > T4346C,C10376T,C14708T,C28725T,G29692T\n+B.1.1.179\t533\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > C313T > C5700A > T682C,C900T,G3259T,C4048T,C14937T,C17802T,C23604A,C24130T,C25721T,G25767T,G28903T\n+N.1\t545\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > T29148C > G25793T,T27299C > T25793G > C25916T,C29769T\n+N.4\t546\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > T29148C > G25793T,T27299C > T25793G > A2475G\n+N.3\t547\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > T29148C > G25793T,T27299C > T25793G > G26416T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_14_path_mutations.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_14_path_mutations.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1097 @@\n+sample_id\tpath_from_root\n+England/BRIS-1853249/2020|20-04-02\t (1) > C24034T (2) > C29518T\n+Wales/PHWC-25B04/2020|20-03-24\t (1) > C875T (3) > A20637G\n+NPL/61-TW/2020|MT072688.1|20-01-13\t (1) > C24034T (2) > \n+Wales/LIVE-A6831/2020|20-03-16\t (1) > C875T (3) > T14859C\n+Scotland/EDB1317/2020|20-04-09\t (1) > C7423T (4) > G4207A,T7423C\n+Scotland/EDB354/2020|20-03-30\t (1) > C7423T (4) > A29780C\n+England/SHEF-BFF8B/2020|20-03-25\t (1) > C20270T (5) > C1473T\n+England/LCST-24D7202/2020|20-06-22\t (1) > C20270T (5) > A29683T (6) > A18671G (7) > C4021T,A9963T,T24027C\n+England/SHEF-BFFC7/2020|20-03-25\t (1) > T4949C (8) > G28027T\n+England/PHEC-1E01E/2020|20-04-03\t (1) > T4949C (8) > C22445T\n+DP0476/2020|LC571003.1|20-02-16\t (1) > C29635T (9) > C29592T\n+DP0191/2020|LC570980.1|20-02-15\t (1) > C29635T (9) > A3854G\n+England/LIVE-A5D06/2020|20-03-17\t (1) > A10982G (24) > C6681T,G11801A\n+England/LIVE-A065B/2020|20-05-27\t (1) > A10982G (24) > C823T,C8752T,A9741C,C19961T,C26333T,C26408T\n+USA/CA-CZB-1091/2020|MT460091.1|20-05-01\t (1) > A14940G (660) > C15024T\n+USA/CA-CZB-11876/2020|MW276506.1|20-04-08\t (1) > A14940G (660) > A26120G\n+USA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\t (1) > T514C (662) > C22033A\n+NED/NB02_13KS/2020|MT457397.1|20-04-29\t (1) > T514C (662) > G1607A,A10829G,G12795A,C17410T,A22920T\n+USA/CA-QDX-1986/2020|MW190732.1|20-03-18\t (1) > A12557G,C24904T,A27359G (663) > C11050T\n+USA/CA-CZB-1250/2020|MT534320.1|20-04-12\t (1) > A12557G,C24904T,A27359G (663) > C25916T,G29751T\n+USA/CA-CZB-1015/2020|MT438733.1|20-04-22\t (1) > C25692T (664) > T15867A\n+USA/CA-CZB-1073/2020|MT449664.1|20-04-21\t (1) > C25692T (664) > G10617A,G22225T\n+England/BRIS-1258A2/2020|20-03-29\t (1) > G29032A (665) > C6696T,C9096T,C29754T\n+England/SHEF-BFEBB/2020|20-03-24\t (1) > G29032A (665) > C11747T,T24364G\n+USA/CA-CZB-1041/2020|MT438759.1|20-04-22\t (1) > C10277T (666) > A6313G,T7191C,A7193G\n+USA/CA-CZB-1051/2020|MT449644.1|20-04-06\t (1) > C10277T (666) > G7273A\n+England/LIVE-9E66F/2020|20-04-10\t (1) > C6696T (698) > C7765T,G10256T\n+Scotland/CVR705/2020|20-03-26\t (1) > C6696T (698) > C11001T,G17122T\n+England/SHEF-BFF21/2020|20-03-25\t (1) > C20270T (5) > A29683T (6) > A18671G (7) > \n+England/LIVE-A4C46/2020|20-03-12\t (1) > C20270T (5) > A29683T (6) > G431A,G26754A,C28725T\n+Switzerland/100159/2020|LR884273.1|20-03-16\t (1) > C14805T,G26144T (10) > T17247C (11) > C12400T (12) > C16995T\n+England/EXET-135818/2020|20-04-11\t (1) > C14805T,G26144T (10) > C7703T,T9352C,G27201T\n+France/40002VJ/2020|MT470179.1|20-03\t (1) > C241T (25) > C14408T (26) > C2416T,G12079C,C23220A\n+Wales/PHWC-310CA/2020|20-04-11\t (1) > C241T (25) > C14408T (26) > A23403G (27) > A2480G,A12529G,T14408C,G26144T\n+Scotland/GCVR-171160/2020|20-03-26\t (1) > A1904G,C8090T,C10789T (661) > A3958G,C5826T,C17074T\n+England/BRIS-130E2A/2020|20-03-24\t (1) > A1904G,C8090T,C10789T (661) > C16658A,C17733T\n+USA/WI-UW-298/2020|MT706406.1|20-04-13\t (1) > G29711T (667) > A4838G,C7420T,C14937T,C20148T (669) > C7728T,C21637T\n+USA/WI-UW-314/2020|MT706422.1|20-04-16\t (1) > G29711T (667) > A4838G,C7420T,C14937T,C20148T (669) > G25907T\n+USA/WI-UW-325/2020|MT706432.1|20-04-24\t (1) > G29711T (667) > T2116A (670) > C12880T,C28854T\n+USA/WI-UW-290/2020|MT706398.1|20-04-08\t (1) > G29711T (667) > T2116A (670) > A10070C,G28703C,C28849T\n+Scotland/CVR3488/2020|20-05-12\t (1) > C28854T (671) > C12710T (672) > C10335T,C16428T,G22139C,C27737T\n+Scotland/CVR780/2020|20-03-27\t (1) > C28854T (671) > C12710T (672) > C5997T\n+Scotland/EDB5629/2020|20-03-24\t (1) > C8782T,T28144C (676) > A23403G,C26088T (677) > G23403A (678) > G9928T (679) > G27870T\n+HKG/HKU-904a/2020|MT365032.1|20-01-30\t (1) > C8782T,T28144C (676) > C4158T,C18828T\n+Scotland/EDB5040/2020|20-04-02\t (1) > C8782T,T28144C (676) > A23403G,C26088T (677) > G23403A (678) > G9928T (679) > C593T\n+England/LOND-126031F/2020|20-03-15\t (1) > C14805T,G26144T (10) > T17247C (11) > C12400T (12) > A20511G\n+Scotland/EDB046/2020|20-03-15\t (1) > C14805T,G26144T (10) > T17247C (11) > C9996T,T2'..b'C,A12964G,A27237G,G28077T,T28245C,C28892T\n+England/MILK-F72F49/2021|21-01-05\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G25088T (476) > C12053T (479) > C100T,T10667G,C11824T,G23012A,G28628T,G28975T,C29754T (480) > C556T,C1628A,A8233G,T14313C,A17612G,C25117T,A25575G,C25613G,C28315T,G28378T\n+England/ALDP-94DD07/2020|20-06-19\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > G2447T,G22199T (502) > G3164T,C7528T,G20569T,C29625T\n+England/ALDP-49EC3C/2020|20-05-20\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > G2447T,G22199T (502) > G29392T,C29541T\n+PER/covper024/2020|MW030255.1|20-07-04\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > G29179T (503) > C17436T,G27478T\n+PER/CoV-19_HRL-223/2020|MW185824.1|20-04-08\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > G29179T (503) > A10323G,G27160T\n+PER/covper011/2020|MW030242.1|20-07-04\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > A21131G (504) > C3768T,C14265T,G17721T,C27213T,C27513T\n+PER/covper040/2020|MW030271.1|20-05-05\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > A21131G (504) > C12854T,G20752T\n+England/MILK-B1553B/2020|20-10-23\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > C18747T (505) > C2509T,G5029C,C6781T,G17027T,G20164A,G22992A,A23233G,T23629G,G25606T,G28048A\n+England/MILK-66F889/2020|20-07-03\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > C18747T (505) > G14547A,G14869A,A24879G,C29421T\n+England/QEUH-96BAA2/2020|20-08-14\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > T8323C,C10369T,T14345C,T15437C,G18292T,C25624T (508) > G1042T,C8895T,G25250T\n+Wales/ALDP-B19FFD/2020|20-11-01\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > T8323C,C10369T,T14345C,T15437C,G18292T,C25624T (508) > G922T,T10369C,A23064C,G23608T,C28453T,C29642T\n+SRB/NS19622-16-06/2020|MW327528.1|20-06-15\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > G24794T (509) > \n+PER/covper018/2020|MW030249.1|20-07-03\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > G24794T (509) > G3755T,G11552T,A28356G\n+England/CAMC-C3E586/2020|20-12-10\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > C3373A,C15960T (512) > T15960C (513) > C643T,C4897T,C4898T,C9561T,G22349T,C25904T,C27920T (518) > C3736T,C6336T,G19735T,G23611T,C26735T,C26858T\n+England/CAMC-DE5550/2020|20-12-29\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > C3373A,C15960T (512) > T15960C (513) > C643T,C4897T,C4898T,C9561T,G22349T,C25904T,C27920T (518) > G6320T,C10582T,C12194T,C25603T\n+Japan/TKYE630414_2020/2020|LC593818.1|20-08\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > G28882A,G28883C (426) > G28881A (427) > C313T (521) > C8917T,C18167T,G21518T,G27604A,G28975T,C29679T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_14_sample_names.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_14_sample_names.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1096 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2020|20-12-27\n+Wales/PHWC-4846A4/2020|20-10-24\n+England/QEUH-AD487C/2020|20-10-26\n+England/QEUH-9B7B2C/2020|20-09-03\n+England/CAMB-72B44/2020|20-03-22\n+England/CAMB-822D3/2020|20-04-12\n+Japan/TKYE627000_2020/2020|LC593811.1|20-08\n+Japan/TKYE624705_2020/2020|LC593810.1|20-07\n+England/QEUH-9F9265/2020|20-09-26\n+England/QEUH-98EE43/2020|20-08-25\n+IND/GBRC455b/2020|MW600453.1|20-12-24\n+IND/GBRC455a/2020|MW600436.1|20-12-24\n+USA/FL-BPHL-2014/2020|MW286586.1|20-06-19\n+USA/MA_MGH_00693/2020|MT520290.1|20-04-06\n+CHL/Santiago-PUC_MVL_0491/2020|MW365473.1|20-05-13\n+CHL/Puerto_Montt-PUC_MVL_0534/2020|MW365467.1|20-05-27\n+ARG/Cordoba-2858/2020|MW633904.1|20-09-14\n+ARG/Cordoba-1484/2020|MW633909.1|20-09-17\n+England/MILK-95862C/2020|20-06-11\n+England/ALDP-94EF88/2020|20-06-16\n+Scotland/QEUH-A00DF0/2020|20-10-02\n+England/ALDP-9CC5BD/2020|20-09-15\n+England/ALDP-9BEB16/2020|20-09-09\n+England/ALDP-A95376/2020|20-10-19\n+England/QEUH-B10460/2020|20-11-02\n+Scotland/QEUH-96D5CD/2020|20-08-20\n+England/CAMB-1AE7FF/2020|20-04-29\n+England/CAMB-762D2/2020|20-03-28\n+USA/WA-S1222/2020|MT821613.1|20-05-08\n+USA/WA-S1655/2020|MT834136.1|20-05-29\n+England/MILK-BB0F16/2020|20-11-17\n+England/CAMC-BBDD4C/2020|20-11-22\n+Scotland/EDB11342/2020|20-12-26\n+England/QEUH-CAF17D/2020|20-12-15\n+USA/CA-QDX-3684/2021|MW545275.1|21-01-08\n+USA/CA-LACPHL-AE00058/2020|MW433754.1|20-07-13\n+Scotland/QEUH-969725/2020|20-08-14\n+England/QEUH-AD1648/2020|20-10-26\n+England/MILK-A192C8/2020|20-10-01\n+England/QEUH-9F3FDD/2020|20-09-24\n+England/CAMC-1263B05/2021|21-02-10\n+England/QEUH-AD3822/2020|20-10-26\n+England/MILK-9A94E6/2020|20-09-01\n+England/MILK-566C5A/2020|20-06-12\n+England/CAMC-C2CDFC/2020|20-12-07\n+England/MILK-CAA0EE/2020|20-12-18\n+England/TFCI-26FA9B7/2020|20-12-31\n+England/MILK-B94ACC/2020|20-11-13\n+England/QEUH-96A29C/2020|20-08-13\n+England/ALDP-9EA6D4/2020|20-09-24\n+England/MILK-A6AEC4/2020|20-10-09\n+England/MILK-B889A0/2020|20-11-14\n+England/MILK-ACEE55/2020|20-10-21\n+Switzerland/260079/2020|LR882418.1|20-08-25\n+USA/WI-UW-1288/2020|MW035458.1|20-09-02\n+USA/WA-S2808/2020|MW077495.1|20-08-31\n+England/CAMC-B3582D/2020|20-11-05\n+England/MILK-A796E8/2020|20-10-14\n+England/MILK-BB0031/2020|20-11-18\n+Scotland/QEUH-96B4E0/2020|20-08-17\n+England/PHEC-152C73/2020|20-11-16\n+England/MILK-9AA782/2020|20-08-31\n+England/ALDP-B82A0D/2020|20-11-14\n+USA/MD-MDH-0664/2021|MW524034.1|21-01-04\n+England/MILK-A79D10/2020|20-10-15\n+England/PHEC-148F95/2020|20-10-15\n+England/MILK-A180DE/2020|20-10-01\n+England/NORW-222D0F/2020|20-12-20\n+England/MILK-F72F49/2021|21-01-05\n+England/ALDP-94DD07/2020|20-06-19\n+England/ALDP-49EC3C/2020|20-05-20\n+PER/covper024/2020|MW030255.1|20-07-04\n+PER/CoV-19_HRL-223/2020|MW185824.1|20-04-08\n+PER/covper011/2020|MW030242.1|20-07-04\n+PER/covper040/2020|MW030271.1|20-05-05\n+England/MILK-B1553B/2020|20-10-23\n+England/MILK-66F889/2020|20-07-03\n+England/QEUH-96BAA2/2020|20-08-14\n+Wales/ALDP-B19FFD/2020|20-11-01\n+SRB/NS19622-16-06/2020|MW327528.1|20-06-15\n+PER/covper018/2020|MW030249.1|20-07-03\n+England/CAMC-C3E586/2020|20-12-10\n+England/CAMC-DE5550/2020|20-12-29\n+Japan/TKYE630414_2020/2020|LC593818.1|20-08\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_15_mutation_annotated_tree.pb |
| b |
| Binary file test-data/test_15_mutation_annotated_tree.pb has changed |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_15_subtree.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_15_subtree.json Tue May 11 17:53:49 2021 +0000 |
| [ |
| b'@@ -0,0 +1,16487 @@\n+{\n+"version":"v2",\n+"meta":{\n+"title":"mutation_annotated_tree",\n+"filters": ["country"],\n+"panels": ["tree"],\n+"colorings": [ {"key":"MAT_Clade_0","title":"MAT_Clade","type":"categorical"}, \n+{"key":"MAT_Clade_1","title":"MAT_Clade","type":"categorical"} ],\n+"display_defaults":{"branch_label":"nuc mutations"},"description":"JSON generated by matUtils. If you have metadata you wish to display, you can now drag on a CSV/TSV file and it will be added into this view, [see here](https://docs.nextstrain.org/projects/auspice/en/latest/advanced-functionality/drag-drop-csv-tsv.html) for more info."},\n+"tree":{ "name":"wrapper",\n+"children":[ {\n+"name": "25",\n+"branch_attrs": {\n+ "labels": { "nuc mutations": "C241T" },\n+"mutations": { "nuc" : [ "C241T" ] }\n+ },\n+"node_attrs": {\n+ "div":1, "MAT_Clade_0": {"value": ""}, "MAT_Clade_1": {"value": ""}},\n+"children":[ {\n+"name": "26",\n+"branch_attrs": {\n+ "labels": { "nuc mutations": "C14408T" },\n+"mutations": { "nuc" : [ "C14408T" ] }\n+ },\n+"node_attrs": {\n+ "div":2, "MAT_Clade_0": {"value": ""}, "MAT_Clade_1": {"value": "B.1"}},\n+"children":[ {\n+"name": "France/40002VJ/2020|MT470179.1|20-03",\n+"branch_attrs": {\n+ "labels": { "nuc mutations": "C2416T,G12079C,C23220A" },\n+"mutations": { "nuc" : [ "C2416T","G12079C","C23220A" ] }\n+ },\n+"node_attrs": { "div": 5, "date": {"value": "20-03"}, "country": {"value": "France"}, "MAT_Clade_0": {"value": ""}, "MAT_Clade_1": {"value": ""}}\n+}\n+,\n+{\n+"name": "27",\n+"branch_attrs": {\n+ "labels": { "nuc mutations": "A23403G" },\n+"mutations": { "nuc" : [ "A23403G" ] }\n+ },\n+"node_attrs": {\n+ "div":3, "MAT_Clade_0": {"value": ""}, "MAT_Clade_1": {"value": ""}},\n+"children":[ {\n+"name": "Wales/PHWC-310CA/2020|20-04-11",\n+"branch_attrs": {\n+ "labels": { "nuc mutations": "A2480G,A12529G,T14408C,G26144T" },\n+"mutations": { "nuc" : [ "A2480G","A12529G","T14408C","G26144T" ] }\n+ },\n+"node_attrs": { "div": 7, "date": {"value": "20-04-11"}, "country": {"value": "Wales"}, "MAT_Clade_0": {"value": ""}, "MAT_Clade_1": {"value": ""}}\n+}\n+,\n+{\n+"name": "28",\n+"branch_attrs": {\n+ "labels": { "nuc mutations": "C3037T" },\n+"mutations": { "nuc" : [ "C3037T" ] }\n+ },\n+"node_attrs": {\n+ "div":4, "MAT_Clade_0": {"value": "20A"}, "MAT_Clade_1": {"value": "B.1.108"}},\n+"children":[ {\n+"name": 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"G28851T" },\n+"mutations": { "nuc" : [ "G28851T" ] }\n+ },\n+"node_attrs": {\n+ "div":5, "MAT_Clade_0": {"value": ""}, "MAT_Clade_1": {"value": "B.3.1"}},\n+"children":[ {\n+"name": "Wales/PHWC-31CB7/2020|20-04-14",\n+"branch_attrs": {\n+ "labels": { "nuc mutations": "C9180T,C16466T,G19670A" },\n+"mutations": { "nuc" : [ "C9180T","C16466T","G19670A" ] }\n+ },\n+"node_attrs": { "div": 8, "date": {"value": "20-04-14"}, "country": {"value": "Wales"}, "MAT_Clade_0": {"value": ""}, "MAT_Clade_1": {"value": ""}}\n+}\n+,\n+{\n+"name": "Wales/PHWC-26D2B/2020|20-03-30",\n+"branch_attrs": {\n+ "labels": { "nuc mutations": "C5183T,G18651T" },\n+"mutations": { "nuc" : [ "C5183T","G18651T" ] }\n+ },\n+"node_attrs": { "div": 7, "date": {"value": "20-03-30"}, "country": {"value": "Wales"}, "MAT_Clade_0": {"value": ""}, "MAT_Clade_1": {"value": ""}}\n+}\n+] \n+}\n+] \n+}\n+] \n+}\n+]\n+}\n+}\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_15_subtree_no_genotype.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_15_subtree_no_genotype.vcf Tue May 11 17:53:49 2021 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_15_tree.