changeset 0:5e258fba246c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c67950184792952302f0e89354c311d4e5ed774c"
author iuc
date Fri, 08 May 2020 12:59:27 -0400
parents
children 0bc0009f9ea0
files static/images/table_description.png test-data/Mbovis-01D6_avg_mq.json test-data/Mbovis-01D6_cascade_table.xlsx test-data/Mbovis-01D6_snps.json test-data/Mbovis-01D6_snps.newick test-data/Mbovis-01D6_sort_table.xlsx test-data/Mbovis-01D_avg_mq.json test-data/Mbovis-01D_cascade_table.xlsx test-data/Mbovis-01D_snps.json test-data/Mbovis-01D_snps.newick test-data/Mbovis-01D_sort_table.xlsx test-data/Mbovis-01_avg_mq.json test-data/Mbovis-01_cascade_table.xlsx test-data/Mbovis-01_snps.json test-data/Mbovis-01_snps.newick test-data/Mbovis-01_sort_table.xlsx test-data/cascade_table.xlsx test-data/input_avg_mq_json.json test-data/input_newick.newick test-data/input_snps_json.json test-data/sort_table.xlsx tool-data/vsnp_genbank.loc.sample tool_data_table_conf.xml.sample vsnp_build_tables.py vsnp_build_tables.xml
diffstat 25 files changed, 610 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
Binary file static/images/table_description.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01D6_avg_mq.json	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+{"name":null,"index":["NC_002945.4:1057","NC_002945.4:4480","NC_002945.4:8741","NC_002945.4:29061","NC_002945.4:33788","NC_002945.4:41228","NC_002945.4:41437","NC_002945.4:50470","NC_002945.4:59861","NC_002945.4:69913","NC_002945.4:70082","NC_002945.4:70438","NC_002945.4:79918","NC_002945.4:96244","NC_002945.4:110198","NC_002945.4:114965","NC_002945.4:117800","NC_002945.4:127447","NC_002945.4:130166","NC_002945.4:130237","NC_002945.4:140686","NC_002945.4:143799","NC_002945.4:144992","NC_002945.4:148871","NC_002945.4:159370","NC_002945.4:160535","NC_002945.4:165799","NC_002945.4:166696","NC_002945.4:179885","NC_002945.4:189083","NC_002945.4:192177","NC_002945.4:198890","NC_002945.4:223919","NC_002945.4:230661","NC_002945.4:232188","NC_002945.4:295519","NC_002945.4:299636","NC_002945.4:304339","NC_002945.4:319911","NC_002945.4:332124","NC_002945.4:332128","NC_002945.4:332144","NC_002945.4:332145","NC_002945.4:332154","NC_002945.4:332215","NC_002945.4:332218","NC_002945.4:333010","NC_002945.4:340088","NC_002945.4:340090","NC_002945.4:340091","NC_002945.4:340092","NC_002945.4:340097","NC_002945.4:362818","NC_002945.4:364560","NC_002945.4:364804","NC_002945.4:366022","NC_002945.4:407246","NC_002945.4:430077","NC_002945.4:438482","NC_002945.4:441762","NC_002945.4:449922","NC_002945.4:452398","NC_002945.4:460722","NC_002945.4:467343","NC_002945.4:467402","NC_002945.4:479644","NC_002945.4:483845","NC_002945.4:485584","NC_002945.4:488897","NC_002945.4:490878","NC_002945.4:507929","NC_002945.4:518522","NC_002945.4:519412","NC_002945.4:541571","NC_002945.4:544180","NC_002945.4:577068","NC_002945.4:598704","NC_002945.4:600207","NC_002945.4:611077","NC_002945.4:622386","NC_002945.4:641896","NC_002945.4:642875","NC_002945.4:644245","NC_002945.4:649910","NC_002945.4:652349","NC_002945.4:673880","NC_002945.4:680416","NC_002945.4:685069","NC_002945.4:701329","NC_002945.4:701386","NC_002945.4:712319","NC_002945.4:723170","NC_002945.4:726979","NC_002945.4:737636","NC_002945.4:738102","NC_002945.4:745507","NC_002945.4:760347","NC_002945.4:792617","NC_002945.4:804997","NC_002945.4:808601","NC_002945.4:811737","NC_002945.4:812709","NC_002945.4:828003","NC_002945.4:832093","NC_002945.4:833960","NC_002945.4:839308","NC_002945.4:843812","NC_002945.4:854043","NC_002945.4:865821","NC_002945.4:870116","NC_002945.4:884432","NC_002945.4:889897","NC_002945.4:905912","NC_002945.4:917766","NC_002945.4:920753","NC_002945.4:941068","NC_002945.4:942431","NC_002945.4:943719","NC_002945.4:946102","NC_002945.4:948022","NC_002945.4:948811","NC_002945.4:948974","NC_002945.4:965529","NC_002945.4:967989","NC_002945.4:973459","NC_002945.4:974604","NC_002945.4:976327","NC_002945.4:982301","NC_002945.4:990611","NC_002945.4:998183","NC_002945.4:998196","NC_002945.4:1018313","NC_002945.4:1021422","NC_002945.4:1034434","NC_002945.4:1036102","NC_002945.4:1036530","NC_002945.4:1096802","NC_002945.4:1104019","NC_002945.4:1104291","NC_002945.4:1124266","NC_002945.4:1137800","NC_002945.4:1139489","NC_002945.4:1159390","NC_002945.4:1160992","NC_002945.4:1168458","NC_002945.4:1186381","NC_002945.4:1190076","NC_002945.4:1190080","NC_002945.4:1190084","NC_002945.4:1191092","NC_002945.4:1199529","NC_002945.4:1199530","NC_002945.4:1199951","NC_002945.4:1206896","NC_002945.4:1212203","NC_002945.4:1213847","NC_002945.4:1214540","NC_002945.4:1224899","NC_002945.4:1230875","NC_002945.4:1244746","NC_002945.4:1259250","NC_002945.4:1264712","NC_002945.4:1295457","NC_002945.4:1312836","NC_002945.4:1314197","NC_002945.4:1333537","NC_002945.4:1335092","NC_002945.4:1341613","NC_002945.4:1383731","NC_002945.4:1405922","NC_002945.4:1412824","NC_002945.4:1412828","NC_002945.4:1412885","NC_002945.4:1412893","NC_002945.4:1421904","NC_002945.4:1442194","NC_002945.4:1467394","NC_002945.4:1470606","NC_002945.4:1479827","NC_002945.4:1481327","NC_002945.4:1484942","NC_002945.4:1492328","NC_002945.4:1498639","NC_002945.4:1501932","NC_002945.4:1509487","NC_002945.4:1517866","NC_002945.4:1524526","NC_002945.4:1529147","NC_002945.4:1533175","NC_002945.4:1535299","NC_002945.4:1535303","NC_002945.4:1535366","NC_002945.4:1536267","NC_002945.4:1547426","NC_002945.4:1568090","NC_002945.4:1584881","NC_002945.4:1591357","NC_002945.4:1594398","NC_002945.4:1597464","NC_002945.4:1597847","NC_002945.4:1600443","NC_002945.4:1619153","NC_002945.4:1619361","NC_002945.4:1625561","NC_002945.4:1628068","NC_002945.4:1632869","NC_002945.4:1659174","NC_002945.4:1682044","NC_002945.4:1701507","NC_002945.4:1711760","NC_002945.4:1716413","NC_002945.4:1717086","NC_002945.4:1720220","NC_002945.4:1741553","NC_002945.4:1762390","NC_002945.4:1790296","NC_002945.4:1799442","NC_002945.4:1803035","NC_002945.4:1817260","NC_002945.4:1828312","NC_002945.4:1833330","NC_002945.4:1863248","NC_002945.4:1871114","NC_002945.4:1880430","NC_002945.4:1894922","NC_002945.4:1896107","NC_002945.4:1915461","NC_002945.4:1915936","NC_002945.4:1920100","NC_002945.4:1932972","NC_002945.4:1941781","NC_002945.4:1954048","NC_002945.4:1957978","NC_002945.4:1958977","NC_002945.4:1961656","NC_002945.4:1974665","NC_002945.4:1989922","NC_002945.4:1996251","NC_002945.4:2002061","NC_002945.4:2007303","NC_002945.4:2010421","NC_002945.4:2020061","NC_002945.4:2021640","NC_002945.4:2024890","NC_002945.4:2027869","NC_002945.4:2035774","NC_002945.4:2036697","NC_002945.4:2049171","NC_002945.4:2057553","NC_002945.4:2059249","NC_002945.4:2059920","NC_002945.4:2075405","NC_002945.4:2078648","NC_002945.4:2093479","NC_002945.4:2096812","NC_002945.4:2099043","NC_002945.4:2118096","NC_002945.4:2121160","NC_002945.4:2137049","NC_002945.4:2138896","NC_002945.4:2145868","NC_002945.4:2163576","NC_002945.4:2204661","NC_002945.4:2210027","NC_002945.4:2239061","NC_002945.4:2257546","NC_002945.4:2267557","NC_002945.4:2268821","NC_002945.4:2283200","NC_002945.4:2283218","NC_002945.4:2283220","NC_002945.4:2283227","NC_002945.4:2283235","NC_002945.4:2283236","NC_002945.4:2283350","NC_002945.4:2283353","NC_002945.4:2283355