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_15_tree.nh Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1 @@\n+((France/40002VJ/2020|MT470179.1|20-03:3,(Wales/PHWC-310CA/2020|20-04-11:4,((England/BRIS-123965/2020|20-04-07:2,England/BRIS-125347/2020|20-03-27:0)29:2,(IND/Isolate_9088/2020|MW555597.1|20-06-30:2,IND/763/2020|MT577009.1|20:0)30:1,((England/CAMB-76515/2020|20-03-29:1,England/CAMB-1AE294/2020|20-04-27:3)32:1,(England/LEED-2A8D10/2020|20-03-31:1,England/CAMB-1AC6F4/2020|20-04-21:3)33:1,(((Scotland/EDB2049/2020|20-04-18:1,Scotland/EDB2100/2020|20-04-19:0)36:2,England/CAMB-1AC7D3/2020|20-04-22:1)35:2,England/CAMB-7EBDF/2020|20-04-07:2,(England/MILK-BB0F16/2020|20-11-17:2,England/CAMC-BBDD4C/2020|20-11-22:5)37:7)34:1,(Scotland/CVR2381/2020|20-04-13:1,Scotland/CVR2197/2020|20-04-11:1)38:5,(Scotland/CVR3417/2020|20-05-07:3,Scotland/CVR1519/2020|20-04-03:1)39:1,(England/MILK-93B73B/2020|20-06-21:3,England/MILK-9589F6/2020|20-06-15:2)40:1,(England/BRIS-128441/2020|20-04-16:2,England/CAMB-7C39D/2020|20-04-13:3)41:1,(England/NORW-E8C37/2020|20-04-13:1,England/NORW-E75A6/2020|20-05-04:3)42:2,(Wales/PHWC-3122E/2020|20-04-10:1,Wales/PHWC-1645EC/2020|20-05-10:1)43:2,(England/ALDP-50085E/2020|20-06-27:5,England/PHEC-127E8/2020|20-03-28:0)44:1)31:1,(England/CAMB-75BD8/2020|20-03-29:1,UnitedKingdom/NORW-EB4F0/2020|LR822001.1|20-05-01:5)45:1,(England/ALDP-9ED9F6/2020|20-05-05:4,England/ALDP-944BD9/2020|20-06-07:2)46:2,(USA/MI-MDHHS-SC20612/2020|MT585039.1|20-04-29:1,USA/MI-MDHHS-SC20597/2020|MT585043.1|20-04-29:1)47:2,(USA/WA-S3017/2020|MW474188.1|20-08-15:3,USA/WA-S2852/2020|MW079820.1|20-09-01:2)48:8,(USA/WI-UW-26/2020|MT706147.1|20-03-24:1,USA/IL-QDX-2568/2020|MW191367.1|20-03-14:1)49:1,(USA/ID-QDX-1727/2020|MW190466.1|20-03-17:3,USA/UT-UPHL-201111720/2020|MW265609.1|20-04-30:2)50:1,(USA/IN-QDX-184/2020|MT786818.1|20-04-28:2,USA/WI-UW-558/2020|MT750137.1|20-06-25:0)51:1,(AUS/VIC2260/2020|MT972173.1|20-06-22:4,England/EXET-1358BE/2020|20-04-15:2)52:1,(((USA/FL-BPHL-0553/2020|MT834693.1|20-06-30:5,(USA/FL-BPHL-0540/2020|MT834625.1|20-03-21:2,(USA/COVID20-0537/2020|MT981422.1|20-06-04:1,USA/COVID20-1129/2020|MW067826.1|20-07-10:1)57:1)56:1)55:1,(CHL/Santiago-PUC_MVL_0112/2020|MW365482.1|20-04-02:2,(CHL/Santiago-PUC_MVL_0011/2020|MW365225.1|20-03-18:1,USA/WI-UW-269/2020|MT429191.1|20-04-06:2)59:2)58:1,(England/LEED-2A91D7/2020|20-04-06:3,England/LEED-2A87C7/2020|20-04-03:1)60:1)54:1,EGY/CUNCI-HGC5I033/2020|MT614347.1|20-06-02:1,((USA/CA-CZB-1434/2020|MT628140.1|20-03-25:0,USA/UT-UPHL-201016311/2020|MW181497.1|20-04-09:1)62:1,(USA/VA-DCLS-0676/2020|MT911804.1|20-04:0,USA/MI-QDX-476/2020|MW064508.1|20-03-23:0)63:1,(USA/WA-UW-4105/2020|MT358746.1|20-03-31:2,USA/WA-UW-2220/2020|MT345839.1|20-03-23:3)64:3,(USA/FL-BPHL-1565/2020|MW056116.1|20-09-10:7,USA/FL-BPHL-0510/2020|MT834668.1|20-06-10:4)65:1,(USA/MI-MDHHS-SC20574/2020|MT585034.1|20-04-29:2,USA/MI-MDHHS-SC20587/2020|MT585026.1|20-04-29:1)66:1,(England/CAMB-7A7DF/2020|20-04-02:1,Netherlands/NA_18/2020|LR878352.1|20-03-09:1)67:3,(USA/VA-DCLS-1557/2020|MW208010.1|20-08:1,USA/FL-BPHL-1018/2020|MT966219.1|20-07-17:1)68:2,(USA/CA-CZB-11119/2020|MW276517.1|20-05-29:3,USA/CA-CZB-11132/2020|MW276510.1|20-05-23:2)69:1,((Wales/PHWC-340A9/2020|20-04-20:4,Wales/PHWC-1667A8/2020|20-05-26:7)71:3,(England/CAMB-83FBD/2020|20-04-22:0,England/CAMB-1AD004/2020|20-04-30:1)72:3)70:1,((USA/FL-BPHL-1022/2020|MT966234.1|20-07-20:4,USA/FL-CDC-LC0001066/2020|MW634501.1|20-12-26:9)74:2,(England/PHEC-14F5D8/2020|20-12-29:9,((Scotland/EDB11343/2020|20-12-26:3,Scotland/EDB11342/2020|20-12-26:2)77:3,England/QEUH-CAF17D/2020|20-12-15:2)76:1)75:10)73:1,(England/LIVE-DAB556/2020|20-10-18:7,England/PHEC-14DE93/2020|20-11-11:5)78:7,(Wales/PHWC-1658A6/2020|20-05-19:3,Wales/PHWC-2E0A2/2020|20-04-10:1)79:2,(England/ALDP-952A53/2020|20-06-13:3,England/ALDP-95A745/2020|20-06-13:3)80:3,(Scotland/EDB3137/2020|20-04-06:2,Scotland/EDB2810/2020|20-03-30:2)81:2,(USA/CA-QDX-434/2020|MW064457.1|20-03-20:2,USA/UT-02231/2020|MT444626.1|20-04-15:5)82:2,(USA/WA-S2850/2020|MW079819.1|20-09-01:4,USA/WA-S2746/2020|MT947577.1|20-07-1'..b'A-S1246/2020|MT821587.1|20-05-11:4,USA/WA-S820/2020|MT641503.1|20-04-15:1)611:2)609:1,(England/CAMB-80B43/2020|20-04-11:2,England/CAMB-7666D/2020|20-03-29:2)612:1,(USA/WA-S2573/2020|MT831840.1|20-06-17:0,USA/WA-S2761/2020|MT947580.1|20-07-29:4)613:2,(England/ALDP-9BEB16/2020|20-09-09:1,England/ALDP-A95376/2020|20-10-19:4)614:8,(England/QEUH-A9F5D0/2020|20-10-20:5,England/QEUH-96AEF2/2020|20-08-15:2)615:2,(Scotland/CVR1557/2020|20-04-03:1,Wales/PHWC-34610/2020|20-04-21:1,(Netherlands/NA_436/2020|LR883367.1|20-04-07:1,Netherlands/Friesland_33/2020|LR883315.1|20-04-14:1)617:1)616:2,((England/CAMC-B36516/2020|20-11-05:1,England/CAMC-B362D3/2020|20-11-05:1)619:3,(England/MILK-B3A284/2020|20-11-01:1,England/CAMC-B365AD/2020|20-11-05:1)620:3)618:21,(BGD/BCSIR_NILMRC_104/2020|MT655948.1|20-06-07:1,BGD/BCSIR_NILMRC_133/2020|MT731733.1|20-06-18:2,(AUS/VIC3114/2020|MT972550.1|20-07-06:2,AUS/VIC9664/2020|MW156172.1|20-08-12:2)622:3,(AUS/VIC13094/2020|MW185501.1|20-07-31:1,(AUS/VIC9179/2020|MW153248.1|20-08-21:4,AUS/VIC11646/2020|MW155572.1|20-07-22:1)624:2)623:4)621:1,(England/CAMB-82060/2020|20-04-21:3,England/CAMB-82E1B/2020|20-04-14:1,(covid_hub_pl_ibch_0157|LR991987.1|20-05-19:3,Poland/1/2020|LR899030.1|20-05-20:5)626:4,(England/CAMC-947259/2020|20-07-21:0,England/MILK-9927C9/2020|20-08-27:6)627:8)625:1,(SAU/KFSHRC44/2020|MT820480.1|20-04-11:0,SAU/KAIMRC67/2020|MT820487.1|20-04-01:1)628:2,(Scotland/EDB300/2020|20-03-29:1,Scotland/CVR3194/2020|20-04-28:6)629:1,(England/CAMB-1AA438/2020|20-04-17:0,England/CAMB-1AFB7A/2020|20-05-02:3)630:3,(Wales/PHWC-48212D/2020|20-10-20:2,England/QEUH-9C80B0/2020|20-09-10:2)631:11,(England/MILK-9C4087/2020|20-09-09:1,England/QEUH-96F349/2020|20-08-17:4)632:4,(England/BIRM-5FC3B/2020|20-05-28:5,England/PHEC-13ADF/2020|20-03-13:0)633:2,(England/BIRM-6529A/2020|20-09-30:7,USA/WA-S2831/2020|MW077478.1|20-09-08:13)634:1,(England/NORT-282796/2020|20-03-28:2,England/NORT-2839AE/2020|20-04-01:2)635:1,(England/ALDP-951E49/2020|20-06-10:2,England/ALDP-9557A4/2020|20-06-12:2)636:5,(USA/CA-CZB-2205/2020|MW035956.1|20-05-27:3,USA/CA-CZB-2184/2020|MW035923.1|20-05-26:1)637:2,(IND/GBRC203a/2020|MT669321.1|20-06-07:4,USA/WA-S2809/2020|MW077484.1|20-08-31:10)638:1,(England/QEUH-96E025/2020|20-08-18:2,Scotland/QEUH-94375E/2020|20-08-02:1)639:9,(USA/CA-CZB-4099/2020|MW134393.1|20-08-15:6,USA/UT-UPHL-2009621/2020|MW206324.1|20-07-18:3)640:4,(England/CAMB-7C12A/2020|20-04-13:0,England/CAMB-83348/2020|20-04-15:0)641:5,(Switzerland/220001/2020|LR882220.1|20-07-24:5,England/BIRM-6BECD/2020|20-11-17:12)642:2,(England/CAMC-946506/2020|20-07-15:5,AUS/VIC2173/2020|MT972184.1|20-06-24:3)643:1,(USA/MS-CDC-6546/2020|MW279423.1|20-08-25:1,USA/TX-DSHS-1780/2020|MW425014.1|20-07-07:1)644:2,(England/ALDP-94A63C/2020|20-06-11:5,England/ALDP-52A636/2020|20-06-01:2)645:4,(England/SHEF-D1CE6/2020|20-04-28:4,England/SHEF-C0F96/2020|20-04-15:4)646:1,(England/QEUH-B10460/2020|20-11-02:3,Scotland/QEUH-96D5CD/2020|20-08-20:4)647:4,(ZW-6983|LR963462.1|20-05-01:1,ZW-6978|LR963455.1|20-05-01:1)648:5,(USA/GA-CDC-LC0013501/2021|MW643935.1|21-02-02:1,England/MILK-1169960/2021|21-01-25:8)649:11,(England/ALDP-952A44/2020|20-06-21:2,England/QEUH-9B4A22/2020|20-09-07:5)650:2,(Netherlands/NA_359/2020|LR883961.1|20-04-07:1,Netherlands/NA_589/2020|LR883868.1|20-04-05:2)651:2,(England/CAMB-1AE7FF/2020|20-04-29:1,England/CAMB-762D2/2020|20-03-28:4)652:3)427:1)426:2,(England/ALDP-BCA4B0/2020|20-11-23:0,England/ALDP-119985B/2021|21-01-27:3)653:11,(USA/WA-S1222/2020|MT821613.1|20-05-08:1,USA/WA-S1655/2020|MT834136.1|20-05-29:2,(Spain/R60/2020|LR884131.1|20-04-17:3,USA/CA-CZB-5682/2020|MW276261.1|20-07-23:4,(England/MILK-A06194/2020|20-10-01:2,England/CAMC-B32AA2/2020|20-11-05:4)656:7)655:3)654:7,(USA/FHCRC-19442/2020|MW593677.1|20-07-30:4,USA/CA-LACPHL-AE00022/2020|MW389622.1|20-07-07:3)657:1)28:1)27:1)26:1,(England/CAMB-7772D/2020|20-03-31:3,England/BRIS-12208F/2020|20-03-21:2,(Wales/PHWC-31CB7/2020|20-04-14:3,Wales/PHWC-26D2B/2020|20-03-30:2)659:1)658:3)25:1;\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_16_path_mutations.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_16_path_mutations.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1235 @@\n+sample_id\tpath_from_root\n+England/BRIS-1853249/2020|20-04-02\t (1) > C24034T (2) > C29518T\n+NPL/61-TW/2020|MT072688.1|20-01-13\t (1) > C24034T (2) > \n+Wales/PHWC-25B04/2020|20-03-24\t (1) > C875T (3) > A20637G\n+Wales/LIVE-A6831/2020|20-03-16\t (1) > C875T (3) > T14859C\n+Scotland/EDB1317/2020|20-04-09\t (1) > C7423T (4) > G4207A,T7423C\n+Scotland/EDB354/2020|20-03-30\t (1) > C7423T (4) > A29780C\n+England/SHEF-BFF8B/2020|20-03-25\t (1) > C20270T (5) > C1473T\n+England/SHEF-BFFC7/2020|20-03-25\t (1) > T4949C (8) > G28027T\n+England/PHEC-1E01E/2020|20-04-03\t (1) > T4949C (8) > C22445T\n+DP0476/2020|LC571003.1|20-02-16\t (1) > C29635T (9) > C29592T\n+DP0191/2020|LC570980.1|20-02-15\t (1) > C29635T (9) > A3854G\n+England/EXET-135818/2020|20-04-11\t (1) > C14805T,G26144T (10) > C7703T,T9352C,G27201T\n+England/LIVE-A5D06/2020|20-03-17\t (1) > A10982G (24) > C6681T,G11801A\n+England/LIVE-A065B/2020|20-05-27\t (1) > A10982G (24) > C823T,C8752T,A9741C,C19961T,C26333T,C26408T\n+USA/CA-CZB-1091/2020|MT460091.1|20-05-01\t (1) > A14940G (660) > C15024T\n+USA/CA-CZB-11876/2020|MW276506.1|20-04-08\t (1) > A14940G (660) > A26120G\n+Scotland/GCVR-171160/2020|20-03-26\t (1) > A1904G,C8090T,C10789T (661) > A3958G,C5826T,C17074T\n+England/BRIS-130E2A/2020|20-03-24\t (1) > A1904G,C8090T,C10789T (661) > C16658A,C17733T\n+USA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\t (1) > T514C (662) > C22033A\n+NED/NB02_13KS/2020|MT457397.1|20-04-29\t (1) > T514C (662) > G1607A,A10829G,G12795A,C17410T,A22920T\n+USA/CA-QDX-1986/2020|MW190732.1|20-03-18\t (1) > A12557G,C24904T,A27359G (663) > C11050T\n+USA/CA-CZB-1250/2020|MT534320.1|20-04-12\t (1) > A12557G,C24904T,A27359G (663) > C25916T,G29751T\n+USA/CA-CZB-1015/2020|MT438733.1|20-04-22\t (1) > C25692T (664) > T15867A\n+USA/CA-CZB-1073/2020|MT449664.1|20-04-21\t (1) > C25692T (664) > G10617A,G22225T\n+England/BRIS-1258A2/2020|20-03-29\t (1) > G29032A (665) > C6696T,C9096T,C29754T\n+England/SHEF-BFEBB/2020|20-03-24\t (1) > G29032A (665) > C11747T,T24364G\n+USA/CA-CZB-1041/2020|MT438759.1|20-04-22\t (1) > C10277T (666) > A6313G,T7191C,A7193G\n+USA/CA-CZB-1051/2020|MT449644.1|20-04-06\t (1) > C10277T (666) > G7273A\n+USA/CA-QDX-33/2020|MT614459.1|20-03-15\t (1) > C6312A,C13730T,C23929T,C28311T (674) > C66T\n+USA/DC-HP00063/2020|MT646075.1|20-03-13\t (1) > C6312A,C13730T,C23929T,C28311T (674) > C11455T\n+HKG/HKU-904a/2020|MT365032.1|20-01-30\t (1) > C8782T,T28144C (676) > C4158T,C18828T\n+England/LIVE-9E66F/2020|20-04-10\t (1) > C6696T (698) > C7765T,G10256T\n+Scotland/CVR705/2020|20-03-26\t (1) > C6696T (698) > C11001T,G17122T\n+England/PHEC-1A601/2020|20-03-04\t (1) > G1397A,T28688C,G29742T (699) > A19526G\n+England/PHEC-2275E/2020|20-06-22\t (1) > G1397A,T28688C,G29742T (699) > G2246A,C5512T,C20132T,A23586G,C26822T,T27384C,T27484C,G28975T,G29639T\n+England/LIVE-A4C46/2020|20-03-12\t (1) > C20270T (5) > A29683T (6) > G431A,G26754A,C28725T\n+Scotland/EDB046/2020|20-03-15\t (1) > C14805T,G26144T (10) > T17247C (11) > C9996T,T26144G\n+England/BRIS-12EEB6/2020|20-04-22\t (1) > C14805T,G26144T (10) > G28842T (18) > C15240T,C18086T,T23031C\n+Scotland/EDB199/2020|20-03-26\t (1) > C14805T,G26144T (10) > G28842T (18) > C22713T,G26031T\n+England/CAMB-74A09/2020|20-03-18\t (1) > C14805T,G26144T (10) > C23707T (19) > G6981T,G10112T,G22785T\n+England/ALDP-9EE3AC/2020|20-05-06\t (1) > C14805T,G26144T (10) > C23707T (19) > G20991T\n+England/CAMB-8042A/2020|20-04-10\t (1) > C14805T,G26144T (10) > A2480G,C2558T (20) > A4015T\n+England/CAMB-737B8/2020|20-03-30\t (1) > C14805T,G26144T (10) > A2480G,C2558T (20) > G3971T,G28380T\n+USA/WA-S885/2020|MT642386.1|20-04-22\t (1) > C14805T,G26144T (10) > A4236G,T25655C (21) > G7739T,C25904T\n+USA/UT-QDX-1870/2020|MW190618.1|20-03-16\t (1) > C14805T,G26144T (10) > A4236G,T25655C (21) > A5269G,C9943T\n+USA/WA3-UW1/2020|MT163716.1|20-02-27\t (1) > C14805T,G26144T (10) > G5572T (22) > T2446C,C3411T\n+SouthKorea/KOR-BA-ACH_2719/2020|MT304476.1|20-02-29\t (1) > C14805T,G26144T (10) > G5572T (22) > C28311T\n+England/BRIS-1265AA/2020|20-04-10\t (1) > C14805T,G26144T (1'..b'68G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > G25494T (323) > C25386T (324) > C21302T,C21304A,C26256T,C27119T,C28453T\n+Wales/PHWC-47F3A5/2020|20-10-07\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > G25494T (323) > G28817T (325) > T9655C,G28198T\n+England/ALDP-A85BCC/2020|20-10-17\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > G25494T (323) > G28817T (325) > T209C,T11857C\n+England/ALDP-A2FCA3/2020|20-10-05\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C20451T,G21770A (326) > T7919G (327) > C24734T\n+Scotland/MILK-A69E6B/2020|20-10-09\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C20451T,G21770A (326) > T7919G (327) > A28483G,A28877G\n+England/MILK-A7D1A7/2020|20-10-13\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C20451T,G21770A (326) > G18583A (328) > T4579A,T27835C\n+England/MILK-A91486/2020|20-10-16\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C20451T,G21770A (326) > G18583A (328) > G2272T,G20679T,G24586T\n+AUT/2021006354/2021|MW672357.1|21-02\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C829T,C14697T,C18176T,G19398T,G28083T,G28975T (333) > C878T,C12374T,C20384T,C21639T,C29367T\n+England/MILK-E7F4C6/2021|21-01-02\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C829T,C14697T,C18176T,G19398T,G28083T,G28975T (333) > T9070C,C10296T\n+England/ALDP-AA169C/2020|20-10-22\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > G25218T (331) > C23191T,G23909A\n+England/MILK-A474DA/2020|20-10-06\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > G25218T (331) > A6659G\n+England/ALDP-B483EA/2020|20-11-07\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > T8110C (332) > C10039A,T18402C,C29738T\n+England/QEUH-AA0035/2020|20-10-20\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > T8110C (332) > G11417T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_16_sample_names.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_16_sample_names.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1234 @@\n+England/BRIS-1853249/2020|20-04-02\n+NPL/61-TW/2020|MT072688.1|20-01-13\n+Wales/PHWC-25B04/2020|20-03-24\n+Wales/LIVE-A6831/2020|20-03-16\n+Scotland/EDB1317/2020|20-04-09\n+Scotland/EDB354/2020|20-03-30\n+England/SHEF-BFF8B/2020|20-03-25\n+England/SHEF-BFFC7/2020|20-03-25\n+England/PHEC-1E01E/2020|20-04-03\n+DP0476/2020|LC571003.1|20-02-16\n+DP0191/2020|LC570980.1|20-02-15\n+England/EXET-135818/2020|20-04-11\n+England/LIVE-A5D06/2020|20-03-17\n+England/LIVE-A065B/2020|20-05-27\n+USA/CA-CZB-1091/2020|MT460091.1|20-05-01\n+USA/CA-CZB-11876/2020|MW276506.1|20-04-08\n+Scotland/GCVR-171160/2020|20-03-26\n+England/BRIS-130E2A/2020|20-03-24\n+USA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\n+NED/NB02_13KS/2020|MT457397.1|20-04-29\n+USA/CA-QDX-1986/2020|MW190732.1|20-03-18\n+USA/CA-CZB-1250/2020|MT534320.1|20-04-12\n+USA/CA-CZB-1015/2020|MT438733.1|20-04-22\n+USA/CA-CZB-1073/2020|MT449664.1|20-04-21\n+England/BRIS-1258A2/2020|20-03-29\n+England/SHEF-BFEBB/2020|20-03-24\n+USA/CA-CZB-1041/2020|MT438759.1|20-04-22\n+USA/CA-CZB-1051/2020|MT449644.1|20-04-06\n+USA/CA-QDX-33/2020|MT614459.1|20-03-15\n+USA/DC-HP00063/2020|MT646075.1|20-03-13\n+HKG/HKU-904a/2020|MT365032.1|20-01-30\n+England/LIVE-9E66F/2020|20-04-10\n+Scotland/CVR705/2020|20-03-26\n+England/PHEC-1A601/2020|20-03-04\n+England/PHEC-2275E/2020|20-06-22\n+England/LIVE-A4C46/2020|20-03-12\n+Scotland/EDB046/2020|20-03-15\n+England/BRIS-12EEB6/2020|20-04-22\n+Scotland/EDB199/2020|20-03-26\n+England/CAMB-74A09/2020|20-03-18\n+England/ALDP-9EE3AC/2020|20-05-06\n+England/CAMB-8042A/2020|20-04-10\n+England/CAMB-737B8/2020|20-03-30\n+USA/WA-S885/2020|MT642386.1|20-04-22\n+USA/UT-QDX-1870/2020|MW190618.1|20-03-16\n+USA/WA3-UW1/2020|MT163716.1|20-02-27\n+SouthKorea/KOR-BA-ACH_2719/2020|MT304476.1|20-02-29\n+England/BRIS-1265AA/2020|20-04-10\n+AUS/NT38/2020|MT641726.1|20\n+France/40002VJ/2020|MT470179.1|20-03\n+England/CAMB-7772D/2020|20-03-31\n+England/BRIS-12208F/2020|20-03-21\n+England/ALDP-52C0FA/2020|20-06-01\n+England/LIVE-9D7D6/2020|20-04-15\n+USA/WI-UW-298/2020|MT706406.1|20-04-13\n+USA/WI-UW-314/2020|MT706422.1|20-04-16\n+USA/WI-UW-325/2020|MT706432.1|20-04-24\n+USA/WI-UW-290/2020|MT706398.1|20-04-08\n+Scotland/CVR3488/2020|20-05-12\n+Scotland/CVR780/2020|20-03-27\n+Japan/TKYE63557_2020/2020|LC581365.1|20-03\n+Japan/TKYE64688_2020/2020|LC581375.1|20-03\n+MYS/188407/2020|MT372480.1|20-03-18\n+AUS/VIC961/2020|MT451653.1|20-03-27\n+USA/MN-MDH-1475/2020|MT920008.1|20-03-23\n+USA/CA-CZB-1615/2020|MT628267.1|20-04-14\n+USA/FL-BPHL-0393/2020|MT757005.1|20-03-17\n+USA/COVID20-0008/2020|MT764174.1|20-03-10\n+USA/IL-CDC-IL2/2020|MT044257.1|20-01-28\n+USA/CA-QDX-1421/2020|MW065371.1|20-03-18\n+USA/CA-QDX-2080/2020|MW190832.1|20-03-19\n+AUS/VIC1255/2020|MT451830.1|20-04-11\n+AUS/VIC1878/2020|MT745600.1|20-03-29\n+England/LCST-24D7202/2020|20-06-22\n+England/SHEF-BFF21/2020|20-03-25\n+Switzerland/100159/2020|LR884273.1|20-03-16\n+England/LOND-126031F/2020|20-03-15\n+USA/NY-QDX-1999/2020|MW190795.1|20-03-16\n+USA/NY-QDX-1969/2020|MW190709.1|20-03-15\n+Wales/PHWC-285F4/2020|20-04-01\n+England/BRIS-130965/2020|20-04-13\n+Scotland/CVR44/2020|20-03-13\n+Scotland/CVR839/2020|20-03-27\n+Scotland/GCVR-170107/2020|20-03-23\n+Scotland/CVR207/2020|20-03-18\n+England/NORT-284A9B/2020|20-03-25\n+Scotland/CVR10/2020|20-03-10\n+Wales/PHWC-310CA/2020|20-04-11\n+Wales/PHWC-31CB7/2020|20-04-14\n+Wales/PHWC-26D2B/2020|20-03-30\n+Spain/H12_46/2020|LR884009.1|20-04-08\n+Spain/R11/2020|LR884126.1|20-03-06\n+Spain/LP19_4952/2020|LR884066.1|20-03-07\n+Spain/R10_33/2020|LR884127.1|20-03-02\n+EGY/CUNCI-HGC9I036/2020|MW504609.1|20-12-25\n+EGY/CUNCI-HGC12I049/2021|MW595907.1|21-01-03\n+England/CAMC-C91F38/2020|20-12-11\n+SLE/KGH-G-8626/2020|MT872492.1|20-04-10\n+Scotland/EDB5629/2020|20-03-24\n+Scotland/EDB5040/2020|20-04-02\n+Scotland/EDB1824/2020|20-04-16\n+England/ALDP-CB55B4/2020|20-12-20\n+England/CAMC-CF4B5D/2020|20-12-21\n+USA/WI-UW-06/2020|MT772088.1|20-03-21\n+USA/MI-MDHHS-SC20124/2020|MT439284.1|20-03-24\n+GHA/34927_S20/2020|MT890226.1|20-05-23\n+GHA/35563_S37/2020|MT890230.1|20-05-24\n+GHA/WACCBIP_n'..b'90280/2021|MW667214.1|21-01-27\n+USA/NY-CDC-21712201/2021|MW668883.1|21-02-04\n+England/CAMB-72B44/2020|20-03-22\n+England/CAMB-822D3/2020|20-04-12\n+England/ALDP-94DD07/2020|20-06-19\n+England/ALDP-49EC3C/2020|20-05-20\n+PER/covper024/2020|MW030255.1|20-07-04\n+PER/CoV-19_HRL-223/2020|MW185824.1|20-04-08\n+PER/covper011/2020|MW030242.1|20-07-04\n+PER/covper040/2020|MW030271.1|20-05-05\n+England/MILK-B1553B/2020|20-10-23\n+England/MILK-66F889/2020|20-07-03\n+USA/CO-CDC-STM-000008403/2021|MW617544.1|21-01-31\n+England/LOND-12F65DC/2021|21-01-19\n+Switzerland/310500/2020|LR898805.1|20-10-08\n+Switzerland/300433/2020|LR898634.1|20-09-29\n+England/QEUH-96BAA2/2020|20-08-14\n+Wales/ALDP-B19FFD/2020|20-11-01\n+SRB/NS19622-16-06/2020|MW327528.1|20-06-15\n+PER/covper018/2020|MW030249.1|20-07-03\n+EGY/CUNCI-HGC5I001/2020|MT611527.1|20-06-02\n+EGY/CUNCI-HGC5I011/2020|MT611536.1|20-06-02\n+England/MILK-9A699F/2020|20-09-01\n+England/CAMC-C3E586/2020|20-12-10\n+England/CAMC-DE5550/2020|20-12-29\n+England/ALDP-A525BB/2020|20-10-07\n+ISR/NH_M2_0614/2020|MW194121.1|20-06-14\n+England/MILK-A45AF8/2020|20-10-06\n+Scotland/QEUH-A613BF/2020|20-10-13\n+Switzerland/180039/2020|LR861669.1|20-07-01\n+Switzerland/220022/2020|LR882244.1|20-07-27\n+Japan/TKYE627000_2020/2020|LC593811.1|20-08\n+Japan/TKYE624705_2020/2020|LC593810.1|20-07\n+IND/GBRC455b/2020|MW600453.1|20-12-24\n+IND/GBRC455a/2020|MW600436.1|20-12-24\n+BRA/LRV-SARS.CoV-2.1/2020|MT807936.1|20-05-08\n+USA/WI-UW-114/2020|MT706234.1|20-03-30\n+England/CAMC-947392/2020|20-07-18\n+England/MILK-977469/2020|20-07-24\n+AUS/VIC9179/2020|MW153248.1|20-08-21\n+AUS/VIC11646/2020|MW155572.1|20-07-22\n+Scotland/EDB11343/2020|20-12-26\n+Scotland/EDB11342/2020|20-12-26\n+USA/CA-LACPHL-AF00169/2021|MW485829.1|21-01-08\n+USA/CA-LACPHL-AF00029/2020|MW424876.1|20-12-20\n+England/CAMC-A65DDB/2020|20-10-11\n+England/CAMC-AAF5A0/2020|20-10-22\n+England/MILK-A192C8/2020|20-10-01\n+England/QEUH-9F3FDD/2020|20-09-24\n+England/MILK-ABBF2B/2020|20-10-22\n+England/QEUH-96A85E/2020|20-08-14\n+HongKong/Homo-sapiens/HKG/Case5132/2020|MW181761.1|20-10-06\n+HongKong/Homo-sapiens/HKG/Case5126/2020|MW181753.1|20-10-06\n+England/PHEC-149F0D/2020|20-11-19\n+England/MILK-BE717A/2020|20-11-29\n+CAN/COVID_CRCHUM_Pre_Freeze_6/2020|MW309430.1|20-09-04\n+Scotland/QEUH-BEAF22/2020|20-12-04\n+England/MILK-A230C1/2020|20-10-03\n+Scotland/QEUH-9696CE/2020|20-08-14\n+England/CAMC-B3582D/2020|20-11-05\n+England/MILK-A796E8/2020|20-10-14\n+Northern_Ireland/QEUH-969C53/2020|20-08-14\n+England/ALDP-9E79B0/2020|20-09-24\n+England/MILK-B561FE/2020|20-11-06\n+England/CAMC-9DFBC4/2020|20-09-21\n+England/QEUH-AD1165/2020|20-10-25\n+England/ALDP-FB5E3E/2021|21-01-11\n+England/ALDP-E8756E/2021|21-01-04\n+England/ALDP-A2EAE6/2020|20-10-05\n+Scotland/QEUH-A636C3/2020|20-10-10\n+England/QEUH-A76C07/2020|20-10-12\n+England/MILK-AC7997/2020|20-10-21\n+Scotland/QEUH-9DC927/2020|20-09-22\n+Scotland/QEUH-9B75D3/2020|20-09-04\n+England/CAMC-AEACFF/2020|20-10-25\n+USA/FL-BPHL-2014/2020|MW286586.1|20-06-19\n+USA/MA_MGH_00693/2020|MT520290.1|20-04-06\n+CHL/Santiago-PUC_MVL_0491/2020|MW365473.1|20-05-13\n+CHL/Puerto_Montt-PUC_MVL_0534/2020|MW365467.1|20-05-27\n+ARG/Cordoba-2858/2020|MW633904.1|20-09-14\n+ARG/Cordoba-1484/2020|MW633909.1|20-09-17\n+England/MILK-97356A/2020|20-08-14\n+England/MILK-9A9F7C/2020|20-08-31\n+England/OXON-F42364/2020|20-12-18\n+England/MILK-9C2766/2020|20-09-10\n+England/ALDP-A95A9F/2020|20-10-19\n+England/PHEC-149FA3/2020|20-11-20\n+England/QEUH-C9332B/2020|20-12-17\n+England/CAMC-A649C9/2020|20-10-10\n+England/MILK-B04890/2020|20-10-24\n+England/CAMC-A57F03/2020|20-10-09\n+England/MILK-A7D15C/2020|20-10-13\n+Wales/PHWC-47F3A5/2020|20-10-07\n+England/ALDP-A85BCC/2020|20-10-17\n+England/ALDP-A2FCA3/2020|20-10-05\n+Scotland/MILK-A69E6B/2020|20-10-09\n+England/MILK-A7D1A7/2020|20-10-13\n+England/MILK-A91486/2020|20-10-16\n+AUT/2021006354/2021|MW672357.1|21-02\n+England/MILK-E7F4C6/2021|21-01-02\n+England/ALDP-AA169C/2020|20-10-22\n+England/MILK-A474DA/2020|20-10-06\n+England/ALDP-B483EA/2020|20-11-07\n+England/QEUH-AA0035/2020|20-10-20\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_17_all_paths.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_17_all_paths.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1935 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4-02\tC593T\n+Scotland/EDB1824/2020|20-04-16\tC8240T,T8941C,C9438T,C19185T,G27358T\n+Spain/H12_46/2020|LR884009.1|20-04-08\tC7967T,C16694T\n+680\tC3037T,A20268G\n+Spain/R11/2020|LR884126.1|20-03-06\tT3037C\n+Spain/LP19_4952/2020|LR884066.1|20-03-07\t\n+HKG/HKU-904a/2020|MT365032.1|20-01-30\tC4158T,C18828T\n+681\tA17858G,C18060T\n+USA/MN-MDH-1475/2020|MT920008.1|20-03-23\tA7966G,A22422G\n+USA/CA-CZB-1615/2020|MT628267.1|20-04-14\tC4776T,C9491T,C17747T,G28086T\n+682\tT9477A,C14805T,G25979T\n+USA/FL-BPHL-0393/2020|MT757005.1|20-03-17\t\n+683\tC28863T\n+Spain/R10_33/2020|LR884127.1|20-03-02\tT25979G\n+684\tC28657T\n+685\tC4540T\n+686\tC25714T,C26029A\n+Scotland/CVR3062/2020|20-04-24\tG805A,C5673T,C11960T,C27567T\n+Scotland/CVR2435/2020|20-04-14\tC15274T\n+687\tC28311T\n+England/OXON-B0922/2020|20-03-28\tC147A,G6894T,C18928T,A21489C\n+AUS/VIC995/2020|MT451680.1|20-03-31\tG17632A\n+688\tC275T,C1567T,C4543T,A5234G,A5488G,C10029T,G10105T,C11005A,C12815T,C16466T,T16857C,T18417C,A22525G,T22917G,A23403G,G24697A,C25613T,C26681T,A28272T,G28975T,C29421T\n+USA/WA-S4100/2021|MW555971.1|21-01-18\tG5234A,C12890T,C19944T\n+USA/WA-S4074/2021|MW555949.1|21-01-19\tC3165T,T10105G,C11563T,G22525A,G25311T,C27630T\n+689\tG22468T,G28878A,G29742A\n+690\tT22468G\n+691\tC4573T,C10747T,G11230T,G11266T,G11521T,C16575T,C17745T,C22000T,C22033A,G23401T,C23604G,T24097C,G28167A,G28378C\n+England/ALDP-CB55B4/2020|20-12-20\tC4940T,G21867T,C29523T\n+England/CAMC-CF4B5D/2020|20-12-21\tG529A,A963G,G2246A,A5068G,C12525T,G21255C,T23698A,G28881A\n+692\tG16381A,T17877C,G25500T\n+USA/WI-UW-06/2020|MT772088.1|20-03-21\tC1929T,C20316T\n+USA/MI-MDHHS-SC20124/2020|MT439284.1|20-03-24\tC25854T\n+693\tC24370T\n+GHA/34927_S20/2020|MT890226.1|20-05-23\tC27641T,G29402T\n+GHA/35563_S37/2020|MT890230.1|20-05-24\tC2306T,C5672T,C5986T,C13515T,G24926T\n+694\tT1885A,C5907T,C10138T,G11417T,C11824T,C18129T,G18181A,T20100C,T21982C,G22132T,T22917G,G23402A,G25687T,G26062T,C29686T\n+GHA/WACCBIP_nCoV_GS115/2021|MW571124.1|21-01-07\tC1385T,A1395G,A9750G,A26069G\n+USA/GA-CDC-LC0010641/2021|MW640882.1|21-01-26\tA4984T,A7854G,A21062G,A28254C\n+695\tA481G,G521T,C2197T,G10850A,C12469T,C16391T,G17014T,A23064C,C23525T,C25904T,C27294T,A27489G,A28272T,C28377T\n+EGY/CUNCI-HGC9I036/2020|MW504609.1|20-12-25\tG16236A,C16694T,G21624A,A21625C,C22097T,G29773T\n+EGY/CUNCI-HGC12I049/2021|MW595907.1|21-01-03\tC6541T,C9988T,T25904C\n+696\tG9802A,G11230T,A16512G,C19951T,G26428T\n+England/CAMC-C91F38/2020|20-12-11\tC4438T,G6446T,C6638T,C10834T,C12469T,C16466T,C16726T,G17140T,G21210C,T22287C,G23402A,C26299T,T27134C,A28273T,G29227A\n+SLE/KGH-G-8626/2020|MT872492.1|20-04-10\tC10818T,T11230G,C25702T\n+697\tT490A,C3177T,C24034T,T26729C,G28077C\n+USA/COVID20-0008/2020|MT764174.1|20-03-10\tT18736C\n+USA/IL-CDC-IL2/2020|MT044257.1|20-01-28\t\n+698\tC6696T\n+England/LIVE-9E66F/2020|20-04-10\tC7765T,G10256T\n+Scotland/CVR705/2020|20-03-26\tC11001T,G17122T\n+699\tG1397A,T28688C,G29742T\n+England/PHEC-1A601/2020|20-03-04\tA19526G\n+England/PHEC-2275E/2020|20-06-22\tG2246A,C5512T,C20132T,A23586G,C26822T,T27384C,T27484C,G28975T,G29639T\n+700\tA1079C,C9319T,C19862T,T27384C\n+USA/CA-QDX-1421/2020|MW065371.1|20-03-18\tC7764T,C29625T\n+USA/CA-QDX-2080/2020|MW190832.1|20-03-19\tC6701T,T7225C\n+701\tC1076T\n+AUS/VIC1255/2020|MT451830.1|20-04-11\tT13857C,C25469T,C27964T\n+AUS/VIC1878/2020|MT745600.1|20-03-29\tA28955T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_17_path_clades.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_17_path_clades.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,623 @@\n+clade\troot_id\tfrom_tree_root\n+19A\t1\t\n+B\t1\t\n+B.26\t4\t > C7423T\n+B.48\t5\t > C20270T\n+B.15\t8\t > T4949C\n+B.5\t9\t > C29635T\n+B.54\t10\t > C14805T,G26144T\n+B.47\t24\t > A10982G\n+B.20\t660\t > A14940G\n+B.52\t661\t > A1904G,C8090T,C10789T\n+B.11\t662\t > T514C\n+B.46\t663\t > A12557G,C24904T,A27359G\n+B.1.14\t664\t > C25692T\n+B.27\t665\t > G29032A\n+B.19\t666\t > C10277T\n+B.6\t674\t > C6312A,C13730T,C23929T,C28311T\n+19B\t676\t > C8782T,T28144C\n+A\t676\t > C8782T,T28144C\n+B.10\t698\t > C6696T\n+B.4\t699\t > G1397A,T28688C,G29742T\n+B.23\t6\t > C20270T > A29683T\n+B.33\t11\t > C14805T,G26144T > T17247C\n+B.28\t18\t > C14805T,G26144T > G28842T\n+B.29\t19\t > C14805T,G26144T > C23707T\n+B.40\t20\t > C14805T,G26144T > A2480G,C2558T\n+B.30\t21\t > C14805T,G26144T > A4236G,T25655C\n+B.41\t22\t > C14805T,G26144T > G5572T\n+B.31\t23\t > C14805T,G26144T > G13627T,C15540T,A28338G\n+B.1\t26\t > C241T > C14408T\n+B.3\t658\t > C241T > T241C,G1440A,G2891A\n+B.18\t668\t > G29711T > C1218T,G27806T\n+B.13\t669\t > G29711T > A4838G,C7420T,C14937T,C20148T\n+B.51\t670\t > G29711T > T2116A\n+B.45\t672\t > C28854T > C12710T\n+B.12\t673\t > C28854T > C11752T,C25665T,A27700G,T28854C,T28912C\n+B.6.6\t675\t > C6312A,C13730T,C23929T,C28311T > C6310A,C19524T\n+A.1\t681\t > C8782T,T28144C > A17858G,C18060T\n+A.2\t682\t > C8782T,T28144C > T9477A,C14805T,G25979T\n+A.3\t697\t > C8782T,T28144C > T490A,C3177T,C24034T,T26729C,G28077C\n+B.4.4\t700\t > G1397A,T28688C,G29742T > A1079C,C9319T,C19862T,T27384C\n+B.4.5\t701\t > G1397A,T28688C,G29742T > C1076T\n+B.37\t13\t > C14805T,G26144T > T17247C > C8078T\n+B.35\t14\t > C14805T,G26144T > T17247C > A7479G,C25572T\n+B.32\t15\t > C14805T,G26144T > T17247C > A1587G\n+B.34\t16\t > C14805T,G26144T > T17247C > C988T\n+B.39\t17\t > C14805T,G26144T > T17247C > A1515G,C9223T\n+B.3.1\t659\t > C241T > T241C,G1440A,G2891A > G28851T\n+A.5\t678\t > C8782T,T28144C > A23403G,C26088T > G23403A\n+A.10\t680\t > C8782T,T28144C > A23403G,C26088T > C3037T,A20268G\n+A.28\t695\t > C8782T,T28144C > G22468T,G28878A,G29742A > A481G,G521T,C2197T,G10850A,C12469T,C16391T,G17014T,A23064C,C23525T,C25904T,C27294T,A27489G,A28272T,C28377T\n+A.12\t696\t > C8782T,T28144C > G22468T,G28878A,G29742A > G9802A,G11230T,A16512G,C19951T,G26428T\n+20A\t28\t > C241T > C14408T > A23403G > C3037T\n+B.1.108\t28\t > C241T > C14408T > A23403G > C3037T\n+A.23.1\t691\t > C8782T,T28144C > G22468T,G28878A,G29742A > T22468G > C4573T,C10747T,G11230T,G11266T,G11521T,C16575T,C17745T,C22000T,C22033A,G23401T,C23604G,T24097C,G28167A,G28378C\n+A.4\t692\t > C8782T,T28144C > G22468T,G28878A,G29742A > T22468G > G16381A,T17877C,G25500T\n+A.11\t693\t > C8782T,T28144C > G22468T,G28878A,G29742A > T22468G > C24370T\n+A.21\t694\t > C8782T,T28144C > G22468T,G28878A,G29742A > T22468G > T1885A,C5907T,C10138T,G11417T,C11824T,C18129T,G18181A,T20100C,T21982C,G22132T,T22917G,G23402A,G25687T,G26062T,C29686T\n+B.1.105\t45\t > C241T > C14408T > A23403G > C3037T > G28514T\n+B.1.152\t46\t > C241T > C14408T > A23403G > C3037T > G1914A,T16456C\n+B.1.103\t47\t > C241T > C14408T > A23403G > C3037T > C25665T,G28325T\n+B.1.188\t48\t > C241T > C14408T > A23403G > C3037T > C3487T,C11308T,T15264C,C16332T,C19170T,C25791T,C28854T,C29614T\n+B.1.378\t49\t > C241T > C14408T > A23403G > C3037T > G3871T\n+B.1.199\t50\t > C241T > C14408T > A23403G > C3037T > C2939T\n+B.1.139\t51\t > C241T > C14408T > A23403G > C3037T > A696C\n+B.1.91\t52\t > C241T > C14408T > A23403G > C3037T > G24077T\n+B.1.350\t53\t > C241T > C14408T > A23403G > C3037T > G25563T\n+B.1.216\t267\t > C241T > C14408T > A23403G > C3037T > T3011C,G22205T,T27869C,T28853G\n+B.1.221\t268\t > C241T > C14408T > A23403G > C3037T > C3602T,C6941T,C15324T,C21855T,A25505G,G25906C,G25996T,C28651T,C28869T\n+B.1.525\t272\t > C241T > C14408T > A23403G > C3037T > C1498T,G2659A,C6285T,T8593C,C14407T,C18171T,A20724G,A21717G,C21762T,G23012A,G23593C,T24224C,C24748T,C26305T,T26767C,C28308G,A28699G,C28887T,G29543T\n+B.1.222\t273\t > C241T > C14408T > A23403G > C3037T > C1545T,C22879A\n+B.1.379\t274\t > C241T > C14408T > A23403G > C3037T > A11782G,G22203T\n+B.1.182\t275\t > C241T > C14408T > A23403G > C3037T > A20268G\n+B.1.5\t341\t > C241T > C14408T > A2'..b'3037T > G25563T > C18877T > C26735T > C22444T,C28854T > C2836T,G21724T > G61T,C913T,C1541T,C11259T,C25000T,G26144A,G26849T,C29358T\n+20A.EU2\t240\t > C241T > C14408T > A23403G > C3037T > G25563T > C18877T > C26735T > C4543T,G9526T,C11497T,G15766T,A16889G,G17019T,G22992A,C25710T,T26876C,G28975C,G29399A > G13993T > G5629T\n+B.1.258.14\t334\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > C27800A > G18186T,C28854T\n+B.1.258.2\t336\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > G1464A,A10978T,T20799C > G5572T,G28375T\n+B.1.258.3\t338\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > G1464A,A10978T,T20799C > G18803T\n+B.1.177.6\t370\t > C241T > C14408T > A23403G > C3037T > T445C,C6286T,G21255C,C22227T,C28932T,G29645T > C26801G > C27944T > G204T > C21614T > C6317T\n+B.1.177.12\t371\t > C241T > C14408T > A23403G > C3037T > T445C,C6286T,G21255C,C22227T,C28932T,G29645T > C26801G > C27944T > G204T > C21614T > G17944T,C24334T,T24814C,C27769T\n+B.1.177.5\t372\t > C241T > C14408T > A23403G > C3037T > T445C,C6286T,G21255C,C22227T,C28932T,G29645T > C26801G > C27944T > G204T > C21614T > T24769C,C25460T\n+B.1.177.7\t373\t > C241T > C14408T > A23403G > C3037T > T445C,C6286T,G21255C,C22227T,C28932T,G29645T > C26801G > C27944T > G204T > C21614T > C15480T\n+B.1.177.8\t374\t > C241T > C14408T > A23403G > C3037T > T445C,C6286T,G21255C,C22227T,C28932T,G29645T > C26801G > C27944T > G204T > C21614T > G8179T\n+N.1\t545\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > T29148C > G25793T,T27299C > T25793G > C25916T,C29769T\n+N.4\t546\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > T29148C > G25793T,T27299C > T25793G > A2475G\n+N.3\t547\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > T29148C > G25793T,T27299C > T25793G > G26416T\n+B.1.258.16\t321\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > C27800A > C7844T,T24925C,C27920T > C4893T,C29762T\n+G.1\t337\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > G1464A,A10978T,T20799C > G5572T,G28375T > G2072A,C27294T\n+M.1\t517\t > C241T > C14408T > A23403G > C3037T > G28882A,G28883C > G28881A > C3373A,C15960T > T15960C > G1820A,C6883T,G21724A,G28003C > C12249T > G3431T,T25577C,C25626T,C27002T\n+B.1.160.7\t242\t > C241T > C14408T > A23403G > C3037T > G25563T > C18877T > C26735T > C4543T,G9526T,C11497T,G15766T,A16889G,G17019T,G22992A,C25710T,T26876C,G28975C,G29399A > G13993T > G5629T > > C556T,C23525T\n+B.1.258.6\t324\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > C27800A > G12988T,G15598A,G18028T,T24910C,T26972C > G25494T > C25386T\n+B.1.258.7\t325\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > C27800A > G12988T,G15598A,G18028T,T24910C,T26972C > G25494T > G28817T\n+B.1.258.10\t327\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > C27800A > G12988T,G15598A,G18028T,T24910C,T26972C > C20451T,G21770A > T7919G\n+B.1.258.12\t328\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > C27800A > G12988T,G15598A,G18028T,T24910C,T26972C > C20451T,G21770A > G18583A\n+B.1.258.17\t333\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > C27800A > G12988T,G15598A,G18028T,T24910C,T26972C > C16394T,C22127T,G23876A,G25947T > C829T,C14697T,C18176T,G19398T,G28083T,G28975T\n+B.1.258.4\t331\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > C27800A > G12988T,G15598A,G18028T,T24910C,T26972C > C16394T,C22127T,G23876A,G25947T > C29274T > G25218T\n+B.1.258.5\t332\t > C241T > C14408T > A23403G > C3037T > A20268G > G29734C > C17104T > T7767C,C8047T,C22879A > C27800A > G12988T,G15598A,G18028T,T24910C,T26972C > C16394T,C22127T,G23876A,G25947T > C29274T > T8110C\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_17_path_mutations.