","NC_002945.4:2283362","NC_002945.4:2283366","NC_002945.4:2283367","NC_002945.4:2283368","NC_002945.4:2283371","NC_002945.4:2308525","NC_002945.4:2310215","NC_002945.4:2333994","NC_002945.4:2339770","NC_002945.4:2358298","NC_002945.4:2360219","NC_002945.4:2368982","NC_002945.4:2369407","NC_002945.4:2378324","NC_002945.4:2381437","NC_002945.4:2384647","NC_002945.4:2410761","NC_002945.4:2412437","NC_002945.4:2413021","NC_002945.4:2418267","NC_002945.4:2428397","NC_002945.4:2433602","NC_002945.4:2479007","NC_002945.4:2492067","NC_002945.4:2497022","NC_002945.4:2499336","NC_002945.4:2506199","NC_002945.4:2508626","NC_002945.4:2513801","NC_002945.4:2515130","NC_002945.4:2520576","NC_002945.4:2524942","NC_002945.4:2528517","NC_002945.4:2529413","NC_002945.4:2532958","NC_002945.4:2538021","NC_002945.4:2539896","NC_002945.4:2549198","NC_002945.4:2573831","NC_002945.4:2615591","NC_002945.4:2631265","NC_002945.4:2656304","NC_002945.4:2656651","NC_002945.4:2662768","NC_002945.4:2663582","NC_002945.4:2667489","NC_002945.4:2683485","NC_002945.4:2688315","NC_002945.4:2729845","NC_002945.4:2747797","NC_002945.4:2749502","NC_002945.4:2758761","NC_002945.4:2767533","NC_002945.4:2770129","NC_002945.4:2794510","NC_002945.4:2806603","NC_002945.4:2807510","NC_002945.4:2807511","NC_002945.4:2809255","NC_002945.4:2819758","NC_002945.4:2823105","NC_002945.4:2870414","NC_002945.4:2870624","NC_002945.4:2873027","NC_002945.4:2884747","NC_002945.4:2886118","NC_002945.4:2890220","NC_002945.4:2893045","NC_002945.4:2899163","NC_002945.4:2899584","NC_002945.4:2900525","NC_002945.4:2918203","NC_002945.4:2924775","NC_002945.4:2927134","NC_002945.4:2931071","NC_002945.4:2931113","NC_002945.4:2942926","NC_002945.4:2946800","NC_002945.4:2956778","NC_002945.4:2964207","NC_002945.4:2978162","NC_002945.4:2978164","NC_002945.4:2983580","NC_002945.4:2984156","NC_002945.4:3018593","NC_002945.4:3031841","NC_002945.4:3039600","NC_002945.4:3040820","NC_002945.4:3042914","NC_002945.4:3045025","NC_002945.4:3053649","NC_002945.4:3053756","NC_002945.4:3063074","NC_002945.4:3068041","NC_002945.4:3069493","NC_002945.4:3070642","NC_002945.4:3088868","NC_002945.4:3093531","NC_002945.4:3098932","NC_002945.4:3100639","NC_002945.4:3103354","NC_002945.4:3106064","NC_002945.4:3106527","NC_002945.4:3116059","NC_002945.4:3127117","NC_002945.4:3137471","NC_002945.4:3140342","NC_002945.4:3151212","NC_002945.4:3154140","NC_002945.4:3172929","NC_002945.4:3173568","NC_002945.4:3191792","NC_002945.4:3247551","NC_002945.4:3250072","NC_002945.4:3250245","NC_002945.4:3270181","NC_002945.4:3294771","NC_002945.4:3295991","NC_002945.4:3297558","NC_002945.4:3304410","NC_002945.4:3304946","NC_002945.4:3306898","NC_002945.4:3310831","NC_002945.4:3319244","NC_002945.4:3330907","NC_002945.4:3338298","NC_002945.4:3347870","NC_002945.4:3368453","NC_002945.4:3371156","NC_002945.4:3396621","NC_002945.4:3396650","NC_002945.4:3413486","NC_002945.4:3414355","NC_002945.4:3421983","NC_002945.4:3422650","NC_002945.4:3439578","NC_002945.4:3451869","NC_002945.4:3453219","NC_002945.4:3460907","NC_002945.4:3464357","NC_002945.4:3464485","NC_002945.4:3464524","NC_002945.4:3468669","NC_002945.4:3476130","NC_002945.4:3482644","NC_002945.4:3484836","NC_002945.4:3486507","NC_002945.4:3493554","NC_002945.4:3495510","NC_002945.4:3497957","NC_002945.4:3533661","NC_002945.4:3546799","NC_002945.4:3553753","NC_002945.4:3564896","NC_002945.4:3567535","NC_002945.4:3574014","NC_002945.4:3574955","NC_002945.4:3591452","NC_002945.4:3600600","NC_002945.4:3622899","NC_002945.4:3624371","NC_002945.4:3626128","NC_002945.4:3630061","NC_002945.4:3645682","NC_002945.4:3655045","NC_002945.4:3667823","NC_002945.4:3712401","NC_002945.4:3718169","NC_002945.4:3718628","NC_002945.4:3719802","NC_002945.4:3723554","NC_002945.4:3725203","NC_002945.4:3729351","NC_002945.4:3751627","NC_002945.4:3769174","NC_002945.4:3776764","NC_002945.4:3778473","NC_002945.4:3800223","NC_002945.4:3805467","NC_002945.4:3816878","NC_002945.4:3821259","NC_002945.4:3839650","NC_002945.4:3846859","NC_002945.4:3874432","NC_002945.4:3877448","NC_002945.4:3884519","NC_002945.4:3888418","NC_002945.4:3902781","NC_002945.4:3905690","NC_002945.4:3957298","NC_002945.4:3966140","NC_002945.4:3969490","NC_002945.4:3969558","NC_002945.4:3969875","NC_002945.4:4003460","NC_002945.4:4008509","NC_002945.4:4010760","NC_002945.4:4017319","NC_002945.4:4018300","NC_002945.4:4029201","NC_002945.4:4046572","NC_002945.4:4070056","NC_002945.4:4076594","NC_002945.4:4077189","NC_002945.4:4080736","NC_002945.4:4096612","NC_002945.4:4128841","NC_002945.4:4130927","NC_002945.4:4149101","NC_002945.4:4155870","NC_002945.4:4159272","NC_002945.4:4160820","NC_002945.4:4162407","NC_002945.4:4162554","NC_002945.4:4180986","NC_002945.4:4205111","NC_002945.4:4207380","NC_002945.4:4214259","NC_002945.4:4219009","NC_002945.4:4222196","NC_002945.4:4226875","NC_002945.4:4231626","NC_002945.4:4245762","NC_002945.4:4251588","NC_002945.4:4264139","NC_002945.4:4278315","NC_002945.4:4281136","NC_002945.4:4282825","NC_002945.4:4293932","NC_002945.4:4298964","NC_002945.4:4303164","NC_002945.4:4311425","NC_002945.4:4321337","NC_002945.4:4339036","NC_002945.4:4347304","NC_002945.4:228109","NC_002945.4:331051","NC_002945.4:331241","NC_002945.4:331411","NC_002945.4:960995","NC_002945.4:997676","NC_002945.4:1005705","NC_002945.4:1348342","NC_002945.4:1723583","NC_002945.4:1961826","NC_002945.4:3373966","NC_002945.4:3941254","NC_002945.4:4236320","NC_002945.4:1277988","NC_002945.4:1382465","NC_002945.4:1463503","NC_002945.4:1704859","NC_002945.4:1806623","NC_002945.4:1911237","NC_002945.4:3942270"],"data":[60,60,60,59,60,59,60,59,59,60,60,59,60,59,60,60,59,59,60,60,60,60,59,59,59,59,60,59,60,59,60,60,60,60,60,59,60,60,59,59,59,59,59,59,59,59,59,57,57,57,57,57,58,59,60,60,60,59,59,60,59,59,60,59,60,60,59,60,60,59,59,59,59,60,60,59,59,59,59,60,60,60,60,60,59,60,59,60,60,60,60,59,59,60,59,59,59,59,59,59,59,60,60,59,58,60,59,60,59,59,59,59,59,60,59,59,60,59,59,59,60,59,59,59,60,60,60,59,59,60,60,60,59,60,59,59,55,60,60,60,59,59,60,59,60,60,52,55,56,59,59,59,60,59,60,60,59,59,60,60,59,59,60,59,59,59,60,59,60,60,59,59,56,56,59,60,59,58,60,59,59,60,59,59,59,59,59,60,59,58,57,57,60,59,60,60,59,60,59,60,59,59,59,60,59,59,60,60,60,59,60,60,60,60,59,60,59,59,60,60,59,59,59,60,60,59,60,59,60,60,59,59,59,59,60,60,59,59,59,59,59,59,59,59,59,60,60,59,59,60,60,60,59,60,59,59,60,60,59,59,59,59,59,60,60,60,59,60,59,59,59,59,59,59,60,60,60,60,60,60,60,60,59,60,59,60,60,60,59,59,60,59,60,60,60,60,59,60,60,59,60,60,59,59,60,60,60,59,60,60,59,59,60,59,60,60,59,59,60,60,60,59,60,59,59,59,59,60,60,59,59,59,60,60,60,59,59,60,60,59,60,60,60,59,59,59,60,59,59,60,59,59,60,60,60,60,59,60,60,60,59,60,59,59,60,60,60,60,59,60,60,60,59,59,60,59,60,59,59,59,59,59,60,59,60,59,60,59,60,59,59,60,60,60,60,59,59,59,60,60,60,60,58,60,59,60,59,59,60,60,60,59,59,59,59,59,59,60,59,59,60,60,60,59,60,60,59,60,59,60,60,60,60,60,60,60,59,60,59,59,59,59,59,59,59,59,59,59,59,59,60,60,60,60,60,59,60,60,59,59,59,59,59,59,59,60,60,59,60,59,60,60,60,59,60,60,59,59,60,60,59,59,59,60,59,59,59,60,59,59,60,60,59,60,59,60,60,60,59,59,59,60,60,60,59,60,59,59,59,60,59,59,59,60,60,60,59,59,60,60,60,59,59,59,60,56,60,60,59,60,60,60]}
\ No newline at end of file