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_17_path_mutations.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1235 @@\n+sample_id\tpath_from_root\n+England/BRIS-1853249/2020|20-04-02\t (1) > C24034T (2) > C29518T\n+NPL/61-TW/2020|MT072688.1|20-01-13\t (1) > C24034T (2) > \n+Wales/PHWC-25B04/2020|20-03-24\t (1) > C875T (3) > A20637G\n+Wales/LIVE-A6831/2020|20-03-16\t (1) > C875T (3) > T14859C\n+Scotland/EDB1317/2020|20-04-09\t (1) > C7423T (4) > G4207A,T7423C\n+Scotland/EDB354/2020|20-03-30\t (1) > C7423T (4) > A29780C\n+England/SHEF-BFF8B/2020|20-03-25\t (1) > C20270T (5) > C1473T\n+England/SHEF-BFFC7/2020|20-03-25\t (1) > T4949C (8) > G28027T\n+England/PHEC-1E01E/2020|20-04-03\t (1) > T4949C (8) > C22445T\n+DP0476/2020|LC571003.1|20-02-16\t (1) > C29635T (9) > C29592T\n+DP0191/2020|LC570980.1|20-02-15\t (1) > C29635T (9) > A3854G\n+England/EXET-135818/2020|20-04-11\t (1) > C14805T,G26144T (10) > C7703T,T9352C,G27201T\n+England/LIVE-A5D06/2020|20-03-17\t (1) > A10982G (24) > C6681T,G11801A\n+England/LIVE-A065B/2020|20-05-27\t (1) > A10982G (24) > C823T,C8752T,A9741C,C19961T,C26333T,C26408T\n+USA/CA-CZB-1091/2020|MT460091.1|20-05-01\t (1) > A14940G (660) > C15024T\n+USA/CA-CZB-11876/2020|MW276506.1|20-04-08\t (1) > A14940G (660) > A26120G\n+Scotland/GCVR-171160/2020|20-03-26\t (1) > A1904G,C8090T,C10789T (661) > A3958G,C5826T,C17074T\n+England/BRIS-130E2A/2020|20-03-24\t (1) > A1904G,C8090T,C10789T (661) > C16658A,C17733T\n+USA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\t (1) > T514C (662) > C22033A\n+NED/NB02_13KS/2020|MT457397.1|20-04-29\t (1) > T514C (662) > G1607A,A10829G,G12795A,C17410T,A22920T\n+USA/CA-QDX-1986/2020|MW190732.1|20-03-18\t (1) > A12557G,C24904T,A27359G (663) > C11050T\n+USA/CA-CZB-1250/2020|MT534320.1|20-04-12\t (1) > A12557G,C24904T,A27359G (663) > C25916T,G29751T\n+USA/CA-CZB-1015/2020|MT438733.1|20-04-22\t (1) > C25692T (664) > T15867A\n+USA/CA-CZB-1073/2020|MT449664.1|20-04-21\t (1) > C25692T (664) > G10617A,G22225T\n+England/BRIS-1258A2/2020|20-03-29\t (1) > G29032A (665) > C6696T,C9096T,C29754T\n+England/SHEF-BFEBB/2020|20-03-24\t (1) > G29032A (665) > C11747T,T24364G\n+USA/CA-CZB-1041/2020|MT438759.1|20-04-22\t (1) > C10277T (666) > A6313G,T7191C,A7193G\n+USA/CA-CZB-1051/2020|MT449644.1|20-04-06\t (1) > C10277T (666) > G7273A\n+USA/CA-QDX-33/2020|MT614459.1|20-03-15\t (1) > C6312A,C13730T,C23929T,C28311T (674) > C66T\n+USA/DC-HP00063/2020|MT646075.1|20-03-13\t (1) > C6312A,C13730T,C23929T,C28311T (674) > C11455T\n+HKG/HKU-904a/2020|MT365032.1|20-01-30\t (1) > C8782T,T28144C (676) > C4158T,C18828T\n+England/LIVE-9E66F/2020|20-04-10\t (1) > C6696T (698) > C7765T,G10256T\n+Scotland/CVR705/2020|20-03-26\t (1) > C6696T (698) > C11001T,G17122T\n+England/PHEC-1A601/2020|20-03-04\t (1) > G1397A,T28688C,G29742T (699) > A19526G\n+England/PHEC-2275E/2020|20-06-22\t (1) > G1397A,T28688C,G29742T (699) > G2246A,C5512T,C20132T,A23586G,C26822T,T27384C,T27484C,G28975T,G29639T\n+England/LIVE-A4C46/2020|20-03-12\t (1) > C20270T (5) > A29683T (6) > G431A,G26754A,C28725T\n+Scotland/EDB046/2020|20-03-15\t (1) > C14805T,G26144T (10) > T17247C (11) > C9996T,T26144G\n+England/BRIS-12EEB6/2020|20-04-22\t (1) > C14805T,G26144T (10) > G28842T (18) > C15240T,C18086T,T23031C\n+Scotland/EDB199/2020|20-03-26\t (1) > C14805T,G26144T (10) > G28842T (18) > C22713T,G26031T\n+England/CAMB-74A09/2020|20-03-18\t (1) > C14805T,G26144T (10) > C23707T (19) > G6981T,G10112T,G22785T\n+England/ALDP-9EE3AC/2020|20-05-06\t (1) > C14805T,G26144T (10) > C23707T (19) > G20991T\n+England/CAMB-8042A/2020|20-04-10\t (1) > C14805T,G26144T (10) > A2480G,C2558T (20) > A4015T\n+England/CAMB-737B8/2020|20-03-30\t (1) > C14805T,G26144T (10) > A2480G,C2558T (20) > G3971T,G28380T\n+USA/WA-S885/2020|MT642386.1|20-04-22\t (1) > C14805T,G26144T (10) > A4236G,T25655C (21) > G7739T,C25904T\n+USA/UT-QDX-1870/2020|MW190618.1|20-03-16\t (1) > C14805T,G26144T (10) > A4236G,T25655C (21) > A5269G,C9943T\n+USA/WA3-UW1/2020|MT163716.1|20-02-27\t (1) > C14805T,G26144T (10) > G5572T (22) > T2446C,C3411T\n+SouthKorea/KOR-BA-ACH_2719/2020|MT304476.1|20-02-29\t (1) > C14805T,G26144T (10) > G5572T (22) > C28311T\n+England/BRIS-1265AA/2020|20-04-10\t (1) > C14805T,G26144T (1'..b'68G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > G25494T (323) > C25386T (324) > C21302T,C21304A,C26256T,C27119T,C28453T\n+Wales/PHWC-47F3A5/2020|20-10-07\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > G25494T (323) > G28817T (325) > T9655C,G28198T\n+England/ALDP-A85BCC/2020|20-10-17\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > G25494T (323) > G28817T (325) > T209C,T11857C\n+England/ALDP-A2FCA3/2020|20-10-05\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C20451T,G21770A (326) > T7919G (327) > C24734T\n+Scotland/MILK-A69E6B/2020|20-10-09\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C20451T,G21770A (326) > T7919G (327) > A28483G,A28877G\n+England/MILK-A7D1A7/2020|20-10-13\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C20451T,G21770A (326) > G18583A (328) > T4579A,T27835C\n+England/MILK-A91486/2020|20-10-16\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C20451T,G21770A (326) > G18583A (328) > G2272T,G20679T,G24586T\n+AUT/2021006354/2021|MW672357.1|21-02\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C829T,C14697T,C18176T,G19398T,G28083T,G28975T (333) > C878T,C12374T,C20384T,C21639T,C29367T\n+England/MILK-E7F4C6/2021|21-01-02\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C829T,C14697T,C18176T,G19398T,G28083T,G28975T (333) > T9070C,C10296T\n+England/ALDP-AA169C/2020|20-10-22\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > G25218T (331) > C23191T,G23909A\n+England/MILK-A474DA/2020|20-10-06\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > G25218T (331) > A6659G\n+England/ALDP-B483EA/2020|20-11-07\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > T8110C (332) > C10039A,T18402C,C29738T\n+England/QEUH-AA0035/2020|20-10-20\t (1) > C241T (25) > C14408T (26) > A23403G (27) > C3037T (28) > A20268G (275) > G29734C (316) > C17104T (317) > T7767C,C8047T,C22879A (318) > C27800A (319) > G12988T,G15598A,G18028T,T24910C,T26972C (322) > C16394T,C22127T,G23876A,G25947T (329) > C29274T (330) > T8110C (332) > G11417T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_17_sample_names.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_17_sample_names.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1234 @@\n+England/BRIS-1853249/2020|20-04-02\n+NPL/61-TW/2020|MT072688.1|20-01-13\n+Wales/PHWC-25B04/2020|20-03-24\n+Wales/LIVE-A6831/2020|20-03-16\n+Scotland/EDB1317/2020|20-04-09\n+Scotland/EDB354/2020|20-03-30\n+England/SHEF-BFF8B/2020|20-03-25\n+England/SHEF-BFFC7/2020|20-03-25\n+England/PHEC-1E01E/2020|20-04-03\n+DP0476/2020|LC571003.1|20-02-16\n+DP0191/2020|LC570980.1|20-02-15\n+England/EXET-135818/2020|20-04-11\n+England/LIVE-A5D06/2020|20-03-17\n+England/LIVE-A065B/2020|20-05-27\n+USA/CA-CZB-1091/2020|MT460091.1|20-05-01\n+USA/CA-CZB-11876/2020|MW276506.1|20-04-08\n+Scotland/GCVR-171160/2020|20-03-26\n+England/BRIS-130E2A/2020|20-03-24\n+USA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\n+NED/NB02_13KS/2020|MT457397.1|20-04-29\n+USA/CA-QDX-1986/2020|MW190732.1|20-03-18\n+USA/CA-CZB-1250/2020|MT534320.1|20-04-12\n+USA/CA-CZB-1015/2020|MT438733.1|20-04-22\n+USA/CA-CZB-1073/2020|MT449664.1|20-04-21\n+England/BRIS-1258A2/2020|20-03-29\n+England/SHEF-BFEBB/2020|20-03-24\n+USA/CA-CZB-1041/2020|MT438759.1|20-04-22\n+USA/CA-CZB-1051/2020|MT449644.1|20-04-06\n+USA/CA-QDX-33/2020|MT614459.1|20-03-15\n+USA/DC-HP00063/2020|MT646075.1|20-03-13\n+HKG/HKU-904a/2020|MT365032.1|20-01-30\n+England/LIVE-9E66F/2020|20-04-10\n+Scotland/CVR705/2020|20-03-26\n+England/PHEC-1A601/2020|20-03-04\n+England/PHEC-2275E/2020|20-06-22\n+England/LIVE-A4C46/2020|20-03-12\n+Scotland/EDB046/2020|20-03-15\n+England/BRIS-12EEB6/2020|20-04-22\n+Scotland/EDB199/2020|20-03-26\n+England/CAMB-74A09/2020|20-03-18\n+England/ALDP-9EE3AC/2020|20-05-06\n+England/CAMB-8042A/2020|20-04-10\n+England/CAMB-737B8/2020|20-03-30\n+USA/WA-S885/2020|MT642386.1|20-04-22\n+USA/UT-QDX-1870/2020|MW190618.1|20-03-16\n+USA/WA3-UW1/2020|MT163716.1|20-02-27\n+SouthKorea/KOR-BA-ACH_2719/2020|MT304476.1|20-02-29\n+England/BRIS-1265AA/2020|20-04-10\n+AUS/NT38/2020|MT641726.1|20\n+France/40002VJ/2020|MT470179.1|20-03\n+England/CAMB-7772D/2020|20-03-31\n+England/BRIS-12208F/2020|20-03-21\n+England/ALDP-52C0FA/2020|20-06-01\n+England/LIVE-9D7D6/2020|20-04-15\n+USA/WI-UW-298/2020|MT706406.1|20-04-13\n+USA/WI-UW-314/2020|MT706422.1|20-04-16\n+USA/WI-UW-325/2020|MT706432.1|20-04-24\n+USA/WI-UW-290/2020|MT706398.1|20-04-08\n+Scotland/CVR3488/2020|20-05-12\n+Scotland/CVR780/2020|20-03-27\n+Japan/TKYE63557_2020/2020|LC581365.1|20-03\n+Japan/TKYE64688_2020/2020|LC581375.1|20-03\n+MYS/188407/2020|MT372480.1|20-03-18\n+AUS/VIC961/2020|MT451653.1|20-03-27\n+USA/MN-MDH-1475/2020|MT920008.1|20-03-23\n+USA/CA-CZB-1615/2020|MT628267.1|20-04-14\n+USA/FL-BPHL-0393/2020|MT757005.1|20-03-17\n+USA/COVID20-0008/2020|MT764174.1|20-03-10\n+USA/IL-CDC-IL2/2020|MT044257.1|20-01-28\n+USA/CA-QDX-1421/2020|MW065371.1|20-03-18\n+USA/CA-QDX-2080/2020|MW190832.1|20-03-19\n+AUS/VIC1255/2020|MT451830.1|20-04-11\n+AUS/VIC1878/2020|MT745600.1|20-03-29\n+England/LCST-24D7202/2020|20-06-22\n+England/SHEF-BFF21/2020|20-03-25\n+Switzerland/100159/2020|LR884273.1|20-03-16\n+England/LOND-126031F/2020|20-03-15\n+USA/NY-QDX-1999/2020|MW190795.1|20-03-16\n+USA/NY-QDX-1969/2020|MW190709.1|20-03-15\n+Wales/PHWC-285F4/2020|20-04-01\n+England/BRIS-130965/2020|20-04-13\n+Scotland/CVR44/2020|20-03-13\n+Scotland/CVR839/2020|20-03-27\n+Scotland/GCVR-170107/2020|20-03-23\n+Scotland/CVR207/2020|20-03-18\n+England/NORT-284A9B/2020|20-03-25\n+Scotland/CVR10/2020|20-03-10\n+Wales/PHWC-310CA/2020|20-04-11\n+Wales/PHWC-31CB7/2020|20-04-14\n+Wales/PHWC-26D2B/2020|20-03-30\n+Spain/H12_46/2020|LR884009.1|20-04-08\n+Spain/R11/2020|LR884126.1|20-03-06\n+Spain/LP19_4952/2020|LR884066.1|20-03-07\n+Spain/R10_33/2020|LR884127.1|20-03-02\n+EGY/CUNCI-HGC9I036/2020|MW504609.1|20-12-25\n+EGY/CUNCI-HGC12I049/2021|MW595907.1|21-01-03\n+England/CAMC-C91F38/2020|20-12-11\n+SLE/KGH-G-8626/2020|MT872492.1|20-04-10\n+Scotland/EDB5629/2020|20-03-24\n+Scotland/EDB5040/2020|20-04-02\n+Scotland/EDB1824/2020|20-04-16\n+England/ALDP-CB55B4/2020|20-12-20\n+England/CAMC-CF4B5D/2020|20-12-21\n+USA/WI-UW-06/2020|MT772088.1|20-03-21\n+USA/MI-MDHHS-SC20124/2020|MT439284.1|20-03-24\n+GHA/34927_S20/2020|MT890226.1|20-05-23\n+GHA/35563_S37/2020|MT890230.1|20-05-24\n+GHA/WACCBIP_n'..b'90280/2021|MW667214.1|21-01-27\n+USA/NY-CDC-21712201/2021|MW668883.1|21-02-04\n+England/CAMB-72B44/2020|20-03-22\n+England/CAMB-822D3/2020|20-04-12\n+England/ALDP-94DD07/2020|20-06-19\n+England/ALDP-49EC3C/2020|20-05-20\n+PER/covper024/2020|MW030255.1|20-07-04\n+PER/CoV-19_HRL-223/2020|MW185824.1|20-04-08\n+PER/covper011/2020|MW030242.1|20-07-04\n+PER/covper040/2020|MW030271.1|20-05-05\n+England/MILK-B1553B/2020|20-10-23\n+England/MILK-66F889/2020|20-07-03\n+USA/CO-CDC-STM-000008403/2021|MW617544.1|21-01-31\n+England/LOND-12F65DC/2021|21-01-19\n+Switzerland/310500/2020|LR898805.1|20-10-08\n+Switzerland/300433/2020|LR898634.1|20-09-29\n+England/QEUH-96BAA2/2020|20-08-14\n+Wales/ALDP-B19FFD/2020|20-11-01\n+SRB/NS19622-16-06/2020|MW327528.1|20-06-15\n+PER/covper018/2020|MW030249.1|20-07-03\n+EGY/CUNCI-HGC5I001/2020|MT611527.1|20-06-02\n+EGY/CUNCI-HGC5I011/2020|MT611536.1|20-06-02\n+England/MILK-9A699F/2020|20-09-01\n+England/CAMC-C3E586/2020|20-12-10\n+England/CAMC-DE5550/2020|20-12-29\n+England/ALDP-A525BB/2020|20-10-07\n+ISR/NH_M2_0614/2020|MW194121.1|20-06-14\n+England/MILK-A45AF8/2020|20-10-06\n+Scotland/QEUH-A613BF/2020|20-10-13\n+Switzerland/180039/2020|LR861669.1|20-07-01\n+Switzerland/220022/2020|LR882244.1|20-07-27\n+Japan/TKYE627000_2020/2020|LC593811.1|20-08\n+Japan/TKYE624705_2020/2020|LC593810.1|20-07\n+IND/GBRC455b/2020|MW600453.1|20-12-24\n+IND/GBRC455a/2020|MW600436.1|20-12-24\n+BRA/LRV-SARS.CoV-2.1/2020|MT807936.1|20-05-08\n+USA/WI-UW-114/2020|MT706234.1|20-03-30\n+England/CAMC-947392/2020|20-07-18\n+England/MILK-977469/2020|20-07-24\n+AUS/VIC9179/2020|MW153248.1|20-08-21\n+AUS/VIC11646/2020|MW155572.1|20-07-22\n+Scotland/EDB11343/2020|20-12-26\n+Scotland/EDB11342/2020|20-12-26\n+USA/CA-LACPHL-AF00169/2021|MW485829.1|21-01-08\n+USA/CA-LACPHL-AF00029/2020|MW424876.1|20-12-20\n+England/CAMC-A65DDB/2020|20-10-11\n+England/CAMC-AAF5A0/2020|20-10-22\n+England/MILK-A192C8/2020|20-10-01\n+England/QEUH-9F3FDD/2020|20-09-24\n+England/MILK-ABBF2B/2020|20-10-22\n+England/QEUH-96A85E/2020|20-08-14\n+HongKong/Homo-sapiens/HKG/Case5132/2020|MW181761.1|20-10-06\n+HongKong/Homo-sapiens/HKG/Case5126/2020|MW181753.1|20-10-06\n+England/PHEC-149F0D/2020|20-11-19\n+England/MILK-BE717A/2020|20-11-29\n+CAN/COVID_CRCHUM_Pre_Freeze_6/2020|MW309430.1|20-09-04\n+Scotland/QEUH-BEAF22/2020|20-12-04\n+England/MILK-A230C1/2020|20-10-03\n+Scotland/QEUH-9696CE/2020|20-08-14\n+England/CAMC-B3582D/2020|20-11-05\n+England/MILK-A796E8/2020|20-10-14\n+Northern_Ireland/QEUH-969C53/2020|20-08-14\n+England/ALDP-9E79B0/2020|20-09-24\n+England/MILK-B561FE/2020|20-11-06\n+England/CAMC-9DFBC4/2020|20-09-21\n+England/QEUH-AD1165/2020|20-10-25\n+England/ALDP-FB5E3E/2021|21-01-11\n+England/ALDP-E8756E/2021|21-01-04\n+England/ALDP-A2EAE6/2020|20-10-05\n+Scotland/QEUH-A636C3/2020|20-10-10\n+England/QEUH-A76C07/2020|20-10-12\n+England/MILK-AC7997/2020|20-10-21\n+Scotland/QEUH-9DC927/2020|20-09-22\n+Scotland/QEUH-9B75D3/2020|20-09-04\n+England/CAMC-AEACFF/2020|20-10-25\n+USA/FL-BPHL-2014/2020|MW286586.1|20-06-19\n+USA/MA_MGH_00693/2020|MT520290.1|20-04-06\n+CHL/Santiago-PUC_MVL_0491/2020|MW365473.1|20-05-13\n+CHL/Puerto_Montt-PUC_MVL_0534/2020|MW365467.1|20-05-27\n+ARG/Cordoba-2858/2020|MW633904.1|20-09-14\n+ARG/Cordoba-1484/2020|MW633909.1|20-09-17\n+England/MILK-97356A/2020|20-08-14\n+England/MILK-9A9F7C/2020|20-08-31\n+England/OXON-F42364/2020|20-12-18\n+England/MILK-9C2766/2020|20-09-10\n+England/ALDP-A95A9F/2020|20-10-19\n+England/PHEC-149FA3/2020|20-11-20\n+England/QEUH-C9332B/2020|20-12-17\n+England/CAMC-A649C9/2020|20-10-10\n+England/MILK-B04890/2020|20-10-24\n+England/CAMC-A57F03/2020|20-10-09\n+England/MILK-A7D15C/2020|20-10-13\n+Wales/PHWC-47F3A5/2020|20-10-07\n+England/ALDP-A85BCC/2020|20-10-17\n+England/ALDP-A2FCA3/2020|20-10-05\n+Scotland/MILK-A69E6B/2020|20-10-09\n+England/MILK-A7D1A7/2020|20-10-13\n+England/MILK-A91486/2020|20-10-16\n+AUT/2021006354/2021|MW672357.1|21-02\n+England/MILK-E7F4C6/2021|21-01-02\n+England/ALDP-AA169C/2020|20-10-22\n+England/MILK-A474DA/2020|20-10-06\n+England/ALDP-B483EA/2020|20-11-07\n+England/QEUH-AA0035/2020|20-10-20\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_18_all_paths.