Binary file test-data/Mbovis-01D6_cascade_table.xlsx has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01D6_snps.json	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+{"columns":["NC_002945.4:1005705","NC_002945.4:1348342","NC_002945.4:1382465","NC_002945.4:1463503","NC_002945.4:1704859","NC_002945.4:1723583","NC_002945.4:1911237","NC_002945.4:1961826","NC_002945.4:228109","NC_002945.4:2412437","NC_002945.4:2413021","NC_002945.4:3069493","NC_002945.4:3319244","NC_002945.4:3373966","NC_002945.4:3413486","NC_002945.4:3941254","NC_002945.4:3942270","NC_002945.4:4236320","NC_002945.4:4278315","NC_002945.4:960995","NC_002945.4:997676"],"index":["SRR1792265_zc","SRR1792272_zc","SRR1792271_zc","SRR8073662_zc","SRR1791772_zc","SRR1791698_zc_vcf","root"],"data":[["C","G","G","A","C","G","C","G","C","R","C","A","C","G","A","G","A","G","T","T","C"],["G","A","G","A","C","A","C","C","T","A","T","C","A","A","G","A","A","A","C","G","T"],["G","A","G","A","C","A","C","C","T","A","T","C","A","A","G","A","A","A","C","G","T"],["G","A","G","A","C","G","C","C","T","A","T","C","A","G","G","G","A","G","C","G","T"],["G","A","C","G","T","G","C","C","T","A","T","C","A","G","G","G","A","G","C","G","T"],["G","A","G","A","C","G","T","C","T","A","T","C","A","G","G","G","C","G","C","G","T"],["C","G","G","A","C","G","C","G","C","G","T","C","A","G","G","G","A","G","C","T","C"]]}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01D6_snps.newick	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+(root,((((SRR1792271_zc,SRR1792272_zc),SRR1791772_zc),SRR8073662_zc),SRR1791698_zc_vcf),SRR1792265_zc);
Binary file test-data/Mbovis-01D6_sort_table.xlsx has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01D_avg_mq.json	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+{"name":null,"index":["NC_002945.4:1057","NC_002945.4:4480","NC_002945.4:8741","NC_002945.4:29061","NC_002945.4:33788","NC_002945.4:41228","NC_002945.4:41437","NC_002945.4:50470","NC_002945.4:59861","NC_002945.4:69913","NC_002945.4:70082","NC_002945.4:70438","NC_002945.4:79918","NC_002945.4:96244","NC_002945.4:110198","NC_002945.4:114965","NC_002945.4:117800","NC_002945.4:127447","NC_002945.4:130166","NC_002945.4:130237","NC_002945.4:140686","NC_002945.4:143799","NC_002945.4:144992","NC_002945.4:148871","NC_002945.4:159370","NC_002945.4:160535","NC_002945.4:165799","NC_002945.4:166696","NC_002945.4:179885","NC_002945.4:189083","NC_002945.4:192177","NC_002945.4:198890","NC_002945.4:223919","NC_002945.4:230661","NC_002945.4:232188","NC_002945.4:295519","NC_002945.4:299636","NC_002945.4:304339","NC_002945.4:319911","NC_002945.4:332124","NC_002945.4:332128","NC_002945.4:332144","NC_002945.4:332145","NC_002945.4:332154","NC_002945.4:332215","NC_002945.4:332218","NC_002945.4:333010","NC_002945.4:340088","NC_002945.4:340090","NC_002945.4:340091","NC_002945.4:340092","NC_002945.4:340097","NC_002945.4:362818","NC_002945.4:364560","NC_002945.4:364804","NC_002945.4:366022","NC_002945.4:407246","NC_002945.4:430077","NC_002945.4:438482","NC_002945.4:441762","NC_002945.4:449922","NC_002945.4:452398","NC_002945.4:460722","NC_002945.4:467343","NC_002945.4:467402","NC_002945.4:479644","NC_002945.4:483845","NC_002945.4:485584","NC_002945.4:488897","NC_002945.4:490878","NC_002945.4:507929","NC_002945.4:518522","NC_002945.4:519412","NC_002945.4:541571","NC_002945.4:544180","NC_002945.4:577068","NC_002945.4:598704","NC_002945.4:600207","NC_002945.4:611077","NC_002945.4:622386","NC_002945.4:641896","NC_002945.4:642875","NC_002945.4:644245","NC_002945.4:649910","NC_002945.4:652349","NC_002945.4:673880","NC_002945.4:680416","NC_002945.4:685069","NC_002945.4:701329","NC_002945.4:701386","NC_002945.4:712319","NC_002945.4:723170","NC_002945.4:726979","NC_002945.4:737636","NC_002945.4:738102","NC_002945.4:745507","NC_002945.4:760347","NC_002945.4:792617","NC_002945.4:804997","NC_002945.4:808601","NC_002945.4:811737","NC_002945.4:812709","NC_002945.4:828003","NC_002945.4:832093","NC_002945.4:833960","NC_002945.4:839308","NC_002945.4:843812","NC_002945.4:854043","NC_002945.4:865821","NC_002945.4:870116","NC_002945.4:884432","NC_002945.4:889897","NC_002945.4:905912","NC_002945.4:917766","NC_002945.4:920753","NC_002945.4:941068","NC_002945.4:942431","NC_002945.4:943719","NC_002945.4:946102","NC_002945.4:948022","NC_002945.4:948811","NC_002945.4:948974","NC_002945.4:965529","NC_002945.4:967989","NC_002945.4:973459","NC_002945.4:974604","NC_002945.4:976327","NC_002945.4:982301","NC_002945.4:990611","NC_002945.4:998183","NC_002945.4:998196","NC_002945.4:1018313","NC_002945.4:1021422","NC_002945.4:1034434","NC_002945.4:1036102","NC_002945.4:1036530","NC_002945.4:1096802","NC_002945.4:1104019","NC_002945.4:1104291","NC_002945.4:1124266","NC_002945.4:1137800","NC_002945.4:1139489","NC_002945.4:1159390","NC_002945.4:1160992","NC_002945.4:1168458","NC_002945.4:1186381","NC_002945.4:1190076","NC_002945.4:1190080","NC_002945.4:1190084","NC_002945.4:1191092","NC_002945.4:1199529","NC_002945.4:1199530","NC_002945.4:1199951","NC_002945.4:1206896","NC_002945.4:1212203","NC_002945.4:1213847","NC_002945.4:1214540","NC_002945.4:1224899","NC_002945.4:1230875","NC_002945.4:1244746","NC_002945.4:1259250","NC_002945.4:1264712","NC_002945.4:1295457","NC_002945.4:1312836","NC_002945.4:1314197","NC_002945.4:1333537","NC_002945.4:1335092","NC_002945.4:1341613","NC_002945.4:1383731","NC_002945.4:1405922","NC_002945.4:1412824","NC_002945.4:1412828","NC_002945.4:1412885","NC_002945.4:1412893","NC_002945.4:1421904","NC_002945.4:1442194","NC_002945.4:1467394","NC_002945.4:1470606","NC_002945.4:1479827","NC_002945.4:1481327","NC_002945.4:1484942","NC_002945.4:1492328","NC_002945.4:1498639","NC_002945.4:1501932","NC_002945.4:1509487","NC_002945.4:1517866","NC_002945.4:1524526","NC_002945.4:1529147","NC_002945.4:1533175","NC_002945.4:1535299","NC_002945.4:1535303","NC_002945.4:1535366","NC_002945.4:1536267","NC_002945.4:1547426","NC_002945.4:1568090","NC_002945.4:1584881","NC_002945.4:1591357","NC_002945.4:1594398","NC_002945.4:1597464","NC_002945.4:1597847","NC_002945.4:1600443","NC_002945.4:1619153","NC_002945.4:1619361","NC_002945.4:1625561","NC_002945.4:1628068","NC_002945.4:1632869","NC_002945.4:1659174","NC_002945.4:1682044","NC_002945.4:1701507","NC_002945.4:1711760","NC_002945.4:1716413","NC_002945.4:1717086","NC_002945.4:1720220","NC_002945.4:1741553","NC_002945.4:1762390","NC_002945.4:1790296","NC_002945.4:1799442","NC_002945.4:1803035","NC_002945.4:1817260","NC_002945.4:1828312","NC_002945.4:1833330","NC_002945.4:1863248","NC_002945.4:1871114","NC_002945.4:1880430","NC_002945.4:1894922","NC_002945.4:1896107","NC_002945.4:1915461","NC_002945.4:1915936","NC_002945.4:1920100","NC_002945.4:1932972","NC_002945.4:1941781","NC_002945.4:1954048","NC_002945.4:1957978","NC_002945.4:1958977","NC_002945.4:1961656","NC_002945.4:1974665","NC_002945.4:1989922","NC_002945.4:1996251","NC_002945.4:2002061","NC_002945.4:2007303","NC_002945.4:2010421","NC_002945.4:2020061","NC_002945.4:2021640","NC_002945.4:2024890","NC_002945.4:2027869","NC_002945.4:2035774","NC_002945.4:2036697","NC_002945.4:2049171","NC_002945.4:2057553","NC_002945.4:2059249","NC_002945.4:2059920","NC_002945.4:2075405","NC_002945.4:2078648","NC_002945.4:2093479","NC_002945.4:2096812","NC_002945.4:2099043","NC_002945.4:2118096","NC_002945.4:2121160","NC_002945.4:2137049","NC_002945.4:2138896","NC_002945.4:2145868","NC_002945.4:2163576","NC_002945.4:2204661","NC_002945.4:2210027","NC_002945.4:2239061","NC_002945.4:2257546","NC_002945.4:2267557","NC_002945.4:2268821","NC_002945.4:2283200","NC_002945.4:2283218","NC_002945.4:2283220","NC_002945.4:2283227","NC_002945.4:2283235","NC_002945.4:2283236","NC_002945.4:2283350","NC_002945.4:2283353","NC_002945.4:2283355","NC_002945.4:2283362","NC_002945.4:2283366","NC_002945.4:2283367","NC_002945.4:2283368","NC_002945.4:2283371","NC_002945.4:2308525","NC_002945.4:2310215","NC_002945.4:2333994","NC_002945.4:2339770","NC_002945.4:2358298","NC_002945.4:2360219","NC_002945.4:2368982","NC_002945.4:2369407","NC_002945.4:2378324","NC_002945.4:2381437","NC_002945.4:2384647","NC_002945.4:2410761","NC_002945.4:2412437","NC_002945.4:2413021","NC_002945.4:2418267","NC_002945.4:2428397","NC_002945.4:2433602","NC_002945.4:2479007","NC_002945.4:2492067","NC_002945.4:2497022","NC_002945.4:2499336","NC_002945.4:2506199","NC_002945.4:2508626","NC_002945.4:2513801","NC_002945.4:2515130","NC_002945.4:2520576","NC_002945.4:2524942","NC_002945.4:2528517","NC_002945.4:2529413","NC_002945.4:2532958","NC_002945.4:2538021","NC_002945.4:2539896","NC_002945.4:2549198","NC_002945.4:2573831","NC_002945.4:2615591","NC_002945.4:2631265","NC_002945.4:2656304","NC_002945.4:2656651","NC_002945.4:2662768","NC_002945.4:2663582","NC_002945.4:2667489","NC_002945.4:2683485","NC_002945.4:2688315","NC_002945.4:2729845","NC_002945.4:2747797","NC_002945.4:2749502","NC_002945.4:2758761","NC_002945.4:2767533","NC_002945.4:2770129","NC_002945.4:2794510","NC_002945.4:2806603","NC_002945.4:2807510","NC_002945.4:2807511","NC_002945.4:2809255","NC_002945.4:2819758","NC_002945.4:2823105","NC_002945.4:2870414","NC_002945.4:2870624","NC_002945.4:2873027","NC_002945.4:2884747","NC_002945.4:2886118","NC_002945.4:2890220","NC_002945.4:2893045","NC_002945.4:2899163","NC_002945.4:2899584","NC_002945.4:2900525","NC_002945.4:2918203","NC_002945.4:2924775","NC_002945.4:2927134","NC_002945.4:2931071","NC_002945.4:2931113","NC_002945.4:2942926","NC_002945.4:2946800","NC_002945.4:2956778","NC_002945.4:2964207","NC_002945.4:2978162","NC_002945.4:2978164","NC_002945.4:2983580","NC_002945.4:2984156","NC_002945.4:3018593","NC_002945.4:3031841","NC_002945.4:3039600","NC_002945.4:3040820","NC_002945.4:3042914","NC_002945.4:3045025","NC_002945.4:3053649","NC_002945.4:3053756","NC_002945.4:3063074","NC_002945.4:3068041","NC_002945.4:3069493","NC_002945.4:3070642","NC_002945.4:3088868","NC_002945.4:3093531","NC_002945.4:3098932","NC_002945.4:3100639","NC_002945.4:3103354","NC_002945.4:3106064","NC_002945.4:3106527","NC_002945.4:3116059","NC_002945.4:3127117","NC_002945.4:3137471","NC_002945.4:3140342","NC_002945.4:3151212","NC_002945.4:3154140","NC_002945.4:3172929","NC_002945.4:3173568","NC_002945.4:3191792","NC_002945.4:3247551","NC_002945.4:3250072","NC_002945.4:3250245","NC_002945.4:3270181","NC_002945.4:3294771","NC_002945.4:3295991","NC_002945.4:3297558","NC_002945.4:3304410","NC_002945.4:3304946","NC_002945.4:3306898","NC_002945.4:3310831","NC_002945.4:3319244","NC_002945.4:3330907","NC_002945.4:3338298","NC_002945.4:3347870","NC_002945.4:3368453","NC_002945.4:3371156","NC_002945.4:3396621","NC_002945.4:3396650","NC_002945.4:3413486","NC_002945.4:3414355","NC_002945.4:3421983","NC_002945.4:3422650","NC_002945.4:3439578","NC_002945.4:3451869","NC_002945.4:3453219","NC_002945.4:3460907","NC_002945.4:3464357","NC_002945.4:3464485","NC_002945.4:3464524","NC_002945.4:3468669","NC_002945.4:3476130","NC_002945.4:3482644","NC_002945.4:3484836","NC_002945.4:3486507","NC_002945.4:3493554","NC_002945.4:3495510","NC_002945.4:3497957","NC_002945.4:3533661","NC_002945.4:3546799","NC_002945.4:3553753","NC_002945.4:3564896","NC_002945.4:3567535","NC_002945.4:3574014","NC_002945.4:3574955","NC_002945.4:3591452","NC_002945.4:3600600","NC_002945.4:3622899","NC_002945.4:3624371","NC_002945.4:3626128","NC_002945.4:3630061","NC_002945.4:3645682","NC_002945.4:3655045","NC_002945.4:3667823","NC_002945.4:3712401","NC_002945.4:3718169","NC_002945.4:3718628","NC_002945.4:3719802","NC_002945.4:3723554","NC_002945.4:3725203","NC_002945.4:3729351","NC_002945.4:3751627","NC_002945.4:3769174","NC_002945.4:3776764","NC_002945.4:3778473","NC_002945.4:3800223","NC_002945.4:3805467","NC_002945.4:3816878","NC_002945.4:3821259","NC_002945.4:3839650","NC_002945.4:3846859","NC_002945.4:3874432","NC_002945.4:3877448","NC_002945.4:3884519","NC_002945.4:3888418","NC_002945.4:3902781","NC_002945.4:3905690","NC_002945.4:3957298","NC_002945.4:3966140","NC_002945.4:3969490","NC_002945.4:3969558","NC_002945.4:3969875","NC_002945.4:4003460","NC_002945.4:4008509","NC_002945.4:4010760","NC_002945.4:4017319","NC_002945.4:4018300","NC_002945.4:4029201","NC_002945.4:4046572","NC_002945.4:4070056","NC_002945.4:4076594","NC_002945.4:4077189","NC_002945.4:4080736","NC_002945.4:4096612","NC_002945.4:4128841","NC_002945.4:4130927","NC_002945.4:4149101","NC_002945.4:4155870","NC_002945.4:4159272","NC_002945.4:4160820","NC_002945.4:4162407","NC_002945.4:4162554","NC_002945.4:4180986","NC_002945.4:4205111","NC_002945.4:4207380","NC_002945.4:4214259","NC_002945.4:4219009","NC_002945.4:4222196","NC_002945.4:4226875","NC_002945.4:4231626","NC_002945.4:4245762","NC_002945.4:4251588","NC_002945.4:4264139","NC_002945.4:4278315","NC_002945.4:4281136","NC_002945.4:4282825","NC_002945.4:4293932","NC_002945.4:4298964","NC_002945.4:4303164","NC_002945.4:4311425","NC_002945.4:4321337","NC_002945.4:4339036","NC_002945.4:4347304","NC_002945.4:228109","NC_002945.4:331051","NC_002945.4:331241","NC_002945.4:331411","NC_002945.4:960995","NC_002945.4:997676","NC_002945.4:1005705","NC_002945.4:1348342","NC_002945.4:1723583","NC_002945.4:1961826","NC_002945.4:3373966","NC_002945.4:3941254","NC_002945.4:4236320","NC_002945.4:1277988","NC_002945.4:1382465","NC_002945.4:1463503","NC_002945.4:1704859","NC_002945.4:1806623","NC_002945.4:1911237","NC_002945.4:3942270"],"data":[60,60,60,59,60,59,60,59,59,60,60,59,60,59,60,60,59,59,60,60,60,60,59,59,59,59,60,59,60,59,60,60,60,60,60,59,60,60,59,59,59,59,59,59,59,59,59,57,57,57,57,57,58,59,60,60,60,59,59,60,59,59,60,59,60,60,59,60,60,59,59,59,59,60,60,59,59,59,59,60,60,60,60,60,59,60,59,60,60,60,60,59,59,60,59,59,59,59,59,59,59,60,60,59,58,60,59,60,59,59,59,59,59,60,59,59,60,59,59,59,60,59,59,59,60,60,60,59,59,60,60,60,59,60,59,59,55,60,60,60,59,59,60,59,60,60,52,55,56,59,59,59,60,59,60,60,59,59,60,60,59,59,60,59,59,59,60,59,60,60,59,59,56,56,59,60,59,58,60,59,59,60,59,59,59,59,59,60,59,58,57,57,60,59,60,60,59,60,59,60,59,59,59,60,59,59,60,60,60,59,60,60,60,60,59,60,59,59,60,60,59,59,59,60,60,59,60,59,60,60,59,59,59,59,60,60,59,59,59,59,59,59,59,59,59,60,60,59,59,60,60,60,59,60,59,59,60,60,59,59,59,59,59,60,60,60,59,60,59,59,59,59,59,59,60,60,60,60,60,60,60,60,59,60,59,60,60,60,59,59,60,59,60,60,60,60,59,60,60,59,60,60,59,59,60,60,60,59,60,60,59,59,60,59,60,60,59,59,60,60,60,59,60,59,59,59,59,60,60,59,59,59,60,60,60,59,59,60,60,59,60,60,60,59,59,59,60,59,59,60,59,59,60,60,60,60,59,60,60,60,59,60,59,59,60,60,60,60,59,60,60,60,59,59,60,59,60,59,59,59,59,59,60,59,60,59,60,59,60,59,59,60,60,60,60,59,59,59,60,60,60,60,58,60,59,60,59,59,60,60,60,59,59,59,59,59,59,60,59,59,60,60,60,59,60,60,59,60,59,60,60,60,60,60,60,60,59,60,59,59,59,59,59,59,59,59,59,59,59,59,60,60,60,60,60,59,60,60,59,59,59,59,59,59,59,60,60,59,60,59,60,60,60,59,60,60,59,59,60,60,59,59,59,60,59,59,59,60,59,59,60,60,59,60,59,60,60,60,59,59,59,60,60,60,59,60,59,59,59,60,59,59,59,60,60,60,59,59,60,60,60,59,59,59,60,56,60,60,59,60,60,60]}