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_18_all_paths.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,595 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C22987T\n+625\tC19488T\n+England/CAMB-82E1B/2020|20-04-14\tA8374T\n+England/CAMC-947259/2020|20-07-21\tA8244G,G8408A,G12191T,T26171A,C28500T,G29254A,G29474T,G29751C\n+628\tA11869G,T27484C\n+SAU/KFSHRC44/2020|MT820480.1|20-04-11\t\n+SAU/KAIMRC67/2020|MT820487.1|20-04-01\tG29422T\n+Scotland/EDB300/2020|20-03-29\tC2399T,C15240T\n+England/CAMB-1AA438/2020|20-04-17\tT4149C,C12525T,G25599T\n+England/MILK-9C4087/2020|20-09-09\tT1543A,C1938T,T4369C,T22020C,C27911T\n+England/PHEC-13ADF/2020|20-03-13\tT15978C,G24794T\n+USA/CA-CZB-2184/2020|MW035923.1|20-05-26\tC21205T,G21255C,G28960T\n+Scotland/QEUH-94375E/2020|20-08-02\tG5554T,G19891T,C22938A,C24034T,G25249T,G25785T,G26152T,C27532T,G28321T,C29614T\n+641\tT3615C,G22256T,C23802T,A27403T,C27741T\n+England/CAMB-7C12A/2020|20-04-13\t\n+England/CAMB-83348/2020|20-04-15\t\n+644\tG596T,T18231C\n+USA/MS-CDC-6546/2020|MW279423.1|20-08-25\tG1589T\n+USA/TX-DSHS-1780/2020|MW425014.1|20-07-07\tT3127C\n+648\tG5950T,C19164T,A21137G,T27447C,T29661C\n+ZW-6983|LR963462.1|20-05-01\tC10341T\n+ZW-6978|LR963455.1|20-05-01\tA13833G\n+USA/GA-CDC-LC0013501/2021|MW643935.1|21-02-02\tA3852T,C3961T,G7798T,C9891T,C10116T,C21846T,G23012A,T23287C,C23604A,C25276A,T26767C,C28720T\n+Netherlands/NA_359/2020|LR883961.1|20-04-07\tC7095T,C13502T,A16179G\n+England/CAMB-1AE7FF/2020|20-04-29\tG4207T,A4208C,C6033T,G11842T\n+England/ALDP-BCA4B0/2020|20-11-23\tG1599T,C4965T,A6466G,A6616G,A7319G,G7954T,C12651T,G14371A,G21624T,G23587T,G28914T\n+USA/WA-S1222/2020|MT821613.1|20-05-08\tC186T,C15933T,G16968T,T19839C,G28881A,G28882A,G28883C,C29784T\n+660\tA14940G\n+USA/CA-CZB-1091/2020|MT460091.1|20-05-01\tC15024T\n+USA/CA-CZB-11876/2020|MW276506.1|20-04-08\tA26120G\n+USA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\tT514C,C22033A\n+USA/CA-QDX-1986/2020|MW190732.1|20-03-18\tC11050T,A12557G,C24904T,A27359G\n+USA/CA-CZB-1015/2020|MT438733.1|20-04-22\tT15867A,C25692T\n+USA/CA-CZB-1051/2020|MT449644.1|20-04-06\tG7273A,C10277T\n+667\tG29711T\n+England/LIVE-9D7D6/2020|20-04-15\tC1218T,C27493T,G27806T\n+USA/WI-UW-314/2020|MT706422.1|20-04-16\tA4838G,C7420T,C14937T,C20148T,G25907T\n+671\tC28854T\n+Scotland/CVR780/2020|20-03-27\tC5997T,C12710T\n+Japan/TKYE63557_2020/2020|LC581365.1|20-03\tC11752T,C25665T,C26447T,A27700G,T28854C,T28912C\n+674\tC6312A,C13730T,C23929T,C28311T\n+USA/CA-QDX-33/2020|MT614459.1|20-03-15\tC66T\n+USA/DC-HP00063/2020|MT646075.1|20-03-13\tC11455T\n+MYS/188407/2020|MT372480.1|20-03-18\tC6310A,C19524T,T25473C\n+676\tC8782T,T28144C\n+677\tA23403G,C26088T\n+679\tG9928T,G23403A\n+Scotland/EDB5629/2020|20-03-24\tG27870T\n+Scotland/EDB5040/2020|20-04-02\tC593T\n+680\tC3037T,A20268G\n+Spain/R11/2020|LR884126.1|20-03-06\tT3037C\n+Spain/LP19_4952/2020|LR884066.1|20-03-07\t\n+682\tT9477A,C14805T,G25979T\n+USA/FL-BPHL-0393/2020|MT757005.1|20-03-17\t\n+683\tC28863T\n+Spain/R10_33/2020|LR884127.1|20-03-02\tT25979G\n+685\tC4540T,C28657T\n+Scotland/CVR2435/2020|20-04-14\tC15274T,C25714T,C26029A\n+AUS/VIC995/2020|MT451680.1|20-03-31\tG17632A,C28311T\n+USA/MI-MDHHS-SC20124/2020|MT439284.1|20-03-24\tG16381A,T17877C,G25500T,C25854T,G28878A,G29742A\n+697\tT490A,C3177T,C24034T,T26729C,G28077C\n+USA/COVID20-0008/2020|MT764174.1|20-03-10\tT18736C\n+USA/IL-CDC-IL2/2020|MT044257.1|20-01-28\t\n+699\tG1397A,T28688C,G29742T\n+England/PHEC-1A601/2020|20-03-04\tA19526G\n+AUS/VIC1878/2020|MT745600.1|20-03-29\tC1076T,A28955T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_18_path_clades.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_18_path_clades.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,360 @@\n+clade\troot_id\tfrom_tree_root\n+19A\t1\t\n+B\t1\t\n+B.26\tScotland/EDB354/2020|20-03-30\t > C7423T,A29780C\n+B.48\t5\t > C20270T\n+B.15\t8\t > T4949C\n+B.5\t9\t > C29635T\n+B.54\t10\t > C14805T,G26144T\n+20A\t28\t > C241T,C3037T,C14408T,A23403G\n+B.1.108\t28\t > C241T,C3037T,C14408T,A23403G\n+B.20\t660\t > A14940G\n+B.11\tUSA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\t > T514C,C22033A\n+B.46\tUSA/CA-QDX-1986/2020|MW190732.1|20-03-18\t > C11050T,A12557G,C24904T,A27359G\n+B.1.14\tUSA/CA-CZB-1015/2020|MT438733.1|20-04-22\t > T15867A,C25692T\n+B.19\tUSA/CA-CZB-1051/2020|MT449644.1|20-04-06\t > G7273A,C10277T\n+B.6\t674\t > C6312A,C13730T,C23929T,C28311T\n+19B\t676\t > C8782T,T28144C\n+A\t676\t > C8782T,T28144C\n+B.4\t699\t > G1397A,T28688C,G29742T\n+B.23\tEngland/SHEF-BFF21/2020|20-03-25\t > C20270T > A18671G,A29683T\n+B.33\t11\t > C14805T,G26144T > T17247C\n+B.29\tEngland/ALDP-9EE3AC/2020|20-05-06\t > C14805T,G26144T > G20991T,C23707T\n+B.40\tEngland/CAMB-8042A/2020|20-04-10\t > C14805T,G26144T > A2480G,C2558T,A4015T\n+B.41\tSouthKorea/KOR-BA-ACH_2719/2020|MT304476.1|20-02-29\t > C14805T,G26144T > G5572T,C28311T\n+B.1.105\tEngland/CAMB-75BD8/2020|20-03-29\t > C241T,C3037T,C14408T,A23403G > C18060T,G28514T\n+B.1.103\t47\t > C241T,C3037T,C14408T,A23403G > C25665T,G28325T\n+B.1.378\t49\t > C241T,C3037T,C14408T,A23403G > G3871T\n+B.1.139\tUSA/WI-UW-558/2020|MT750137.1|20-06-25\t > C241T,C3037T,C14408T,A23403G > A696C\n+B.1.350\t53\t > C241T,C3037T,C14408T,A23403G > G25563T\n+B.1.221.1\t269\t > C241T,C3037T,C14408T,A23403G > C3602T,G4442T,C6525T,C6941T,C15324T,A16044T,C21855T,A25505G,G25906C,G25996T,C28651T,C28869T\n+B.1.222\tScotland/GCVR-172150/2020|20-03-30\t > C241T,C3037T,C14408T,A23403G > C1545T,C22879A\n+B.1.379\tEngland/BRIS-122C4F/2020|20-04-02\t > C241T,C3037T,C14408T,A23403G > A11782G,G22203T,G27754T\n+B.1.182\t275\t > C241T,C3037T,C14408T,A23403G > A20268G\n+B.1.5\t341\t > C241T,C3037T,C14408T,A23403G > C15324T\n+B.1.215\tScotland/GCVR-173C30/2020|20-04-07\t > C241T,C3037T,C14408T,A23403G > G3831A,T7441C\n+20E.EU1\t361\t > C241T,C3037T,C14408T,A23403G > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T\n+B.1.177.14\t361\t > C241T,C3037T,C14408T,A23403G > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T\n+B.1.179\tEngland/ALDP-4A2A77/2020|20-05-22\t > C241T,C3037T,C14408T,A23403G > C7834T,C16997T,G25429T\n+B.1.81\tEngland/BRIS-12468B/2020|20-04-09\t > C241T,C3037T,C14408T,A23403G > C1909T,T27576C\n+B.1.201\tEngland/NORW-E9DF7/2020|20-05-02\t > C241T,C3037T,C14408T,A23403G > C2940T,C7765T\n+B.1.395\t398\t > C241T,C3037T,C14408T,A23403G > C6990T\n+B.1.67\tWales/PHWC-29E43/2020|20-04-04\t > C241T,C3037T,C14408T,A23403G > G9220A,T26512C\n+B.1.98\tEngland/LOND-D3534/2020|20-03-27\t > C241T,C3037T,C14408T,A23403G > C25350T,T27280C\n+B.1.76\tEngland/LIVE-A63E5/2020|20-03-18\t > C241T,C3037T,C14408T,A23403G > G680T,T17835C\n+B.1.376\tWales/PHWC-27461/2020|20-03-31\t > C241T,C3037T,C14408T,A23403G > C5506T,G14241T,C19374T\n+B.1.23\tAUS/VIC1056/2020|MT451723.1|20-04-03\t > C241T,C3037T,C14408T,A23403G > T7438C,A21944T,C29353T\n+B.1.153\tEngland/LIVE-A65EF/2020|20-03-19\t > C241T,C3037T,C14408T,A23403G > G10523C,G14580T\n+B.1.113\tIND/GBRC209a/2020|MT664202.1|20-06-11\t > C241T,C3037T,C14408T,A23403G > A2292C,C2836T,G4300T,C18568T,C18877T,G21724T,G25563T,C29750T\n+B.1.70\tScotland/CVR30/2020|20-03-13\t > C241T,C3037T,C14408T,A23403G > C1884T,T26497C\n+B.1.145\tIND/GBRC99/2020|MT509504.1|20-05-06\t > C241T,C3037T,C14408T,A23403G > G4866T,C14425A,A21511G\n+B.1.197\tAUS/VIC1239/2020|MT451821.1|20-04-02\t > C241T,C3037T,C14408T,A23403G > C6723T,T26094C,G28476T\n+B.1.143\tIND/GBRC128/2020|MT539172.1|20-05-02\t > C241T,C3037T,C14408T,A23403G > C4084T,G5572T\n+B.1.187\tPOL/PL_MCB_75/2020|MW273857.1|20-04-16\t > C241T,C3037T,C14408T,A23403G > A544G,C17104T\n+B.1.414\tNetherlands/NA_302/2020|LR878041.1|20-04-01\t > C241T,C3037T,C14408T,A23403G > A3058G,G20275A\n+B.1.206\tUSA/TX-DSHS-0975/2020|MW217385.1|20-06-16\t > C241T,C3037T,C14408T,A23403G > G2282A,T9742C,C17639T,G20160T\n+B.1.69\t423\t > C241T,C3037T,C14408T,A23403G > C23422T,T23849C,C29686T\n+20B\t426\t > C241T,C3037T,C14408T,A'..b'037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > A20553G,G22487C\n+B.1.499\tUSA/NY-QDX-2365/2020|MW191144.1|20-03-16\t > C241T,C3037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > C28863T\n+B.1.508\tUSA/CA-CZB-2139/2020|MT750510.1|20-05-21\t > C241T,C3037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > C5540A,C19145T\n+B.1.501\tUSA/NC-QDX-174/2020|MT786825.1|20-04-27\t > C241T,C3037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > C10458T,C18693A,G26828T\n+B.1.505\tEngland/MILK-6166F0/2020|20-07-05\t > C241T,C3037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > C66A,C4455T,C7768T,A8773G,C17304T,T22912G,T24805C,C26270T\n+B.1.282\tEngland/ALDP-955F15/2020|20-06-08\t > C241T,C3037T,C14408T,A23403G > G25563T > C2416T > G8371T > C22477T > C882T,C17746T,G19962T,G25793A,G28907T\n+B.1.477\tEngland/ALDP-94EB75/2020|20-06-17\t > C241T,C3037T,C14408T,A23403G > G25563T > C2416T > G8371T > C22477T > C3811T,G22225A\n+B.1.36.20\t221\t > C241T,C3037T,C14408T,A23403G > G25563T > C18877T > C26735T > C22444T > C593T,T3118C,T10200C,A12547G,C21772T,C28854T\n+B.1.36.21\tEngland/PHEC-149F0D/2020|20-11-19\t > C241T,C3037T,C14408T,A23403G > G25563T > C18877T > C26735T > C22444T,C28854T > C1122T,T4057C,G6077T,A10323G,G13858T,G21724T,C27092T,C27434T,G28975T\n+B.1.36.23\tEngland/MILK-970CE0/2020|20-08-18\t > C241T,C3037T,C14408T,A23403G > G25563T > C18877T > C26735T > C22444T,C28854T > C6312T,C12513T,G14122T,A20559G,C23127T,G26389T,T26876C,C28311T,A28900C\n+B.1.36.24\tEngland/SHEF-10CC3AA/2020|20-12-17\t > C241T,C3037T,C14408T,A23403G > G25563T > C18877T > C26735T > C22444T,C28854T > A749G,C1420T,C2113T,C6268A,C6701T,C7318T,C9438T,C14724T,A17637G,C20555T,C21660A,G22201T,C22480A,G23522C,A25856C\n+B.1.36.12\tEngland/MILK-566C5A/2020|20-06-12\t > C241T,C3037T,C14408T,A23403G > G25563T > C18877T > C26735T > C22444T,C28854T > C11514T,C13168T,G24764T\n+B.1.36.10\t237\t > C241T,C3037T,C14408T,A23403G > G25563T > C18877T > C26735T > C22444T,C28854T > C2898T,C6681T,C7728T,G12191T,T16993C,G25311T\n+B.1.177.7\t373\t > C241T,C3037T,C14408T,A23403G > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > C27944T > G204T > C21614T > C15480T\n+B.1.177.8\tScotland/QEUH-9B75D3/2020|20-09-04\t > C241T,C3037T,C14408T,A23403G > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T > C27944T > G204T > C21614T > G8179T,G29778T\n+B.1.1.289\tWales/PHWC-260AA/2020|20-03-24\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > T19839C > G25552T > T7168C,G11801A\n+B.1.1.2\t434\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > T19839C > G25552T > A26332G,A28877T,G28878C\n+C.5\tSwitzerland/300433/2020|LR898634.1|20-09-29\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > G2995T,T4871C,C6449T,C10252T,C19366T,G27382T,T27808C\n+C.4\tSRB/NS19622-16-06/2020|MW327528.1|20-06-15\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > G24794T\n+B.1.36.1\tEngland/CAMC-A65DDB/2020|20-10-11\t > C241T,C3037T,C14408T,A23403G > G25563T > C18877T > C26735T > C22444T,C28854T > T1947C > G2659T,G5008T,G19549T,C25349A,G25947C,G26062T\n+B.1.36.28\tEngland/QEUH-9F3FDD/2020|20-09-24\t > C241T,C3037T,C14408T,A23403G > G25563T > C18877T > C26735T > C22444T,C28854T > T1947C > T7292C,T8410C,C10833T,C11572T,C16293T,T23986C\n+B.1.36.17\tEngland/QEUH-96A85E/2020|20-08-14\t > C241T,C3037T,C14408T,A23403G > G25563T > C18877T > C26735T > C22444T,C28854T > T1947C > C7528T,T23986C,C29555T\n+B.1.36.27\t228\t > C241T,C3037T,C14408T,A23403G > G25563T > C18877T > C26735T > C22444T,C28854T > T1947C > G922A,G3431T,T5653C,G5950A,C7504T,T24175C,C26060T\n+N.1\tUSA/MA_MGH_00693/2020|MT520290.1|20-04-06\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > T29148C > G25793T,T27299C > T25793G > C25916T,T28360C,C29769T\n+N.4\tCHL/Santiago-PUC_MVL_0491/2020|MW365473.1|20-05-13\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > T29148C > G25793T,T27299C > T25793G > A2475G,C14805T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_18_path_mutations.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_18_path_mutations.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,442 @@\n+sample_id\tpath_from_root\n+England/BRIS-1853249/2020|20-04-02\t (1) > C24034T (2) > C29518T\n+NPL/61-TW/2020|MT072688.1|20-01-13\t (1) > C24034T (2) > \n+Wales/PHWC-25B04/2020|20-03-24\t (1) > C875T (3) > A20637G\n+Wales/LIVE-A6831/2020|20-03-16\t (1) > C875T (3) > T14859C\n+Scotland/EDB354/2020|20-03-30\t (1) > C7423T,A29780C\n+England/SHEF-BFF8B/2020|20-03-25\t (1) > C20270T (5) > C1473T\n+England/SHEF-BFFC7/2020|20-03-25\t (1) > T4949C (8) > G28027T\n+England/PHEC-1E01E/2020|20-04-03\t (1) > T4949C (8) > C22445T\n+DP0476/2020|LC571003.1|20-02-16\t (1) > C29635T (9) > C29592T\n+DP0191/2020|LC570980.1|20-02-15\t (1) > C29635T (9) > A3854G\n+USA/CA-CZB-1091/2020|MT460091.1|20-05-01\t (1) > A14940G (660) > C15024T\n+USA/CA-CZB-11876/2020|MW276506.1|20-04-08\t (1) > A14940G (660) > A26120G\n+USA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\t (1) > T514C,C22033A\n+USA/CA-QDX-1986/2020|MW190732.1|20-03-18\t (1) > C11050T,A12557G,C24904T,A27359G\n+USA/CA-CZB-1015/2020|MT438733.1|20-04-22\t (1) > T15867A,C25692T\n+USA/CA-CZB-1051/2020|MT449644.1|20-04-06\t (1) > G7273A,C10277T\n+USA/CA-QDX-33/2020|MT614459.1|20-03-15\t (1) > C6312A,C13730T,C23929T,C28311T (674) > C66T\n+USA/DC-HP00063/2020|MT646075.1|20-03-13\t (1) > C6312A,C13730T,C23929T,C28311T (674) > C11455T\n+England/PHEC-1A601/2020|20-03-04\t (1) > G1397A,T28688C,G29742T (699) > A19526G\n+England/ALDP-9EE3AC/2020|20-05-06\t (1) > C14805T,G26144T (10) > G20991T,C23707T\n+England/CAMB-8042A/2020|20-04-10\t (1) > C14805T,G26144T (10) > A2480G,C2558T,A4015T\n+SouthKorea/KOR-BA-ACH_2719/2020|MT304476.1|20-02-29\t (1) > C14805T,G26144T (10) > G5572T,C28311T\n+England/LIVE-9D7D6/2020|20-04-15\t (1) > G29711T (667) > C1218T,C27493T,G27806T\n+USA/WI-UW-314/2020|MT706422.1|20-04-16\t (1) > G29711T (667) > A4838G,C7420T,C14937T,C20148T,G25907T\n+Scotland/CVR780/2020|20-03-27\t (1) > C28854T (671) > C5997T,C12710T\n+Japan/TKYE63557_2020/2020|LC581365.1|20-03\t (1) > C28854T (671) > C11752T,C25665T,C26447T,A27700G,T28854C,T28912C\n+MYS/188407/2020|MT372480.1|20-03-18\t (1) > C6312A,C13730T,C23929T,C28311T (674) > C6310A,C19524T,T25473C\n+USA/FL-BPHL-0393/2020|MT757005.1|20-03-17\t (1) > C8782T,T28144C (676) > T9477A,C14805T,G25979T (682) > \n+USA/COVID20-0008/2020|MT764174.1|20-03-10\t (1) > C8782T,T28144C (676) > T490A,C3177T,C24034T,T26729C,G28077C (697) > T18736C\n+USA/IL-CDC-IL2/2020|MT044257.1|20-01-28\t (1) > C8782T,T28144C (676) > T490A,C3177T,C24034T,T26729C,G28077C (697) > \n+AUS/VIC1878/2020|MT745600.1|20-03-29\t (1) > G1397A,T28688C,G29742T (699) > C1076T,A28955T\n+England/SHEF-BFF21/2020|20-03-25\t (1) > C20270T (5) > A18671G,A29683T\n+Switzerland/100159/2020|LR884273.1|20-03-16\t (1) > C14805T,G26144T (10) > T17247C (11) > C12400T (12) > C16995T\n+England/LOND-126031F/2020|20-03-15\t (1) > C14805T,G26144T (10) > T17247C (11) > C12400T (12) > A20511G\n+USA/NY-QDX-1999/2020|MW190795.1|20-03-16\t (1) > C14805T,G26144T (10) > T17247C (11) > C8078T (13) > G10754A\n+USA/NY-QDX-1969/2020|MW190709.1|20-03-15\t (1) > C14805T,G26144T (10) > T17247C (11) > C8078T (13) > \n+Scotland/CVR44/2020|20-03-13\t (1) > C14805T,G26144T (10) > T17247C (11) > G443A,A1587G\n+Scotland/CVR207/2020|20-03-18\t (1) > C14805T,G26144T (10) > T17247C (11) > C988T,G12832A\n+Spain/R11/2020|LR884126.1|20-03-06\t (1) > C8782T,T28144C (676) > A23403G,C26088T (677) > C3037T,A20268G (680) > T3037C\n+Spain/LP19_4952/2020|LR884066.1|20-03-07\t (1) > C8782T,T28144C (676) > A23403G,C26088T (677) > C3037T,A20268G (680) > \n+Spain/R10_33/2020|LR884127.1|20-03-02\t (1) > C8782T,T28144C (676) > T9477A,C14805T,G25979T (682) > C28863T (683) > T25979G\n+Scotland/EDB5629/2020|20-03-24\t (1) > C8782T,T28144C (676) > A23403G,C26088T (677) > G9928T,G23403A (679) > G27870T\n+Scotland/EDB5040/2020|20-04-02\t (1) > C8782T,T28144C (676) > A23403G,C26088T (677) > G9928T,G23403A (679) > C593T\n+USA/MI-MDHHS-SC20124/2020|MT439284.1|20-03-24\t (1) > C8782T,T28144C (676) > G16381A,T17877C,G25500T,C25854T,G28878A,G29742A\n+England/BRIS-125347/2020|20-03-27\t (1) > C241T,C3037T,C14408T,A23403G (28) > G7042T,G8861T'..b'> G25793T,T27299C (543) > T25793G (544) > C28969T\n+England/CAMC-947392/2020|20-07-18\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > G26918T,T29464C (572) > C7843T,G15438T,C25207T,T25949C,C28453T\n+AUS/VIC11646/2020|MW155572.1|20-07-22\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > A1163T (621) > T7540C,G16647T,G22992A,G23401A (623) > G6617T,C18555T,C22987T\n+England/CAMC-A65DDB/2020|20-10-11\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C18877T (211) > C26735T (212) > C22444T,C28854T (223) > T1947C (224) > G2659T,G5008T,G19549T,C25349A,G25947C,G26062T\n+England/QEUH-9F3FDD/2020|20-09-24\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C18877T (211) > C26735T (212) > C22444T,C28854T (223) > T1947C (224) > T7292C,T8410C,C10833T,C11572T,C16293T,T23986C\n+England/QEUH-96A85E/2020|20-08-14\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C18877T (211) > C26735T (212) > C22444T,C28854T (223) > T1947C (224) > C7528T,T23986C,C29555T\n+HongKong/Homo-sapiens/HKG/Case5132/2020|MW181761.1|20-10-06\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C18877T (211) > C26735T (212) > C22444T,C28854T (223) > T1947C (224) > G922A,G3431T,T5653C,G5950A,C7504T,T24175C,C26060T (228) > C14724T\n+HongKong/Homo-sapiens/HKG/Case5126/2020|MW181753.1|20-10-06\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C18877T (211) > C26735T (212) > C22444T,C28854T (223) > T1947C (224) > G922A,G3431T,T5653C,G5950A,C7504T,T24175C,C26060T (228) > A6391G\n+England/PHEC-149F0D/2020|20-11-19\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C18877T (211) > C26735T (212) > C22444T,C28854T (223) > C1122T,T4057C,G6077T,A10323G,G13858T,G21724T,C27092T,C27434T,G28975T\n+England/MILK-A230C1/2020|20-10-03\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C18877T (211) > C26735T (212) > C4543T,G5629T,G9526T,C11497T,G13993T,G15766T,A16889G,G17019T,G22992A,C25710T,T26876C,G28975C,G29399A (240) > A2175G\n+England/QEUH-A76C07/2020|20-10-12\t (1) > C241T,C3037T,C14408T,A23403G (28) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > C27944T (366) > G204T (367) > C21614T (369) > C15480T (373) > G21777A\n+England/MILK-AC7997/2020|20-10-21\t (1) > C241T,C3037T,C14408T,A23403G (28) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > C27944T (366) > G204T (367) > C21614T (369) > C15480T (373) > C125T\n+Scotland/QEUH-9B75D3/2020|20-09-04\t (1) > C241T,C3037T,C14408T,A23403G (28) > T445C,C6286T,G21255C,C22227T,C26801G,C28932T,G29645T (361) > C27944T (366) > G204T (367) > C21614T (369) > G8179T,G29778T\n+USA/MA_MGH_00693/2020|MT520290.1|20-04-06\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > T29148C (542) > G25793T,T27299C (543) > T25793G (544) > C25916T,T28360C,C29769T\n+CHL/Santiago-PUC_MVL_0491/2020|MW365473.1|20-05-13\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > T29148C (542) > G25793T,T27299C (543) > T25793G (544) > A2475G,C14805T\n+England/MILK-97356A/2020|20-08-14\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C18877T (211) > C26735T (212) > C4543T,G5629T,G9526T,C11497T,G13993T,G15766T,A16889G,G17019T,G22992A,C25710T,T26876C,G28975C,G29399A (240) > C15720T\n+England/ALDP-A2FCA3/2020|20-10-05\t (1) > C241T,C3037T,C14408T,A23403G (28) > A20268G (275) > T7767C,C8047T,G12988T,G15598A,C17104T,G18028T,C22879A,T24910C,T26972C,C27800A,G29734C (322) > T7919G,C20451T,G21770A,C24734T\n+England/MILK-A474DA/2020|20-10-06\t (1) > C241T,C3037T,C14408T,A23403G (28) > A20268G (275) > T7767C,C8047T,G12988T,G15598A,C17104T,G18028T,C22879A,T24910C,T26972C,C27800A,G29734C (322) > C16394T,C22127T,G23876A,G25947T,C29274T (330) > A6659G,G25218T\n+England/QEUH-AA0035/2020|20-10-20\t (1) > C241T,C3037T,C14408T,A23403G (28) > A20268G (275) > T7767C,C8047T,G12988T,G15598A,C17104T,G18028T,C22879A,T24910C,T26972C,C27800A,G29734C (322) > C16394T,C22127T,G23876A,G25947T,C29274T (330) > T8110C,G11417T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_18_sample_names.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_18_sample_names.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,441 @@\n+England/BRIS-1853249/2020|20-04-02\n+NPL/61-TW/2020|MT072688.1|20-01-13\n+Wales/PHWC-25B04/2020|20-03-24\n+Wales/LIVE-A6831/2020|20-03-16\n+Scotland/EDB354/2020|20-03-30\n+England/SHEF-BFF8B/2020|20-03-25\n+England/SHEF-BFFC7/2020|20-03-25\n+England/PHEC-1E01E/2020|20-04-03\n+DP0476/2020|LC571003.1|20-02-16\n+DP0191/2020|LC570980.1|20-02-15\n+USA/CA-CZB-1091/2020|MT460091.1|20-05-01\n+USA/CA-CZB-11876/2020|MW276506.1|20-04-08\n+USA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\n+USA/CA-QDX-1986/2020|MW190732.1|20-03-18\n+USA/CA-CZB-1015/2020|MT438733.1|20-04-22\n+USA/CA-CZB-1051/2020|MT449644.1|20-04-06\n+USA/CA-QDX-33/2020|MT614459.1|20-03-15\n+USA/DC-HP00063/2020|MT646075.1|20-03-13\n+England/PHEC-1A601/2020|20-03-04\n+England/ALDP-9EE3AC/2020|20-05-06\n+England/CAMB-8042A/2020|20-04-10\n+SouthKorea/KOR-BA-ACH_2719/2020|MT304476.1|20-02-29\n+England/LIVE-9D7D6/2020|20-04-15\n+USA/WI-UW-314/2020|MT706422.1|20-04-16\n+Scotland/CVR780/2020|20-03-27\n+Japan/TKYE63557_2020/2020|LC581365.1|20-03\n+MYS/188407/2020|MT372480.1|20-03-18\n+USA/FL-BPHL-0393/2020|MT757005.1|20-03-17\n+USA/COVID20-0008/2020|MT764174.1|20-03-10\n+USA/IL-CDC-IL2/2020|MT044257.1|20-01-28\n+AUS/VIC1878/2020|MT745600.1|20-03-29\n+England/SHEF-BFF21/2020|20-03-25\n+Switzerland/100159/2020|LR884273.1|20-03-16\n+England/LOND-126031F/2020|20-03-15\n+USA/NY-QDX-1999/2020|MW190795.1|20-03-16\n+USA/NY-QDX-1969/2020|MW190709.1|20-03-15\n+Scotland/CVR44/2020|20-03-13\n+Scotland/CVR207/2020|20-03-18\n+Spain/R11/2020|LR884126.1|20-03-06\n+Spain/LP19_4952/2020|LR884066.1|20-03-07\n+Spain/R10_33/2020|LR884127.1|20-03-02\n+Scotland/EDB5629/2020|20-03-24\n+Scotland/EDB5040/2020|20-04-02\n+USA/MI-MDHHS-SC20124/2020|MT439284.1|20-03-24\n+England/BRIS-125347/2020|20-03-27\n+IND/763/2020|MT577009.1|20\n+England/CAMB-75BD8/2020|20-03-29\n+USA/MI-MDHHS-SC20612/2020|MT585039.1|20-04-29\n+USA/MI-MDHHS-SC20597/2020|MT585043.1|20-04-29\n+USA/WI-UW-26/2020|MT706147.1|20-03-24\n+USA/IL-QDX-2568/2020|MW191367.1|20-03-14\n+USA/WI-UW-558/2020|MT750137.1|20-06-25\n+EGY/CUNCI-HGC5I033/2020|MT614347.1|20-06-02\n+Scotland/GCVR-172150/2020|20-03-30\n+England/BRIS-122C4F/2020|20-04-02\n+USA/RI-CDC-0556/2020|MT304488.1|20-03-01\n+Switzerland/100198/2020|LR884312.1|20-03-17\n+USA/WI-UW-37/2020|MT706158.1|20-03-22\n+Scotland/GCVR-173C30/2020|20-04-07\n+England/ALDP-4A2A77/2020|20-05-22\n+England/BRIS-12468B/2020|20-04-09\n+England/NORW-E9DF7/2020|20-05-02\n+Wales/PHWC-27B20/2020|20-03-30\n+Wales/PHWC-2624A/2020|20-03-27\n+Wales/PHWC-29E43/2020|20-04-04\n+England/LOND-D3534/2020|20-03-27\n+England/LIVE-A63E5/2020|20-03-18\n+Wales/PHWC-27461/2020|20-03-31\n+AUS/VIC1056/2020|MT451723.1|20-04-03\n+England/LIVE-A65EF/2020|20-03-19\n+IND/GBRC209a/2020|MT664202.1|20-06-11\n+Scotland/CVR30/2020|20-03-13\n+IND/GBRC99/2020|MT509504.1|20-05-06\n+AUS/VIC1239/2020|MT451821.1|20-04-02\n+IND/GBRC128/2020|MT539172.1|20-05-02\n+POL/PL_MCB_75/2020|MW273857.1|20-04-16\n+Netherlands/NA_302/2020|LR878041.1|20-04-01\n+USA/TX-DSHS-0975/2020|MW217385.1|20-06-16\n+Scotland/CVR129/2020|20-03-13\n+Scotland/CVR52/2020|20-03-14\n+Poland/covid_hub_pl_ibch_0033/2020|LR899101.1|20-05-20\n+England/ALDP-BCA4B0/2020|20-11-23\n+USA/WA-S1222/2020|MT821613.1|20-05-08\n+England/CAMB-76515/2020|20-03-29\n+England/LEED-2A8D10/2020|20-03-31\n+Scotland/CVR2381/2020|20-04-13\n+Scotland/CVR2197/2020|20-04-11\n+Scotland/CVR1519/2020|20-04-03\n+England/NORW-E8C37/2020|20-04-13\n+Wales/PHWC-3122E/2020|20-04-10\n+Wales/PHWC-1645EC/2020|20-05-10\n+England/PHEC-127E8/2020|20-03-28\n+England/MILK-9A8AB8/2020|20-08-31\n+IND/GBRC174b/2020|MT607610.1|20-06-05\n+France/10036BG/2020|MT470106.1|20-03\n+POL/PL_MCB_97/2020|MW273879.1|20-05-10\n+Scotland/CVR3629/2020|20-05-24\n+Scotland/QEUH-5456F9/2020|20-05-13\n+England/QEUH-990752/2020|20-08-29\n+AUS/VIC38/2020|MT450953.1|20-03-11\n+IHUCOVID-0133|LR794459.1|?\n+Switzerland/240009/2020|LR880588.1|20-08-07\n+USA/MN67-MDH67/2020|MT911566.1|20-03-14\n+Netherlands/NA_292/2020|LR878032.1|20-04-01\n+Switzerland/101166/2020|LR824397.1|20-03-31\n+Switzerland/100154/2020|LR824311.1|20-03-16\n+PER/covper09'..b'HEC-149635/2020|20-10-28\n+England/ALDP-9E75E9/2020|20-09-25\n+England/ALDP-A68CF9/2020|20-10-12\n+England/MILK-9F1898/2020|20-09-25\n+Wales/PHWC-4815AA/2020|20-10-13\n+England/QEUH-7A4BBB/2020|20-07-14\n+USA/WA-S1922/2020|MT831459.1|20-06-03\n+USA/WA-S1775/2020|MT834200.1|20-06-01\n+England/ALDP-B82A0D/2020|20-11-14\n+England/BRIS-12A70A/2020|20-05-01\n+England/CAMB-77F61/2020|20-04-01\n+England/NORW-EE34B/2020|20-03-24\n+Northern_Ireland/NIRE-FBB52/2020|20-04-13\n+Northern_Ireland/NIRE-FAC7E/2020|20-04-15\n+England/CAMB-81070/2020|20-04-20\n+Scotland/CVR41/2020|20-03-13\n+England/QEUH-96E605/2020|20-08-17\n+USA/ME-HETL-J0061/2020|MT886346.1|20-03-20\n+USA/FL-BPHL-0303/2020|MT757111.1|20-05-30\n+Japan/TKYE622411_2020/2020|LC593808.1|20-07\n+England/MILK-A18C8F/2020|20-10-03\n+Wales/PHWC-30957/2020|20-04-08\n+LC573289.2|20-06\n+TUR/Kafkas-SARSCoV2-0036/2020|MT787743.1|20-07-15\n+England/CAMB-74D5B/2020|20-03-19\n+England/BRIS-125D67/2020|20-03-29\n+England/ALDP-94D8F7/2020|20-06-20\n+England/NOTT-111BFB/2020|20-05-29\n+England/MILK-8664D7/2020|20-07-17\n+England/CAMC-A40F67/2020|20-10-06\n+England/QEUH-9B6EAC/2020|20-09-09\n+England/NORT-2A4CAE/2020|20-09-17\n+Northern_Ireland/NIRE-FB369/2020|20-08-31\n+England/LEED-2AA394/2020|20-03-31\n+England/WSFT-25C13CB/2020|20-04-17\n+England/PORT-2F5D9C/2020|20-06-05\n+England/ALDP-5D52BE/2020|20-06-18\n+England/ALDP-4A2BFC/2020|20-05-22\n+England/ALDP-49F5B8/2020|20-05-22\n+USA/WA-S2598/2020|MT831859.1|20-06-18\n+USA/WA-S820/2020|MT641503.1|20-04-15\n+Netherlands/NA_436/2020|LR883367.1|20-04-07\n+Netherlands/Friesland_33/2020|LR883315.1|20-04-14\n+England/CAMC-B36516/2020|20-11-05\n+England/CAMC-B362D3/2020|20-11-05\n+England/MILK-B3A284/2020|20-11-01\n+England/CAMC-B365AD/2020|20-11-05\n+AUS/VIC13094/2020|MW185501.1|20-07-31\n+England/CAMC-947259/2020|20-07-21\n+USA/COVID20-0537/2020|MT981422.1|20-06-04\n+USA/COVID20-1129/2020|MW067826.1|20-07-10\n+USA/VA-DCLS-1147/2020|MT992749.1|20-04\n+USA/NY-QDX-2365/2020|MW191144.1|20-03-16\n+USA/CA-CZB-2139/2020|MT750510.1|20-05-21\n+USA/NC-QDX-174/2020|MT786825.1|20-04-27\n+England/MILK-6166F0/2020|20-07-05\n+USA/WI-UW-1194/2020|MT981478.1|20-08-11\n+England/ALDP-955F15/2020|20-06-08\n+England/ALDP-94EB75/2020|20-06-17\n+England/SHEF-10B22B9/2020|20-04-20\n+Scotland/QEUH-A9E7BD/2020|20-10-20\n+Scotland/EDB7778/2020|20-09-16\n+England/MILK-970CE0/2020|20-08-18\n+England/SHEF-10CC3AA/2020|20-12-17\n+England/MILK-566C5A/2020|20-06-12\n+England/CAMC-C2CDFC/2020|20-12-07\n+England/MILK-CAA0EE/2020|20-12-18\n+England/QEUH-96A29C/2020|20-08-13\n+England/ALDP-9BE8B5/2020|20-09-09\n+Scotland/CVR4309/2020|20-09-14\n+England/ALDP-9BECB9/2020|20-09-10\n+England/MILK-9A9D09/2020|20-09-01\n+England/CAMC-AEA62E/2020|20-10-25\n+Wales/PHWC-260AA/2020|20-03-24\n+England/BRIS-185470D/2020|20-05-01\n+England/BRIS-12AF02/2020|20-05-01\n+USA/MA-Broad_CRSP-00367/2021|MW599505.1|21-01-08\n+USA/MA-MGH-03951/2021|MW617773.1|21-01-22\n+USA/MD-MDH-0841/2021|MW621433.1|21-01-17\n+England/CAMB-72B44/2020|20-03-22\n+England/CAMB-822D3/2020|20-04-12\n+Switzerland/300433/2020|LR898634.1|20-09-29\n+SRB/NS19622-16-06/2020|MW327528.1|20-06-15\n+EGY/CUNCI-HGC5I001/2020|MT611527.1|20-06-02\n+EGY/CUNCI-HGC5I011/2020|MT611536.1|20-06-02\n+Japan/TKYE627000_2020/2020|LC593811.1|20-08\n+IND/GBRC455a/2020|MW600436.1|20-12-24\n+BRA/LRV-SARS.CoV-2.1/2020|MT807936.1|20-05-08\n+England/CAMC-947392/2020|20-07-18\n+AUS/VIC11646/2020|MW155572.1|20-07-22\n+England/CAMC-A65DDB/2020|20-10-11\n+England/QEUH-9F3FDD/2020|20-09-24\n+England/QEUH-96A85E/2020|20-08-14\n+HongKong/Homo-sapiens/HKG/Case5132/2020|MW181761.1|20-10-06\n+HongKong/Homo-sapiens/HKG/Case5126/2020|MW181753.1|20-10-06\n+England/PHEC-149F0D/2020|20-11-19\n+England/MILK-A230C1/2020|20-10-03\n+England/QEUH-A76C07/2020|20-10-12\n+England/MILK-AC7997/2020|20-10-21\n+Scotland/QEUH-9B75D3/2020|20-09-04\n+USA/MA_MGH_00693/2020|MT520290.1|20-04-06\n+CHL/Santiago-PUC_MVL_0491/2020|MW365473.1|20-05-13\n+England/MILK-97356A/2020|20-08-14\n+England/ALDP-A2FCA3/2020|20-10-05\n+England/MILK-A474DA/2020|20-10-06\n+England/QEUH-AA0035/2020|20-10-20\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_19_path_clades.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_19_path_clades.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,305 @@\n+clade\troot_id\tfrom_tree_root\n+19A\t1\t\n+B\t1\t\n+B.26\t4\t > C7423T\n+B.48\t5\t > C20270T\n+B.15\t8\t > T4949C\n+B.5\t9\t > C29635T\n+B.54\t10\t > C14805T,G26144T\n+B.47\tEngland/LIVE-A5D06/2020|20-03-17\t > C6681T,A10982G,G11801A\n+20A\t28\t > C241T,C3037T,C14408T,A23403G\n+B.1.108\t28\t > C241T,C3037T,C14408T,A23403G\n+B.20\t660\t > A14940G\n+B.11\tUSA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\t > T514C,C22033A\n+B.1.14\t664\t > C25692T\n+B.27\tEngland/SHEF-BFEBB/2020|20-03-24\t > C11747T,T24364G,G29032A\n+B.19\tUSA/CA-CZB-1051/2020|MT449644.1|20-04-06\t > G7273A,C10277T\n+B.45\tScotland/CVR780/2020|20-03-27\t > C5997T,C12710T,C28854T\n+19B\t676\t > C8782T,T28144C\n+A\t676\t > C8782T,T28144C\n+B.10\t698\t > C6696T\n+B.23\tEngland/SHEF-BFF21/2020|20-03-25\t > C20270T > A18671G,A29683T\n+B.33\t11\t > C14805T,G26144T > T17247C\n+B.28\tScotland/EDB199/2020|20-03-26\t > C14805T,G26144T > C22713T,G26031T,G28842T\n+B.29\tEngland/ALDP-9EE3AC/2020|20-05-06\t > C14805T,G26144T > G20991T,C23707T\n+B.40\t20\t > C14805T,G26144T > A2480G,C2558T\n+B.30\t21\t > C14805T,G26144T > A4236G,T25655C\n+B.41\t22\t > C14805T,G26144T > G5572T\n+B.1.105\tEngland/CAMB-75BD8/2020|20-03-29\t > C241T,C3037T,C14408T,A23403G > C18060T,G28514T\n+B.1.152\tEngland/ALDP-944BD9/2020|20-06-07\t > C241T,C3037T,C14408T,A23403G > G1914A,G4399T,T16456C,G27746T\n+B.1.103\t47\t > C241T,C3037T,C14408T,A23403G > C25665T,G28325T\n+B.1.378\t49\t > C241T,C3037T,C14408T,A23403G > G3871T\n+B.1.199\tUSA/UT-UPHL-201111720/2020|MW265609.1|20-04-30\t > C241T,C3037T,C14408T,A23403G > C2939T,T11698C,C18322T\n+B.1.139\t51\t > C241T,C3037T,C14408T,A23403G > A696C\n+B.1.91\tEngland/EXET-1358BE/2020|20-04-15\t > C241T,C3037T,C14408T,A23403G > A20092G,G24077T,T28630G\n+B.1.350\t53\t > C241T,C3037T,C14408T,A23403G > G25563T\n+B.1.222\tScotland/GCVR-172150/2020|20-03-30\t > C241T,C3037T,C14408T,A23403G > C1545T,C22879A\n+B.1.379\t274\t > C241T,C3037T,C14408T,A23403G > A11782G,G22203T\n+B.1.182\t275\t > C241T,C3037T,C14408T,A23403G > A20268G\n+B.1.5\t341\t > C241T,C3037T,C14408T,A23403G > C15324T\n+B.1.215\tScotland/GCVR-173C30/2020|20-04-07\t > C241T,C3037T,C14408T,A23403G > G3831A,T7441C\n+B.1.81\tEngland/BRIS-12468B/2020|20-04-09\t > C241T,C3037T,C14408T,A23403G > C1909T,T27576C\n+B.1.201\tEngland/NORW-E9DF7/2020|20-05-02\t > C241T,C3037T,C14408T,A23403G > C2940T,C7765T\n+B.1.395\t398\t > C241T,C3037T,C14408T,A23403G > C6990T\n+B.1.67\tWales/PHWC-29E43/2020|20-04-04\t > C241T,C3037T,C14408T,A23403G > G9220A,T26512C\n+B.1.98\tEngland/LOND-D3534/2020|20-03-27\t > C241T,C3037T,C14408T,A23403G > C25350T,T27280C\n+B.1.76\tEngland/LIVE-A63E5/2020|20-03-18\t > C241T,C3037T,C14408T,A23403G > G680T,T17835C\n+B.1.383\tWales/PHWC-260C8/2020|20-03-26\t > C241T,C3037T,C14408T,A23403G > C12242T,C22264T,A25575C\n+B.1.142\tWales/PHWC-16C6F0/2020|20-06-09\t > C241T,C3037T,C14408T,A23403G > T8944C,C14741T,G25552T\n+B.1.376\t407\t > C241T,C3037T,C14408T,A23403G > C5506T,G14241T\n+B.1.23\t408\t > C241T,C3037T,C14408T,A23403G > T7438C,C29353T\n+B.1.198\tEngland/BRIS-128DCE/2020|20-04-14\t > C241T,C3037T,C14408T,A23403G > A187G,C12213T,C19066A\n+B.1.153\t412\t > C241T,C3037T,C14408T,A23403G > G14580T\n+B.1.70\t414\t > C241T,C3037T,C14408T,A23403G > C1884T,T26497C\n+B.1.145\tIND/GBRC99/2020|MT509504.1|20-05-06\t > C241T,C3037T,C14408T,A23403G > G4866T,C14425A,A21511G\n+B.1.197\tAUS/VIC1239/2020|MT451821.1|20-04-02\t > C241T,C3037T,C14408T,A23403G > C6723T,T26094C,G28476T\n+B.1.143\t417\t > C241T,C3037T,C14408T,A23403G > C4084T\n+B.1.187\tPOL/PL_MCB_75/2020|MW273857.1|20-04-16\t > C241T,C3037T,C14408T,A23403G > A544G,C17104T\n+B.1.414\t419\t > C241T,C3037T,C14408T,A23403G > G20275A\n+B.1.93\tEngland/NORT-289814/2020|20-04-01\t > C241T,C3037T,C14408T,A23403G > C9165T,C13862T,T21033C,C28836T\n+B.1.78\tNorthern_Ireland/NIRE-1022CB/2020|20-03-25\t > C241T,C3037T,C14408T,A23403G > C1997T,C28708T,G29422T\n+20B\t426\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C\n+B.18\tEngland/LIVE-9D7D6/2020|20-04-15\t > G29711T > C1218T,C27493T,G27806T\n+B.51\tUSA/WI-UW-325/2020|MT706432.1|20-04-24\t > G29711T > T2116A,C12880T,C28854T\n+A.1\tUSA/MN-MDH-1475/2020|MT920008.1|20-03-23\t > C8782T'..b'land/MILK-ACCF27/2020|20-10-21\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > A8072G > T3873C,G3880A,C18131T,G26640T\n+B.1.1.279\tEngland/BRIS-125D67/2020|20-03-29\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G21624T > C6347T,G18859T\n+B.1.1.207\t576\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > A10948G > T9172C,G26730T\n+B.1.1.41\tWales/PHWC-162751/2020|20-05-27\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > A10948G > C6312A,G18538T,A20136G\n+B.1.1.308\tEngland/CAMC-A40F67/2020|20-10-06\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G25617T > G1590T,A11120G,A12529G\n+B.1.1.309\t586\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G25617T > C835T\n+B.1.1.310\t587\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G25617T > A6900G\n+B.1.1.260\t590\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G21724T > G11230T,G23587C\n+B.1.1.199\t591\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G21724T > T7792C\n+B.1.1.259\t592\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G21724T > G17302T,C25046T\n+B.1.1.300\t600\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G10265A > T13794G\n+B.1.1.299\tEngland/ALDP-4A2BFC/2020|20-05-22\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G10265A > A20826G,A23207G\n+B.1.1.301\tEngland/ALDP-49F5B8/2020|20-05-22\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G10265A > A19650G,T21368C\n+B.1.1.233\tUSA/WA-S2598/2020|MT831859.1|20-06-18\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G16813A > C6445T,G16852T,G29254T\n+B.1.1.65\tUSA/WA-S820/2020|MT641503.1|20-04-15\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G16813A > A5538T,G17261A,T25783C\n+L.2\t617\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > C19170T,G19509A > C26313T\n+B.1.507\tUSA/VA-DCLS-1147/2020|MT992749.1|20-04\t > C241T,C3037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > A20553G,G22487C\n+B.1.503\tUSA/CA-CZB-1275/2020|MT533209.1|20-04-16\t > C241T,C3037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > C23685T,G25947C,G27703T\n+B.1.499\tUSA/NY-QDX-2365/2020|MW191144.1|20-03-16\t > C241T,C3037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > C28863T\n+B.1.508\tUSA/CA-CZB-2139/2020|MT750510.1|20-05-21\t > C241T,C3037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > C5540A,C19145T\n+B.1.502\tUSA/FL-BPHL-1988/2020|MW286761.1|20-04-18\t > C241T,C3037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > G3638A,T13914C,C16217T\n+B.1.501\tUSA/NC-QDX-174/2020|MT786825.1|20-04-27\t > C241T,C3037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > C10458T,C18693A,G26828T\n+B.1.504\tISR/hCov-19-Israel-CVL-n-9434/2020|MW674838.1|20-04-19\t > C241T,C3037T,C14408T,A23403G > G25563T > C1059T > C11916T > C18998T,G29540A > C21731T,G26217T,G29645T\n+B.1.36.17\t227\t > C241T,C3037T,C14408T,A23403G > G25563T > C18877T > C26735T > C22444T,C28854T > T1947C,C7528T,C29555T\n+C.3\tEngland/ALDP-49EC3C/2020|20-05-20\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > G2447T,G22199T,G29392T,C29541T\n+C.14\t503\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > G29179T\n+C.13\tPER/covper040/2020|MW030271.1|20-05-05\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > C12854T,G20752T,A21131G\n+C.4\tSRB/NS19622-16-06/2020|MW327528.1|20-06-15\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > G10097A,C23731T > C4002T,C13536T > G24794T\n+N.1\tUSA/MA_MGH_00693/2020|MT520290.1|20-04-06\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > T29148C > G25793T,T27299C > T25793G > C25916T,T28360C,C29769T\n+N.4\tCHL/Santiago-PUC_MVL_0491/2020|MW365473.1|20-05-13\t > C241T,C3037T,C14408T,A23403G > G28882A,G28883C > G28881A > T29148C > G25793T,T27299C > T25793G > A2475G,C14805T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_19_path_mutations.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_19_path_mutations.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,438 @@\n+sample_id\tpath_from_root\n+England/BRIS-1853249/2020|20-04-02\t (1) > C24034T (2) > C29518T\n+NPL/61-TW/2020|MT072688.1|20-01-13\t (1) > C24034T (2) > \n+Wales/PHWC-25B04/2020|20-03-24\t (1) > C875T (3) > A20637G\n+Wales/LIVE-A6831/2020|20-03-16\t (1) > C875T (3) > T14859C\n+Scotland/EDB1317/2020|20-04-09\t (1) > C7423T (4) > G4207A,T7423C\n+Scotland/EDB354/2020|20-03-30\t (1) > C7423T (4) > A29780C\n+England/SHEF-BFF8B/2020|20-03-25\t (1) > C20270T (5) > C1473T\n+England/SHEF-BFFC7/2020|20-03-25\t (1) > T4949C (8) > G28027T\n+England/PHEC-1E01E/2020|20-04-03\t (1) > T4949C (8) > C22445T\n+DP0476/2020|LC571003.1|20-02-16\t (1) > C29635T (9) > C29592T\n+DP0191/2020|LC570980.1|20-02-15\t (1) > C29635T (9) > A3854G\n+England/LIVE-A5D06/2020|20-03-17\t (1) > C6681T,A10982G,G11801A\n+USA/CA-CZB-1091/2020|MT460091.1|20-05-01\t (1) > A14940G (660) > C15024T\n+USA/CA-CZB-11876/2020|MW276506.1|20-04-08\t (1) > A14940G (660) > A26120G\n+USA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\t (1) > T514C,C22033A\n+USA/CA-CZB-1015/2020|MT438733.1|20-04-22\t (1) > C25692T (664) > T15867A\n+USA/CA-CZB-1073/2020|MT449664.1|20-04-21\t (1) > C25692T (664) > G10617A,G22225T\n+England/SHEF-BFEBB/2020|20-03-24\t (1) > C11747T,T24364G,G29032A\n+USA/CA-CZB-1051/2020|MT449644.1|20-04-06\t (1) > G7273A,C10277T\n+HKG/HKU-904a/2020|MT365032.1|20-01-30\t (1) > C8782T,T28144C (676) > C4158T,C18828T\n+England/LIVE-9E66F/2020|20-04-10\t (1) > C6696T (698) > C7765T,G10256T\n+Scotland/CVR705/2020|20-03-26\t (1) > C6696T (698) > C11001T,G17122T\n+Scotland/EDB046/2020|20-03-15\t (1) > C14805T,G26144T (10) > T17247C (11) > C9996T,T26144G\n+Scotland/EDB199/2020|20-03-26\t (1) > C14805T,G26144T (10) > C22713T,G26031T,G28842T\n+England/ALDP-9EE3AC/2020|20-05-06\t (1) > C14805T,G26144T (10) > G20991T,C23707T\n+England/CAMB-8042A/2020|20-04-10\t (1) > C14805T,G26144T (10) > A2480G,C2558T (20) > A4015T\n+England/CAMB-737B8/2020|20-03-30\t (1) > C14805T,G26144T (10) > A2480G,C2558T (20) > G3971T,G28380T\n+USA/WA-S885/2020|MT642386.1|20-04-22\t (1) > C14805T,G26144T (10) > A4236G,T25655C (21) > G7739T,C25904T\n+USA/UT-QDX-1870/2020|MW190618.1|20-03-16\t (1) > C14805T,G26144T (10) > A4236G,T25655C (21) > A5269G,C9943T\n+USA/WA3-UW1/2020|MT163716.1|20-02-27\t (1) > C14805T,G26144T (10) > G5572T (22) > T2446C,C3411T\n+SouthKorea/KOR-BA-ACH_2719/2020|MT304476.1|20-02-29\t (1) > C14805T,G26144T (10) > G5572T (22) > C28311T\n+England/LIVE-9D7D6/2020|20-04-15\t (1) > G29711T (667) > C1218T,C27493T,G27806T\n+USA/WI-UW-325/2020|MT706432.1|20-04-24\t (1) > G29711T (667) > T2116A,C12880T,C28854T\n+Scotland/CVR780/2020|20-03-27\t (1) > C5997T,C12710T,C28854T\n+USA/MN-MDH-1475/2020|MT920008.1|20-03-23\t (1) > C8782T,T28144C (676) > A7966G,A17858G,C18060T,A22422G\n+England/SHEF-BFF21/2020|20-03-25\t (1) > C20270T (5) > A18671G,A29683T\n+Switzerland/100159/2020|LR884273.1|20-03-16\t (1) > C14805T,G26144T (10) > T17247C (11) > C12400T (12) > C16995T\n+England/LOND-126031F/2020|20-03-15\t (1) > C14805T,G26144T (10) > T17247C (11) > C12400T (12) > A20511G\n+USA/NY-QDX-1999/2020|MW190795.1|20-03-16\t (1) > C14805T,G26144T (10) > T17247C (11) > C8078T (13) > G10754A\n+USA/NY-QDX-1969/2020|MW190709.1|20-03-15\t (1) > C14805T,G26144T (10) > T17247C (11) > C8078T (13) > \n+England/BRIS-130965/2020|20-04-13\t (1) > C14805T,G26144T (10) > T17247C (11) > A7479G,C10741T,C25572T,C27498T\n+Scotland/CVR44/2020|20-03-13\t (1) > C14805T,G26144T (10) > T17247C (11) > A1587G (15) > G443A\n+Scotland/CVR839/2020|20-03-27\t (1) > C14805T,G26144T (10) > T17247C (11) > A1587G (15) > T7816A,C24023T\n+Scotland/CVR207/2020|20-03-18\t (1) > C14805T,G26144T (10) > T17247C (11) > C988T,G12832A\n+England/NORT-284A9B/2020|20-03-25\t (1) > C14805T,G26144T (10) > T17247C (11) > A1515G,C9223T (17) > G28655A,C28657T\n+Scotland/CVR10/2020|20-03-10\t (1) > C14805T,G26144T (10) > T17247C (11) > A1515G,C9223T (17) > T9223C,A21625G\n+Spain/H12_46/2020|LR884009.1|20-04-08\t (1) > C8782T,T28144C (676) > A23403G,C26088T (677) > G23403A (678) > C7967T,C16694T\n+Spain/R11/2020|LR884126.1|20-03-06\t (1) > C8782T,T'..b'1T,C3037T,C14408T,A23403G (28) > G25563T (53) > C1059T (61) > C11916T (86) > C18998T,G29540A (91) > C28863T\n+USA/CA-CZB-2139/2020|MT750510.1|20-05-21\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C1059T (61) > C11916T (86) > C18998T,G29540A (91) > C5540A,C19145T\n+USA/FL-BPHL-1988/2020|MW286761.1|20-04-18\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C1059T (61) > C11916T (86) > C18998T,G29540A (91) > G3638A,T13914C,C16217T\n+USA/NC-QDX-174/2020|MT786825.1|20-04-27\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C1059T (61) > C11916T (86) > C18998T,G29540A (91) > C10458T,C18693A,G26828T\n+ISR/hCov-19-Israel-CVL-n-9434/2020|MW674838.1|20-04-19\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C1059T (61) > C11916T (86) > C18998T,G29540A (91) > C21731T,G26217T,G29645T\n+England/ALDP-94EB75/2020|20-06-17\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C2416T (191) > G8371T (193) > C3811T,G22225A,C22477T (197) > \n+England/ALDP-6E2806/2020|20-07-01\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C2416T (191) > G8371T (193) > C3811T,G22225A,C22477T (197) > T16456G,C27769G\n+Wales/PHWC-360A7/2020|20-04-29\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > T19839C (429) > G11801A,G25552T (433) > T4330C,T24063C\n+Wales/PHWC-260AA/2020|20-03-24\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > T19839C (429) > G11801A,G25552T (433) > T7168C\n+England/CAMB-72B44/2020|20-03-22\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > T28110C (501) > \n+England/CAMB-822D3/2020|20-04-12\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > T28110C (501) > \n+England/ALDP-49EC3C/2020|20-05-20\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > G2447T,G22199T,G29392T,C29541T\n+PER/covper024/2020|MW030255.1|20-07-04\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > G29179T (503) > C17436T,G27478T\n+PER/CoV-19_HRL-223/2020|MW185824.1|20-04-08\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > G29179T (503) > A10323G,G27160T\n+PER/covper040/2020|MW030271.1|20-05-05\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > C12854T,G20752T,A21131G\n+SRB/NS19622-16-06/2020|MW327528.1|20-06-15\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > G10097A,C23731T (499) > C4002T,C13536T (500) > G24794T\n+BRA/LRV-SARS.CoV-2.1/2020|MT807936.1|20-05-08\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > T29148C (542) > G25793T,T27299C (543) > T25793G (544) > C28969T\n+USA/WI-UW-114/2020|MT706234.1|20-03-30\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > T29148C (542) > G25793T,T27299C (543) > T25793G (544) > A14330G,A27989G\n+England/MILK-ABBF2B/2020|20-10-22\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C18877T (211) > C26735T (212) > C22444T,C28854T (223) > T1947C,C7528T,C29555T (227) > C10474T,C13536T\n+England/QEUH-96A85E/2020|20-08-14\t (1) > C241T,C3037T,C14408T,A23403G (28) > G25563T (53) > C18877T (211) > C26735T (212) > C22444T,C28854T (223) > T1947C,C7528T,C29555T (227) > T23986C\n+USA/MA_MGH_00693/2020|MT520290.1|20-04-06\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > T29148C (542) > G25793T,T27299C (543) > T25793G (544) > C25916T,T28360C,C29769T\n+CHL/Santiago-PUC_MVL_0491/2020|MW365473.1|20-05-13\t (1) > C241T,C3037T,C14408T,A23403G (28) > G28882A,G28883C (426) > G28881A (427) > T29148C (542) > G25793T,T27299C (543) > T25793G (544) > A2475G,C14805T\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_19_sample_names.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_19_sample_names.