\ No newline at end of file
Binary file test-data/Mbovis-01D_cascade_table.xlsx has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01D_snps.json	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+{"columns":["NC_002945.4:1005705","NC_002945.4:1348342","NC_002945.4:1382465","NC_002945.4:1463503","NC_002945.4:1704859","NC_002945.4:1723583","NC_002945.4:1911237","NC_002945.4:1961826","NC_002945.4:228109","NC_002945.4:2412437","NC_002945.4:2413021","NC_002945.4:3069493","NC_002945.4:3319244","NC_002945.4:3373966","NC_002945.4:3413486","NC_002945.4:3941254","NC_002945.4:3942270","NC_002945.4:4236320","NC_002945.4:4278315","NC_002945.4:960995","NC_002945.4:997676"],"index":["SRR1792265_zc","SRR1792272_zc","SRR1792271_zc","SRR8073662_zc","SRR1791772_zc","SRR1791698_zc_vcf","root"],"data":[["C","G","G","A","C","G","C","G","C","R","C","A","C","G","A","G","A","G","T","T","C"],["G","A","G","A","C","A","C","C","T","A","T","C","A","A","G","A","A","A","C","G","T"],["G","A","G","A","C","A","C","C","T","A","T","C","A","A","G","A","A","A","C","G","T"],["G","A","G","A","C","G","C","C","T","A","T","C","A","G","G","G","A","G","C","G","T"],["G","A","C","G","T","G","C","C","T","A","T","C","A","G","G","G","A","G","C","G","T"],["G","A","G","A","C","G","T","C","T","A","T","C","A","G","G","G","C","G","C","G","T"],["C","G","G","A","C","G","C","G","C","G","T","C","A","G","G","G","A","G","C","T","C"]]}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01D_snps.newick	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+(root,((((SRR1792271_zc,SRR1792272_zc),SRR1791772_zc),SRR8073662_zc),SRR1791698_zc_vcf),SRR1792265_zc);
Binary file test-data/Mbovis-01D_sort_table.xlsx has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01_avg_mq.json	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+{"name":null,"index":["NC_002945.4:1057","NC_002945.4:4480","NC_002945.4:8741","NC_002945.4:29061","NC_002945.4:33788","NC_002945.4:41228","NC_002945.4:41437","NC_002945.4:50470","NC_002945.4:59861","NC_002945.4:69913","NC_002945.4:70082","NC_002945.4:70438","NC_002945.4:75274","NC_002945.4:79918","NC_002945.4:96244","NC_002945.4:110198","NC_002945.4:114965","NC_002945.4:117800","NC_002945.4:127447","NC_002945.4:130166","NC_002945.4:130237","NC_002945.4:140686","NC_002945.4:143799","NC_002945.4:144992","NC_002945.4:148871","NC_002945.4:159370","NC_002945.4:160535","NC_002945.4:165799","NC_002945.4:166696","NC_002945.4:179885","NC_002945.4:189083","NC_002945.4:192177","NC_002945.4:198890","NC_002945.4:223919","NC_002945.4:230661","NC_002945.4:232188","NC_002945.4:249090","NC_002945.4:295519","NC_002945.4:299636","NC_002945.4:304339","NC_002945.4:319911","NC_002945.4:332124","NC_002945.4:332128","NC_002945.4:332215","NC_002945.4:332218","NC_002945.4:333010","NC_002945.4:340088","NC_002945.4:340090","NC_002945.4:340091","NC_002945.4:340092","NC_002945.4:340097","NC_002945.4:364560","NC_002945.4:364804","NC_002945.4:366022","NC_002945.4:407246","NC_002945.4:430077","NC_002945.4:438482","NC_002945.4:441762","NC_002945.4:449922","NC_002945.4:452398","NC_002945.4:460722","NC_002945.4:467343","NC_002945.4:467402","NC_002945.4:479644","NC_002945.4:483845","NC_002945.4:485584","NC_002945.4:488897","NC_002945.4:490878","NC_002945.4:507929","NC_002945.4:518522","NC_002945.4:519412","NC_002945.4:541571","NC_002945.4:544180","NC_002945.4:577068","NC_002945.4:598704","NC_002945.4:600207","NC_002945.4:611077","NC_002945.4:622386","NC_002945.4:642172","NC_002945.4:642875","NC_002945.4:644245","NC_002945.4:649910","NC_002945.4:652349","NC_002945.4:680416","NC_002945.4:685069","NC_002945.4:701329","NC_002945.4:701386","NC_002945.4:707522","NC_002945.4:712319","NC_002945.4:723170","NC_002945.4:726979","NC_002945.4:737636","NC_002945.4:738102","NC_002945.4:745507","NC_002945.4:760347","NC_002945.4:792617","NC_002945.4:804997","NC_002945.4:808601","NC_002945.4:811737","NC_002945.4:812709","NC_002945.4:828003","NC_002945.4:832093","NC_002945.4:833960","NC_002945.4:843812","NC_002945.4:854043","NC_002945.4:865821","NC_002945.4:870116","NC_002945.4:884432","NC_002945.4:889897","NC_002945.4:905912","NC_002945.4:917766","NC_002945.4:920753","NC_002945.4:941068","NC_002945.4:942431","NC_002945.4:943719","NC_002945.4:946102","NC_002945.4:948022","NC_002945.4:948811","NC_002945.4:948974","NC_002945.4:965529","NC_002945.4:967989","NC_002945.4:973459","NC_002945.4:974604","NC_002945.4:976327","NC_002945.4:982301","NC_002945.4:990611","NC_002945.4:998183","NC_002945.4:998196","NC_002945.4:1018313","NC_002945.4:1021422","NC_002945.4:1034434","NC_002945.4:1036102","NC_002945.4:1036530","NC_002945.4:1096802","NC_002945.4:1104019","NC_002945.4:1104291","NC_002945.4:1124266","NC_002945.4:1137800","NC_002945.4:1139489","NC_002945.4:1159390","NC_002945.4:1160992","NC_002945.4:1168458","NC_002945.4:1186381","NC_002945.4:1191092","NC_002945.4:1199529","NC_002945.4:1199530","NC_002945.4:1199951","NC_002945.4:1206896","NC_002945.4:1212203","NC_002945.4:1214540","NC_002945.4:1224899","NC_002945.4:1230875","NC_002945.4:1244746","NC_002945.4:1259250","NC_002945.4:1264712","NC_002945.4:1295457","NC_002945.4:1312836","NC_002945.4:1314197","NC_002945.4:1333537","NC_002945.4:1335092","NC_002945.4:1341613","NC_002945.4:1383731","NC_002945.4:1405922","NC_002945.4:1412824","NC_002945.4:1412828","NC_002945.4:1412885","NC_002945.4:1412893","NC_002945.4:1421904","NC_002945.4:1442194","NC_002945.4:1462755","NC_002945.4:1467394","NC_002945.4:1470606","NC_002945.4:1479827","NC_002945.4:1481327","NC_002945.4:1484942","NC_002945.4:1492328","NC_002945.4:1498639","NC_002945.4:1501932","NC_002945.4:1509487","NC_002945.4:1517866","NC_002945.4:1524526","NC_002945.4:1529147","NC_002945.4:1533175","NC_002945.4:1535299","NC_002945.4:1535303","NC_002945.4:1535366","NC_002945.4:1536267","NC_002945.4:1547426","NC_002945.4:1568090","NC_002945.4:1584881","NC_002945.4:1591357","NC_002945.4:1594398","NC_002945.4:1597464","NC_002945.4:1597847","NC_002945.4:1600443","NC_002945.4:1619153","NC_002945.4:1619361","NC_002945.4:1625561","NC_002945.4:1628068","NC_002945.4:1632869","NC_002945.4:1659174","NC_002945.4:1682044","NC_002945.4:1701507","NC_002945.4:1717086","NC_002945.4:1720220","NC_002945.4:1723479","NC_002945.4:1741553","NC_002945.4:1762390","NC_002945.4:1790296","NC_002945.4:1796727","NC_002945.4:1803035","NC_002945.4:1817260","NC_002945.4:1828312","NC_002945.4:1833330","NC_002945.4:1863248","NC_002945.4:1871114","NC_002945.4:1880430","NC_002945.4:1894922","NC_002945.4:1896107","NC_002945.4:1915461","NC_002945.4:1915936","NC_002945.4:1920100","NC_002945.4:1932972","NC_002945.4:1941781","NC_002945.4:1954048","NC_002945.4:1957978","NC_002945.4:1958977","NC_002945.4:1961656","NC_002945.4:1967341","NC_002945.4:1974665","NC_002945.4:2002061","NC_002945.4:2007303","NC_002945.4:2010421","NC_002945.4:2020061","NC_002945.4:2021640","NC_002945.4:2024890","NC_002945.4:2027869","NC_002945.4:2035774","NC_002945.4:2036697","NC_002945.4:2049171","NC_002945.4:2051968","NC_002945.4:2057553","NC_002945.4:2059249","NC_002945.4:2059920","NC_002945.4:2075405","NC_002945.4:2078648","NC_002945.4:2093479","NC_002945.4:2096812","NC_002945.4:2099043","NC_002945.4:2118096","NC_002945.4:2121160","NC_002945.4:2137049","NC_002945.4:2138896","NC_002945.4:2145868","NC_002945.4:2163576","NC_002945.4:2178975","NC_002945.4:2204661","NC_002945.4:2239061","NC_002945.4:2257546","NC_002945.4:2267557","NC_002945.4:2268821","NC_002945.4:2283200","NC_002945.4:2283218","NC_002945.4:2283220","NC_002945.4:2283227","NC_002945.4:2283235","NC_002945.4:2283236","NC_002945.4:2283350","NC_002945.4:2283353","NC_002945.4:2283355","NC_002945.4:2283362","NC_002945.4:2283366","NC_002945.4:2283367","NC_002945.4:2283368","NC_002945.4:2283371","NC_002945.4:2308525","NC_002945.4:2310215","NC_002945.4:2333994","NC_002945.4:2339770","NC_002945.4:2358298","NC_002945.4:2360219","NC_002945.4:2368982","NC_002945.4:2369407","NC_002945.4:2378324","NC_002945.4:2381437","NC_002945.4:2384647","NC_002945.4:2410761","NC_002945.4:2412437","NC_002945.4:2418267","NC_002945.4:2428397","NC_002945.4:2429853","NC_002945.4:2433602","NC_002945.4:2479007","NC_002945.4:2492067","NC_002945.4:2497022","NC_002945.4:2499336","NC_002945.4:2506199","NC_002945.4:2508626","NC_002945.4:2513801","NC_002945.4:2515130","NC_002945.4:2520576","NC_002945.4:2524942","NC_002945.4:2528517","NC_002945.4:2529413","NC_002945.4:2532958","NC_002945.4:2538021","NC_002945.4:2539896","NC_002945.4:2549198","NC_002945.4:2573831","NC_002945.4:2615591","NC_002945.4:2631265","NC_002945.4:2656304","NC_002945.4:2656651","NC_002945.4:2662768","NC_002945.4:2663582","NC_002945.4:2667489","NC_002945.4:2683485","NC_002945.4:2688315","NC_002945.4:2729845","NC_002945.4:2747797","NC_002945.4:2749502","NC_002945.4:2758761","NC_002945.4:2767533","NC_002945.4:2770129","NC_002945.4:2794510","NC_002945.4:2806603","NC_002945.4:2807510","NC_002945.4:2807511","NC_002945.4:2809255","NC_002945.4:2819758","NC_002945.4:2823105","NC_002945.4:2870414","NC_002945.4:2870624","NC_002945.4:2873027","NC_002945.4:2886118","NC_002945.4:2890220","NC_002945.4:2893045","NC_002945.4:2899163","NC_002945.4:2899584","NC_002945.4:2900525","NC_002945.4:2918203","NC_002945.4:2924775","NC_002945.4:2927134","NC_002945.4:2931071","NC_002945.4:2931113","NC_002945.4:2942926","NC_002945.4:2946800","NC_002945.4:2956778","NC_002945.4:2964207","NC_002945.4:2978162","NC_002945.4:2978164","NC_002945.4:2983580","NC_002945.4:2984156","NC_002945.4:3018593","NC_002945.4:3031841","NC_002945.4:3039600","NC_002945.4:3040820","NC_002945.4:3042914","NC_002945.4:3043695","NC_002945.4:3045025","NC_002945.4:3053649","NC_002945.4:3053756","NC_002945.4:3063074","NC_002945.4:3068041","NC_002945.4:3070642","NC_002945.4:3088868","NC_002945.4:3093531","NC_002945.4:3098932","NC_002945.4:3100639","NC_002945.4:3103354","NC_002945.4:3106064","NC_002945.4:3106527","NC_002945.4:3116059","NC_002945.4:3127117","NC_002945.4:3137471","NC_002945.4:3140342","NC_002945.4:3151212","NC_002945.4:3154140","NC_002945.4:3172929","NC_002945.4:3173568","NC_002945.4:3191792","NC_002945.4:3247551","NC_002945.4:3250072","NC_002945.4:3250245","NC_002945.4:3252431","NC_002945.4:3270181","NC_002945.4:3294771","NC_002945.4:3295991","NC_002945.4:3297558","NC_002945.4:3304410","NC_002945.4:3304946","NC_002945.4:3306898","NC_002945.4:3309513","NC_002945.4:3310831","NC_002945.4:3330907","NC_002945.4:3338298","NC_002945.4:3347870","NC_002945.4:3368453","NC_002945.4:3371156","NC_002945.4:3396621","NC_002945.4:3396650","NC_002945.4:3414355","NC_002945.4:3421983","NC_002945.4:3422650","NC_002945.4:3439578","NC_002945.4:3451869","NC_002945.4:3453219","NC_002945.4:3460907","NC_002945.4:3464357","NC_002945.4:3464524","NC_002945.4:3468669","NC_002945.4:3476130","NC_002945.4:3482644","NC_002945.4:3484836","NC_002945.4:3486507","NC_002945.4:3488828","NC_002945.4:3493554","NC_002945.4:3495510","NC_002945.4:3497957","NC_002945.4:3533661","NC_002945.4:3546799","NC_002945.4:3564896","NC_002945.4:3567535","NC_002945.4:3574014","NC_002945.4:3574955","NC_002945.4:3591452","NC_002945.4:3600600","NC_002945.4:3622899","NC_002945.4:3624371","NC_002945.4:3626128","NC_002945.4:3630061","NC_002945.4:3645682","NC_002945.4:3655045","NC_002945.4:3667823","NC_002945.4:3672841","NC_002945.4:3712401","NC_002945.4:3718169","NC_002945.4:3718628","NC_002945.4:3719802","NC_002945.4:3723554","NC_002945.4:3725203","NC_002945.4:3729351","NC_002945.4:3751627","NC_002945.4:3769174","NC_002945.4:3776764","NC_002945.4:3778473","NC_002945.4:3800223","NC_002945.4:3805467","NC_002945.4:3816878","NC_002945.4:3821259","NC_002945.4:3825329","NC_002945.4:3839650","NC_002945.4:3846859","NC_002945.4:3872596","NC_002945.4:3874432","NC_002945.4:3877448","NC_002945.4:3884519","NC_002945.4:3888418","NC_002945.4:3902781","NC_002945.4:3905690","NC_002945.4:3957298","NC_002945.4:3966140","NC_002945.4:3969490","NC_002945.4:3969558","NC_002945.4:3969875","NC_002945.4:3993571","NC_002945.4:4003460","NC_002945.4:4008509","NC_002945.4:4010760","NC_002945.4:4017319","NC_002945.4:4017949","NC_002945.4:4018300","NC_002945.4:4029201","NC_002945.4:4046572","NC_002945.4:4052766","NC_002945.4:4070056","NC_002945.4:4076594","NC_002945.4:4077189","NC_002945.4:4080736","NC_002945.4:4096612","NC_002945.4:4128841","NC_002945.4:4130927","NC_002945.4:4149101","NC_002945.4:4155870","NC_002945.4:4159272","NC_002945.4:4160820","NC_002945.4:4162407","NC_002945.4:4162554","NC_002945.4:4180986","NC_002945.4:4205111","NC_002945.4:4207380","NC_002945.4:4214259","NC_002945.4:4219009","NC_002945.4:4222196","NC_002945.4:4226875","NC_002945.4:4231626","NC_002945.4:4245762","NC_002945.4:4264139","NC_002945.4:4281136","NC_002945.4:4282825","NC_002945.4:4298964","NC_002945.4:4303164","NC_002945.4:4311425","NC_002945.4:4321337","NC_002945.4:4339036","NC_002945.4:4347304","NC_002945.4:332144","NC_002945.4:332145","NC_002945.4:332154","NC_002945.4:362818","NC_002945.4:641896","NC_002945.4:673880","NC_002945.4:839308","NC_002945.4:1190076","NC_002945.4:1190080","NC_002945.4:1190084","NC_002945.4:1213847","NC_002945.4:1711760","NC_002945.4:1716413","NC_002945.4:1799442","NC_002945.4:1989922","NC_002945.4:1996251","NC_002945.4:2210027","NC_002945.4:2413021","NC_002945.4:2884747","NC_002945.4:3069493","NC_002945.4:3319244","NC_002945.4:3413486","NC_002945.4:3464485","NC_002945.4:3553753","NC_002945.4:4251588","NC_002945.4:4278315","NC_002945.4:4293932","NC_002945.4:228109","NC_002945.4:331051","NC_002945.4:331241","NC_002945.4:331411","NC_002945.4:960995","NC_002945.4:997676","NC_002945.4:1005705","NC_002945.4:1348342","NC_002945.4:1723583","NC_002945.4:1961826","NC_002945.4:3373966","NC_002945.4:3941254","NC_002945.4:4236320","NC_002945.4:1277988","NC_002945.4:1382465","NC_002945.4:1463503","NC_002945.4:1704859","NC_002945.4:1806623","NC_002945.4:1911237","NC_002945.4:3942270"],"data":[60,60,60,59,60,59,60,59,59,60,60,59,60,60,59,60,60,59,59,60,60,60,60,59,59,59,59,60,59,60,59,60,60,60,60,60,60,59,60,60,59,59,59,59,59,59,57,57,