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,437 @@\n+England/BRIS-1853249/2020|20-04-02\n+NPL/61-TW/2020|MT072688.1|20-01-13\n+Wales/PHWC-25B04/2020|20-03-24\n+Wales/LIVE-A6831/2020|20-03-16\n+Scotland/EDB1317/2020|20-04-09\n+Scotland/EDB354/2020|20-03-30\n+England/SHEF-BFF8B/2020|20-03-25\n+England/SHEF-BFFC7/2020|20-03-25\n+England/PHEC-1E01E/2020|20-04-03\n+DP0476/2020|LC571003.1|20-02-16\n+DP0191/2020|LC570980.1|20-02-15\n+England/LIVE-A5D06/2020|20-03-17\n+USA/CA-CZB-1091/2020|MT460091.1|20-05-01\n+USA/CA-CZB-11876/2020|MW276506.1|20-04-08\n+USA/CDC-CruiseA-18/2020|MT159716.2|20-02-24\n+USA/CA-CZB-1015/2020|MT438733.1|20-04-22\n+USA/CA-CZB-1073/2020|MT449664.1|20-04-21\n+England/SHEF-BFEBB/2020|20-03-24\n+USA/CA-CZB-1051/2020|MT449644.1|20-04-06\n+HKG/HKU-904a/2020|MT365032.1|20-01-30\n+England/LIVE-9E66F/2020|20-04-10\n+Scotland/CVR705/2020|20-03-26\n+Scotland/EDB046/2020|20-03-15\n+Scotland/EDB199/2020|20-03-26\n+England/ALDP-9EE3AC/2020|20-05-06\n+England/CAMB-8042A/2020|20-04-10\n+England/CAMB-737B8/2020|20-03-30\n+USA/WA-S885/2020|MT642386.1|20-04-22\n+USA/UT-QDX-1870/2020|MW190618.1|20-03-16\n+USA/WA3-UW1/2020|MT163716.1|20-02-27\n+SouthKorea/KOR-BA-ACH_2719/2020|MT304476.1|20-02-29\n+England/LIVE-9D7D6/2020|20-04-15\n+USA/WI-UW-325/2020|MT706432.1|20-04-24\n+Scotland/CVR780/2020|20-03-27\n+USA/MN-MDH-1475/2020|MT920008.1|20-03-23\n+England/SHEF-BFF21/2020|20-03-25\n+Switzerland/100159/2020|LR884273.1|20-03-16\n+England/LOND-126031F/2020|20-03-15\n+USA/NY-QDX-1999/2020|MW190795.1|20-03-16\n+USA/NY-QDX-1969/2020|MW190709.1|20-03-15\n+England/BRIS-130965/2020|20-04-13\n+Scotland/CVR44/2020|20-03-13\n+Scotland/CVR839/2020|20-03-27\n+Scotland/CVR207/2020|20-03-18\n+England/NORT-284A9B/2020|20-03-25\n+Scotland/CVR10/2020|20-03-10\n+Spain/H12_46/2020|LR884009.1|20-04-08\n+Spain/R11/2020|LR884126.1|20-03-06\n+Spain/LP19_4952/2020|LR884066.1|20-03-07\n+Scotland/EDB5629/2020|20-03-24\n+Scotland/EDB5040/2020|20-04-02\n+England/BRIS-123965/2020|20-04-07\n+England/BRIS-125347/2020|20-03-27\n+IND/Isolate_9088/2020|MW555597.1|20-06-30\n+IND/763/2020|MT577009.1|20\n+England/CAMB-75BD8/2020|20-03-29\n+England/ALDP-944BD9/2020|20-06-07\n+USA/MI-MDHHS-SC20612/2020|MT585039.1|20-04-29\n+USA/MI-MDHHS-SC20597/2020|MT585043.1|20-04-29\n+USA/WI-UW-26/2020|MT706147.1|20-03-24\n+USA/IL-QDX-2568/2020|MW191367.1|20-03-14\n+USA/UT-UPHL-201111720/2020|MW265609.1|20-04-30\n+USA/IN-QDX-184/2020|MT786818.1|20-04-28\n+USA/WI-UW-558/2020|MT750137.1|20-06-25\n+England/EXET-1358BE/2020|20-04-15\n+EGY/CUNCI-HGC5I033/2020|MT614347.1|20-06-02\n+Scotland/GCVR-172150/2020|20-03-30\n+England/BRIS-124885/2020|20-03-24\n+England/BRIS-122C4F/2020|20-04-02\n+USA/RI-CDC-0556/2020|MT304488.1|20-03-01\n+Switzerland/100198/2020|LR884312.1|20-03-17\n+USA/WI-UW-37/2020|MT706158.1|20-03-22\n+Scotland/GCVR-173C30/2020|20-04-07\n+England/BRIS-12468B/2020|20-04-09\n+England/NORW-E9DF7/2020|20-05-02\n+Wales/PHWC-27B20/2020|20-03-30\n+Wales/PHWC-2624A/2020|20-03-27\n+Wales/PHWC-29E43/2020|20-04-04\n+England/LOND-D3534/2020|20-03-27\n+England/LIVE-A63E5/2020|20-03-18\n+Wales/PHWC-260C8/2020|20-03-26\n+Wales/PHWC-16C6F0/2020|20-06-09\n+Wales/PHWC-27461/2020|20-03-31\n+Wales/PHWC-29F13/2020|20-04-01\n+AUS/VIC989/2020|MT451674.1|20-03-31\n+AUS/VIC1056/2020|MT451723.1|20-04-03\n+England/LIVE-A65EF/2020|20-03-19\n+Wales/PHWC-2B7CE/2020|20-04-12\n+Scotland/GCVR-1725BE/2020|20-04-04\n+Scotland/CVR30/2020|20-03-13\n+IND/GBRC99/2020|MT509504.1|20-05-06\n+AUS/VIC1239/2020|MT451821.1|20-04-02\n+IND/GBRC128/2020|MT539172.1|20-05-02\n+IND/GBRC123/2020|MT539176.1|20-05-02\n+POL/PL_MCB_75/2020|MW273857.1|20-04-16\n+England/CAMB-7BED9/2020|20-04-04\n+Netherlands/NA_302/2020|LR878041.1|20-04-01\n+England/NORT-289814/2020|20-04-01\n+Northern_Ireland/NIRE-1022CB/2020|20-03-25\n+Poland/covid_hub_pl_ibch_0033/2020|LR899101.1|20-05-20\n+England/CAMB-76515/2020|20-03-29\n+England/LEED-2A8D10/2020|20-03-31\n+England/CAMB-7EBDF/2020|20-04-07\n+Scotland/CVR1519/2020|20-04-03\n+England/MILK-9589F6/2020|20-06-15\n+England/BRIS-128441/2020|20-04-16\n+England/NORW-E8C37/2020|20-04-13\n+Wales/PHWC-3122E/2020|20-04-10\n+Wales/PHWC-1645EC/2020|'..b'4-07\n+Netherlands/NA_589/2020|LR883868.1|20-04-05\n+Scotland/EDB2049/2020|20-04-18\n+Scotland/EDB2100/2020|20-04-19\n+USA/FL-BPHL-0540/2020|MT834625.1|20-03-21\n+CHL/Santiago-PUC_MVL_0011/2020|MW365225.1|20-03-18\n+USA/WI-UW-269/2020|MT429191.1|20-04-06\n+USA/NY-QDX-1993/2020|MW190794.1|20-03-18\n+USA/FL-BPHL-0321/2020|MT757040.1|20-04-16\n+USA/FL-BPHL-1841/2020|MW206510.1|20-04-08\n+USA/SEARCH-0792-SAN/2020|MT811373.1|20-04-06\n+USA/WA-S1037/2020|MT642186.1|20-05-03\n+USA/MN-QDX-981/2020|MW065078.1|20-03-15\n+USA/MD-MDH-0164/2020|MT937827.1|20-07-15\n+USA/CA-QDX-2685/2020|MW191430.1|20-03-17\n+USA/MN-QDX-1328/2020|MW065415.1|20-03-15\n+USA/TX-DSHS-1210/2020|MW246004.1|20-03-18\n+USA/UT-00495/2020|MT444543.1|20-04-02\n+USA/UT-00353/2020|MT444564.1|20-03-27\n+Scotland/EDB3598/2020|20-04-27\n+Scotland/EDB2451/2020|20-04-23\n+England/LIVE-A91F7/2020|20-03-25\n+England/BRIS-127AD7/2020|20-04-16\n+BHR/920262933_S19_L001/2020|MW228054.1|20-06-19\n+IND/GBRC-366a/2020|MT951170.1|20-06-18\n+SAU/596/2020|MT755893.1|20-02-18\n+BHR/920265546_S18_L001/2020|MW228055.1|20-06-21\n+SAU/578/2020|MT755891.1|20-02-17\n+USA/SEARCH-1094-SAN/2020|MT811526.1|20-06-19\n+Switzerland/300264/2020|LR898541.1|20-10-01\n+England/QEUH-963433/2020|20-08-10\n+USA/WA-S2264/2020|MT831437.1|20-06-09\n+USA/WA-S1922/2020|MT831459.1|20-06-03\n+USA/WA-S1775/2020|MT834200.1|20-06-01\n+England/LOND-D6EBE/2020|20-04-03\n+USA/WA-S860/2020|MT642111.1|20-04-24\n+England/BRIS-12A70A/2020|20-05-01\n+England/CAMB-77F61/2020|20-04-01\n+England/NORW-EE34B/2020|20-03-24\n+England/NORW-E8693/2020|20-04-16\n+Northern_Ireland/NIRE-FBB52/2020|20-04-13\n+Northern_Ireland/NIRE-FAC7E/2020|20-04-15\n+England/CAMB-81070/2020|20-04-20\n+Scotland/CVR41/2020|20-03-13\n+England/NORW-E8709/2020|20-04-18\n+USA/ME-HETL-J0061/2020|MT886346.1|20-03-20\n+USA/FL-BPHL-0905/2020|MT966149.1|20-06-24\n+USA/FL-BPHL-0303/2020|MT757111.1|20-05-30\n+England/CAMB-7CBD1/2020|20-04-05\n+Wales/PHWC-30957/2020|20-04-08\n+LC573289.2|20-06\n+USA/CA-CZB-4049/2020|MW134382.1|20-08-21\n+England/CAMB-74D5B/2020|20-03-19\n+England/MILK-ACCF27/2020|20-10-21\n+England/BRIS-125D67/2020|20-03-29\n+England/MILK-8664D7/2020|20-07-17\n+USA/VA-DCLS-1073/2020|MT981458.1|20-06\n+USA/VA-DCLS-0120/2020|MT482111.1|20-04\n+Wales/PHWC-162751/2020|20-05-27\n+England/CAMC-A40F67/2020|20-10-06\n+England/QEUH-9B6EAC/2020|20-09-09\n+England/NORT-2A4CAE/2020|20-09-17\n+Northern_Ireland/NIRE-FB3A5/2020|20-08-29\n+Northern_Ireland/NIRE-FB369/2020|20-08-31\n+England/LEED-2AA4EC/2020|20-04-06\n+England/LEED-2AA394/2020|20-03-31\n+England/BRIS-1854318/2020|20-04-28\n+England/BRIS-12E6FA/2020|20-04-20\n+England/WSFT-25C13CB/2020|20-04-17\n+England/PORT-2F5D9C/2020|20-06-05\n+England/ALDP-5D52BE/2020|20-06-18\n+England/ALDP-6FAF24/2020|20-06-29\n+England/ALDP-4A2BFC/2020|20-05-22\n+England/ALDP-49F5B8/2020|20-05-22\n+USA/WA-S2598/2020|MT831859.1|20-06-18\n+USA/WA-S820/2020|MT641503.1|20-04-15\n+Netherlands/NA_436/2020|LR883367.1|20-04-07\n+Netherlands/Friesland_33/2020|LR883315.1|20-04-14\n+USA/COVID20-0537/2020|MT981422.1|20-06-04\n+USA/COVID20-1129/2020|MW067826.1|20-07-10\n+USA/VA-DCLS-1147/2020|MT992749.1|20-04\n+USA/CA-CZB-1275/2020|MT533209.1|20-04-16\n+USA/NY-QDX-2365/2020|MW191144.1|20-03-16\n+USA/CA-CZB-2139/2020|MT750510.1|20-05-21\n+USA/FL-BPHL-1988/2020|MW286761.1|20-04-18\n+USA/NC-QDX-174/2020|MT786825.1|20-04-27\n+ISR/hCov-19-Israel-CVL-n-9434/2020|MW674838.1|20-04-19\n+England/ALDP-94EB75/2020|20-06-17\n+England/ALDP-6E2806/2020|20-07-01\n+Wales/PHWC-360A7/2020|20-04-29\n+Wales/PHWC-260AA/2020|20-03-24\n+England/CAMB-72B44/2020|20-03-22\n+England/CAMB-822D3/2020|20-04-12\n+England/ALDP-49EC3C/2020|20-05-20\n+PER/covper024/2020|MW030255.1|20-07-04\n+PER/CoV-19_HRL-223/2020|MW185824.1|20-04-08\n+PER/covper040/2020|MW030271.1|20-05-05\n+SRB/NS19622-16-06/2020|MW327528.1|20-06-15\n+BRA/LRV-SARS.CoV-2.1/2020|MT807936.1|20-05-08\n+USA/WI-UW-114/2020|MT706234.1|20-03-30\n+England/MILK-ABBF2B/2020|20-10-22\n+England/QEUH-96A85E/2020|20-08-14\n+USA/MA_MGH_00693/2020|MT520290.1|20-04-06\n+CHL/Santiago-PUC_MVL_0491/2020|MW365473.1|20-05-13\n' |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_20_general_stats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_20_general_stats.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Total Nodes in Tree: 1935 +Total Samples in Tree: 1234 +Total Condensed Nodes in Tree: 10 +Total Samples in Condensed Nodes: 20 +Total Tree Parsimony: 5362 |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_21_aberrant_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_21_aberrant_stats.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +NodeID Issue +241 internal-no-mutations |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_21_clades_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_21_clades_stats.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
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| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_21_mutations_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_21_mutations_stats.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,3841 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|
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_21_sample_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_21_sample_stats.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1235 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|
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_22_total_parsimony_tree.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_22_total_parsimony_tree.txt Tue May 11 17:53:49 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +Total Tree Parsimony 5362 |
| b |
| diff -r 000000000000 -r 524cb8f7a69a test-data/test_23_equally_parsimoniou.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_23_equally_parsimoniou.tabular Tue May 11 17:53:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,1097 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| diff -r 000000000000 -r 524cb8f7a69a test-data/test_23_neighbourhood.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_23_neighbourhood.tabular Tue May 11 17:53:49 2021 +0000 |
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| b'@@ -0,0 +1,344 @@\n+<tool id=\'usher\' name=\'UShER\' version=\'@TOOL_VERSION@+@GALAXY_TOOL_VERSION@\' profile=\'20.01\'>\n+ <description>ultrafast sample placement on existing trees</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro=\'edam_ontology\' />\n+ <expand macro=\'requirements\' />\n+ <version_command>usher --version</version_command>\n+ <command detect_errors=\'exit_code\'><![CDATA[\n+ #if $vcf.ext == \'vcf_bgzip\':\n+ ln -s \'$vcf\' input.vcf.gz &&\n+ ln -s \'$vcf.metadata.tabix_index\' input.vcf.gz.tbi &&\n+ #set $input_vcf = \'input.vcf.gz\'\n+ #else:\n+ ln -s \'$vcf\' input.vcf &&\n+ #set $input_vcf = \'input.vcf\'\n+ #end if\n+\n+ usher\n+ -v \'$input_vcf\'\n+ #if $tree\n+ -t \'${tree}\'\n+ #end if\n+ #if $load_mutation_annotated_tree\n+ -i \'${load_mutation_annotated_tree}\'\n+ #end if\n+ $output_options.save_mutation_annotated_tree\n+ $sort_mode\n+ $collapse_options.collapse_tree\n+ $collapse_options.collapse_output_tree\n+ #if $max_uncertainty_per_sample\n+ -e $max_uncertainty_per_sample\n+ #end if\n+ $output_options.write_uncondensed_final_tree\n+ #if $output_options.write_subtrees_size\n+ -k $output_options.write_subtrees_size\n+ #end if\n+ #if $output_options.write_single_subtree\n+ -K $output_options.write_single_subtree\n+ #end if\n+ $output_options.write_parsimony_scores_per_node\n+ #if $output_options.multiple_placements\n+ -M $output_options.multiple_placements\n+ #end if\n+ #if $retain_input_branch_lengths\n+ $retain_input_branch_lengths\n+ #end if\n+ -T \\${GALAXY_SLOTS:-1}\n+ -d ./\n+ #if $output_options.write_subtrees_size\n+ && mkdir -p out_subtrees out_subtrees_expanded out_subtrees_mutations\n+ && mv subtree*expanded.txt ./out_subtrees_expanded\n+ && mv subtree*mutations.txt ./out_subtrees_mutations\n+ && mv subtree*.nh ./out_subtrees\n+ #end if\n+ ]]> </command>\n+ <inputs>\n+ <param name="vcf" type="data" format="vcf,vcf_bgzip" label="VCF file" help="Input VCF file."/>\n+ <param name="tree" type="data" format="newick" optional="True" label="Tree file" help="Input tree file in Newick format."/>\n+ <param argument="--load-mutation-annotated-tree" type="data" format="protobuf3" optional="True" label="Mutation-annotated tree object" help="Load a mutation annotated tree file, in protocol-buffers format (protobuf3)."/>\n+ <param name="sort_mode" type="select" label="Mode of sorting new samples">\n+ <option value="">Default sorting</option>\n+ <option value="--sort-before-placement-1">Sort based on computed parsimony score and then number of optimal placements before the actual placement (-s)</option>\n+ <option value="--sort-before-placement-1 --reverse-sort">Sort based on computed parsimony score and then number of optimal placements before the actual placement [reversed] (-s -r)</option>\n+ <option value="--sort-before-placement-2">Sort based on the number of optimal placements and then the parsimony score before the actual placement (-S)</option>\n+ <option value="--sort-before-placement-2 --reverse-sort">Sort based on the number of optimal placements and then the parsimony score before the actual placement [reversed] (-S -r)</option>\n+ <option value="--sort-before-placement-3">Sort based on the number of ambiguous bases (-A)</option>\n+ </param>\n+ <param argument="--max-uncertainty-per-sample" type="integer" optional="True" min="0" max="10000000" value="" label="Maximum number of equally parsimonious placements" help="Maximum number of equally parsimonious placements allowed per sample beyond which the sample is ignored." />\n+ <param a'..b'S-CoV-2 research groups, including the UCSC Genome Browser team and Rob Lanfear\xe2\x80\x99s global phylogeny releases.\n+\n+----\n+ \n+.. class:: infomark\n+ \n+**How UShER works?**\n+\n+Given existing samples, whose genotypes and phylogenetic tree is known, and the genotypes of new samples, UShER aims to incorporate new samples into the phylogenetic tree while preserving the topology of existing samples and maximizing parsimony. UShER\xe2\x80\x99s algorithm consists of two phases: (i) the pre-processing phase and (ii) the placement phase.\n+\n+In the pre-processing phase, UShER accepts the phylogenetic tree of existing samples in a Newick format and their genotypes, specified as a set of single-nucleotide variants with respect to a reference sequence (UShER currently ignores indels), in a VCF format. For each site in the VCF, UShER uses `Fitch-Sankoff algorithm <https://evolution.gs.washington.edu/gs541/2010/lecture1.pdf>`_ to find the most parsimonious nucleotide assignment for every node of the tree (UShER automatically labels internal tree nodes). \n+\n+When a sample contains ambiguous genotypes, multiple nucleotides may be most parsimonious at a node. To resolve these, UShER assigns it any one of the most parsimonious nucleotides with preference, when possible, given to the reference base. UShER also allows the VCF to specify ambiguous bases in samples using `IUPAC format <https://www.bioinformatics.org/sms/iupac.html>`_, which are also resolved to a unique base using the above strategy. When a node is found to carry a mutation, i.e. the base assigned to the node differs from its parent, the mutation gets added to a list of mutations corresponding to that node. Finally, UShER uses `protocol buffers <https://developers.google.com/protocol-buffers>`_ to store in a file, the Newick string corresponding to the input tree and a list of lists of node mutation, which we refer to as mutation-annotated tree object.\n+\n+The mutation-annotated tree object carries sufficient information to derive parsimony-resolved genotypes for any tip of the tree using the sequence of mutations from the root to that tip. Compared to other tools that use full multiple-sequence alignment (MSA) to guide the placement, UShER\'s mutation-annotated tree object is compact and is what helps make it fast.\n+\n+In the placement phase, UShER loads the pre-processed mutation-annotated tree object and the genotypes of new samples in a VCF format and sequentially adds the new samples to the tree. For each new sample, UShER computes the additional parsimony score required for placing it at every node in the current tree while considering the full path of mutations from the root of the tree to that node. \n+\n+Next, UShER places the new sample at the node that results in the smallest additional parsimony score. When multiple node placements are equally parsimonious, UShER picks the node with a greater number of descendant leaves for placement. If the choice is between a parent and its child node, the parent node would always be selected by this rule. However, a more accurate placement should reflect the number of leaves uniquely attributable to the child versus parent node. Therefore, in these cases, UShER picks the parent node if the number of descendant leaves of the parent that are not shared with the child node exceed the number of descendant leaves of the child. \n+\n+UShER also automatically imputes and reports ambiguous genotypes for the newly added samples and ignores missing bases, such as \'N\' or \'.\' (i.e. missing bases never contribute to the parsimony score).\n+\n+At the end of the placement phase, UShER allows the user to create another protocol-buffer (protobuf) file containing the mutation-annotated tree object for the newly generated tree including added samples. This allows for another round of placements to be carried out over and above the newly added samples.\n+\n+\n+ ]]> </help>\n+ <expand macro="citations" />\n+</tool>\n' |