57,57,57,59,60,60,60,59,59,60,59,59,60,59,60,60,59,60,60,59,59,59,59,60,60,59,59,59,59,60,60,60,60,59,59,59,60,60,60,60,60,59,59,60,59,59,59,59,59,59,59,60,60,59,58,59,60,59,59,59,59,59,60,59,59,60,59,59,59,60,59,59,59,60,60,60,59,59,60,60,60,59,60,59,59,55,60,60,60,59,59,60,59,60,60,59,59,59,60,59,60,59,59,60,60,59,59,60,59,59,59,60,59,60,60,59,59,56,56,59,60,60,59,58,60,59,59,60,59,59,59,59,59,60,59,58,57,56,60,59,60,60,59,60,59,60,59,59,59,60,59,59,59,60,60,60,60,60,60,59,60,60,59,60,60,59,59,59,60,60,59,60,59,60,60,59,59,59,59,60,60,60,59,59,59,59,59,59,59,60,60,59,60,59,60,60,60,59,60,59,59,60,60,59,59,59,59,60,59,60,60,59,60,59,59,59,59,59,59,60,60,60,60,60,60,60,60,59,60,59,60,60,60,59,59,60,59,60,60,60,59,60,60,60,59,60,60,59,59,60,60,60,59,60,60,59,59,60,59,60,60,59,59,60,60,60,59,60,59,59,59,59,60,60,59,59,59,60,60,60,59,59,60,60,59,60,60,59,59,59,60,59,59,60,59,59,60,60,60,60,59,60,60,60,59,60,59,59,60,60,60,60,59,59,60,60,59,59,60,59,60,59,59,59,59,59,60,59,60,59,60,59,60,59,59,60,57,60,60,60,59,59,59,60,60,60,60,58,60,59,60,59,59,60,60,59,59,59,59,59,59,59,59,60,60,60,59,60,60,60,59,60,59,60,60,60,60,60,60,59,60,59,59,59,59,59,60,59,59,59,59,59,59,59,60,60,60,60,60,59,60,60,60,59,59,60,59,59,59,59,59,60,60,59,60,59,60,60,60,60,59,60,60,60,59,59,59,60,60,59,59,59,60,59,59,59,60,59,59,60,60,59,60,59,60,60,60,59,59,60,60,59,59,59,59,60,59,59,59,59,59,58,60,60,60,52,55,56,60,59,60,59,59,59,60,60,60,60,60,60,60,60,59,60,60,59,60,60,60,59,59,60,60,60,59,59,59,60,56,60,60,59,60,60,60]}
\ No newline at end of file
Binary file test-data/Mbovis-01_cascade_table.xlsx has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01_snps.json	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+{"columns":["NC_002945.4:1005705","NC_002945.4:1348342","NC_002945.4:1382465","NC_002945.4:1463503","NC_002945.4:1704859","NC_002945.4:1723583","NC_002945.4:1911237","NC_002945.4:1961826","NC_002945.4:228109","NC_002945.4:2412437","NC_002945.4:2413021","NC_002945.4:3069493","NC_002945.4:3319244","NC_002945.4:3373966","NC_002945.4:3413486","NC_002945.4:3941254","NC_002945.4:3942270","NC_002945.4:4236320","NC_002945.4:4278315","NC_002945.4:960995","NC_002945.4:997676"],"index":["SRR1792265_zc","SRR1792272_zc","SRR1792271_zc","SRR8073662_zc","SRR1791772_zc","SRR1791698_zc_vcf","root"],"data":[["C","G","G","A","C","G","C","G","C","R","C","A","C","G","A","G","A","G","T","T","C"],["G","A","G","A","C","A","C","C","T","A","T","C","A","A","G","A","A","A","C","G","T"],["G","A","G","A","C","A","C","C","T","A","T","C","A","A","G","A","A","A","C","G","T"],["G","A","G","A","C","G","C","C","T","A","T","C","A","G","G","G","A","G","C","G","T"],["G","A","C","G","T","G","C","C","T","A","T","C","A","G","G","G","A","G","C","G","T"],["G","A","G","A","C","G","T","C","T","A","T","C","A","G","G","G","C","G","C","G","T"],["C","G","G","A","C","G","C","G","C","G","T","C","A","G","G","G","A","G","C","T","C"]]}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01_snps.newick	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+(root,((((SRR1792271_zc,SRR1792272_zc),SRR1791772_zc),SRR8073662_zc),SRR1791698_zc_vcf),SRR1792265_zc);
Binary file test-data/Mbovis-01_sort_table.xlsx has changed
Binary file test-data/cascade_table.xlsx has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_avg_mq_json.json	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+{"name":null,"index":["NC_002945.4:1005705","NC_002945.4:1018313","NC_002945.4:1021422","NC_002945.4:1034434","NC_002945.4:1036102","NC_002945.4:1036530","NC_002945.4:1057","NC_002945.4:1096802","NC_002945.4:110198","NC_002945.4:1104019","NC_002945.4:1104291","NC_002945.4:1124266","NC_002945.4:1137800","NC_002945.4:1139489","NC_002945.4:114965","NC_002945.4:1159390","NC_002945.4:1160992","NC_002945.4:1168458","NC_002945.4:117800","NC_002945.4:1186381","NC_002945.4:1190076","NC_002945.4:1190080","NC_002945.4:1190084","NC_002945.4:1191092","NC_002945.4:1199529","NC_002945.4:1199530","NC_002945.4:1199951","NC_002945.4:1206896","NC_002945.4:1212203","NC_002945.4:1213847","NC_002945.4:1214540","NC_002945.4:1224899","NC_002945.4:1230875","NC_002945.4:1244746","NC_002945.4:1259250","NC_002945.4:1264712","NC_002945.4:127447","NC_002945.4:1277988","NC_002945.4:1295457","NC_002945.4:130166","NC_002945.4:130237","NC_002945.4:1312836","NC_002945.4:1314197","NC_002945.4:1333537","NC_002945.4:1335092","NC_002945.4:1341613","NC_002945.4:1348342","NC_002945.4:1382465","NC_002945.4:1383731","NC_002945.4:1405922","NC_002945.4:140686","NC_002945.4:1412824","NC_002945.4:1412828","NC_002945.4:1412885","NC_002945.4:1412893","NC_002945.4:1421904","NC_002945.4:143799","NC_002945.4:1442194","NC_002945.4:144992","NC_002945.4:1463503","NC_002945.4:1467394","NC_002945.4:1470606","NC_002945.4:1479827","NC_002945.4:1481327","NC_002945.4:1484942","NC_002945.4:148871","NC_002945.4:1492328","NC_002945.4:1498639","NC_002945.4:1501932","NC_002945.4:1509487","NC_002945.4:1517866","NC_002945.4:1524526","NC_002945.4:1529147","NC_002945.4:1533175","NC_002945.4:1535299","NC_002945.4:1535303","NC_002945.4:1535366","NC_002945.4:1536267","NC_002945.4:1547426","NC_002945.4:1568090","NC_002945.4:1584881","NC_002945.4:1591357","NC_002945.4:159370","NC_002945.4:1594398","NC_002945.4:1597464","NC_002945.4:1597847","NC_002945.4:1600443","NC_002945.4:160535","NC_002945.4:1619153","NC_002945.4:1619361","NC_002945.4:1625561","NC_002945.4:1628068","NC_002945.4:1632869","NC_002945.4:165799","NC_002945.4:1659174","NC_002945.4:166696","NC_002945.4:1682044","NC_002945.4:1701507","NC_002945.4:1704859","NC_002945.4:1711760","NC_002945.4:1716413","NC_002945.4:1717086","NC_002945.4:1720220","NC_002945.4:1723583","NC_002945.4:1741553","NC_002945.4:1762390","NC_002945.4:1790296","NC_002945.4:179885","NC_002945.4:1799442","NC_002945.4:1803035","NC_002945.4:1806623","NC_002945.4:1817260","NC_002945.4:1828312","NC_002945.4:1833330","NC_002945.4:1863248","NC_002945.4:1871114","NC_002945.4:1880430","NC_002945.4:189083","NC_002945.4:1894922","NC_002945.4:1896107","NC_002945.4:1911237","NC_002945.4:1915461","NC_002945.4:1915936","NC_002945.4:1920100","NC_002945.4:192177","NC_002945.4:1932972","NC_002945.4:1941781","NC_002945.4:1954048","NC_002945.4:1957978","NC_002945.4:1958977","NC_002945.4:1961656","NC_002945.4:1961826","NC_002945.4:1974665","NC_002945.4:198890","NC_002945.4:1989922","NC_002945.4:1996251","NC_002945.4:2002061","NC_002945.4:2007303","NC_002945.4:2010421","NC_002945.4:2020061","NC_002945.4:2021640","NC_002945.4:2024890","NC_002945.4:2027869","NC_002945.4:2035774","NC_002945.4:2036697","NC_002945.4:2049171","NC_002945.4:2057553","NC_002945.4:2059249","NC_002945.4:2059920","NC_002945.4:2075405","NC_002945.4:2078648","NC_002945.4:2093479","NC_002945.4:2096812","NC_002945.4:2099043","NC_002945.4:2118096","NC_002945.4:2121160","NC_002945.4:2137049","NC_002945.4:2138896","NC_002945.4:2145868","NC_002945.4:2163576","NC_002945.4:2204661","NC_002945.4:2210027","NC_002945.4:2239061","NC_002945.4:223919","NC_002945.4:2257546","NC_002945.4:2267557","NC_002945.4:2268821","NC_002945.4:228109","NC_002945.4:2283200","NC_002945.4:2283218","NC_002945.4:2283220","NC_002945.4:2283227","NC_002945.4:2283235","NC_002945.4:2283236","NC_002945.4:2283350","NC_002945.4:2283353","NC_002945.4:2283355","NC_002945.4:2283362","NC_002945.4:2283366","NC_002945.4:2283367","NC_002945.4:2283368","NC_002945.4:2283371","NC_002945.4:230661","NC_002945.4:2308525","NC_002945.4:2310215","NC_002945.4:232188","NC_002945.4:2333994","NC_002945.4:2339770","NC_002945.4:2358298","NC_002945.4:2360219","NC_002945.4:2368982","NC_002945.4:2369407","NC_002945.4:2378324","NC_002945.4:2381437","NC_002945.4:2384647","NC_002945.4:2410761","NC_002945.4:2412437","NC_002945.4:2413021","NC_002945.4:2418267","NC_002945.4:2428397","NC_002945.4:2433602","NC_002945.4:2479007","NC_002945.4:2492067","NC_002945.4:2497022","NC_002945.4:2499336","NC_002945.4:2506199","NC_002945.4:2508626","NC_002945.4:2513801","NC_002945.4:2515130","NC_002945.4:2520576","NC_002945.4:2524942","NC_002945.4:2528517","NC_002945.4:2529413","NC_002945.4:2532958","NC_002945.4:2538021","NC_002945.4:2539896","NC_002945.4:2549198","NC_002945.4:2573831","NC_002945.4:2615591","NC_002945.4:2631265","NC_002945.4:2656304","NC_002945.4:2656651","NC_002945.4:2662768","NC_002945.4:2663582","NC_002945.4:2667489","NC_002945.4:2683485","NC_002945.4:2688315","NC_002945.4:2729845","NC_002945.4:2747797","NC_002945.4:2749502","NC_002945.4:2758761","NC_002945.4:2767533","NC_002945.4:2770129","NC_002945.4:2794510","NC_002945.4:2806603","NC_002945.4:2807510","NC_002945.4:2807511","NC_002945.4:2809255","NC_002945.4:2819758","NC_002945.4:2823105","NC_002945.4:2870414","NC_002945.4:2870624","NC_002945.4:2873027","NC_002945.4:2884747","NC_002945.4:2886118","NC_002945.4:2890220","NC_002945.4:2893045","NC_002945.4:2899163","NC_002945.4:2899584","NC_002945.4:2900525","NC_002945.4:29061","NC_002945.4:2918203","NC_002945.4:2924775","NC_002945.4:2927134","NC_002945.4:2931071","NC_002945.4:2931113","NC_002945.4:2942926","NC_002945.4:2946800","NC_002945.4:295519","NC_002945.4:2956778","NC_002945.4:2964207","NC_002945.4:2978162","NC_002945.4:2978164","NC_002945.4:2983580","NC_002945.4:2984156","NC_002945.4:299636","NC_002945.4:3018593","NC_002945.4:3031841","NC_002945.4:3039600","NC_002945.4:3040820","NC_002945.4:3042914","NC_002945.4:304339","NC_002945.4:3045025","NC_002945.4:3053649","NC_002945.4:3053756","NC_002945.4:3063074","NC_002945.4:3068041","NC_002945.4:3069493","NC_002945.4:3070642","NC_002945.4:3088868","NC_002945.4:3093531","NC_002945.4:3098932","NC_002945.4:3100639","NC_002945.4:3103354","NC_002945.4:3106064","NC_002945.4:3106527","NC_002945.4:3116059","NC_002945.4:3127117","NC_002945.4:3137471","NC_002945.4:3140342","NC_002945.4:3151212","NC_002945.4:3154140","NC_002945.4:3172929","NC_002945.4:3173568","NC_002945.4:3191792","NC_002945.4:319911","NC_002945.4:3247551","NC_002945.4:3250072","NC_002945.4:3250245","NC_002945.4:3270181","NC_002945.4:3294771","NC_002945.4:3295991","NC_002945.4:3297558","NC_002945.4:3304410","NC_002945.4:3304946","NC_002945.4:3306898","NC_002945.4:331051","NC_002945.4:3310831","NC_002945.4:331241","NC_002945.4:331411","NC_002945.4:3319244","NC_002945.4:332124","NC_002945.4:332128","NC_002945.4:332144","NC_002945.4:332145","NC_002945.4:332154","NC_002945.4:332215","NC_002945.4:332218","NC_002945.4:333010","NC_002945.4:3330907","NC_002945.4:3338298","NC_002945.4:3347870","NC_002945.4:3368453","NC_002945.4:3371156","NC_002945.4:3373966","NC_002945.4:33788","NC_002945.4:3396621","NC_002945.4:3396650","NC_002945.4:340088","NC_002945.4:340090","NC_002945.4:340091","NC_002945.4:340092","NC_002945.4:340097","NC_002945.4:3413486","NC_002945.4:3414355","NC_002945.4:3421983","NC_002945.4:3422650","NC_002945.4:3439578","NC_002945.4:3451869","NC_002945.4:3453219","NC_002945.4:3460907","NC_002945.4:3464357","NC_002945.4:3464485","NC_002945.4:3464524","NC_002945.4:3468669","NC_002945.4:3476130","NC_002945.4:3482644","NC_002945.4:3484836","NC_002945.4:3486507","NC_002945.4:3493554","NC_002945.4:3495510","NC_002945.4:3497957","NC_002945.4:3533661","NC_002945.4:3546799","NC_002945.4:3553753","NC_002945.4:3564896","NC_002945.4:3567535","NC_002945.4:3574014","NC_002945.4:3574955","NC_002945.4:3591452","NC_002945.4:3600600","NC_002945.4:3622899","NC_002945.4:3624371","NC_002945.4:3626128","NC_002945.4:362818","NC_002945.4:3630061","NC_002945.4:364560","NC_002945.4:3645682","NC_002945.4:364804","NC_002945.4:3655045","NC_002945.4:366022","NC_002945.4:3667823","NC_002945.4:3712401","NC_002945.4:3718169","NC_002945.4:3718628","NC_002945.4:3719802","NC_002945.4:3723554","NC_002945.4:3725203","NC_002945.4:3729351","NC_002945.4:3751627","NC_002945.4:3769174","NC_002945.4:3776764","NC_002945.4:3778473","NC_002945.4:3800223","NC_002945.4:3805467","NC_002945.4:3816878","NC_002945.4:3821259","NC_002945.4:3839650","NC_002945.4:3846859","NC_002945.4:3874432","NC_002945.4:3877448","NC_002945.4:3884519","NC_002945.4:3888418","NC_002945.4:3902781","NC_002945.4:3905690","NC_002945.4:3941254","NC_002945.4:3942270","NC_002945.4:3957298","NC_002945.4:3966140","NC_002945.4:3969490","NC_002945.4:3969558","NC_002945.4:3969875","NC_002945.4:4003460","NC_002945.4:4008509","NC_002945.4:4010760","NC_002945.4:4017319","NC_002945.4:4018300","NC_002945.4:4029201","NC_002945.4:4046572","NC_002945.4:4070056","NC_002945.4:407246","NC_002945.4:4076594","NC_002945.4:4077189","NC_002945.4:4080736","NC_002945.4:4096612","NC_002945.4:41228","NC_002945.4:4128841","NC_002945.4:4130927","NC_002945.4:41437","NC_002945.4:4149101","NC_002945.4:4155870","NC_002945.4:4159272","NC_002945.4:4160820","NC_002945.4:4162407","NC_002945.4:4162554","NC_002945.4:4180986","NC_002945.4:4205111","NC_002945.4:4207380","NC_002945.4:4214259","NC_002945.4:4219009","NC_002945.4:4222196","NC_002945.4:4226875","NC_002945.4:4231626","NC_002945.4:4236320","NC_002945.4:4245762","NC_002945.4:4251588","NC_002945.4:4264139","NC_002945.4:4278315","NC_002945.4:4281136","NC_002945.4:4282825","NC_002945.4:4293932","NC_002945.4:4298964","NC_002945.4:430077","NC_002945.4:4303164","NC_002945.4:4311425","NC_002945.4:4321337","NC_002945.4:4339036","NC_002945.4:4347304","NC_002945.4:438482","NC_002945.4:441762","NC_002945.4:4480","NC_002945.4:449922","NC_002945.4:452398","NC_002945.4:460722","NC_002945.4:467343","NC_002945.4:467402","NC_002945.4:479644","NC_002945.4:483845","NC_002945.4:485584","NC_002945.4:488897","NC_002945.4:490878","NC_002945.4:50470","NC_002945.4:507929","NC_002945.4:518522","NC_002945.4:519412","NC_002945.4:541571","NC_002945.4:544180","NC_002945.4:577068","NC_002945.4:59861","NC_002945.4:598704","NC_002945.4:600207","NC_002945.4:611077","NC_002945.4:622386","NC_002945.4:641896","NC_002945.4:642875","NC_002945.4:644245","NC_002945.4:649910","NC_002945.4:652349","NC_002945.4:673880","NC_002945.4:680416","NC_002945.4:685069","NC_002945.4:69913","NC_002945.4:70082","NC_002945.4:701329","NC_002945.4:701386","NC_002945.4:70438","NC_002945.4:712319","NC_002945.4:723170","NC_002945.4:726979","NC_002945.4:737636","NC_002945.4:738102","NC_002945.4:745507","NC_002945.4:760347","NC_002945.4:792617","NC_002945.4:79918","NC_002945.4:804997","NC_002945.4:808601","NC_002945.4:811737","NC_002945.4:812709","NC_002945.4:828003","NC_002945.4:832093","NC_002945.4:833960","NC_002945.4:839308","NC_002945.4:843812","NC_002945.4:854043","NC_002945.4:865821","NC_002945.4:870116","NC_002945.4:8741","NC_002945.4:884432","NC_002945.4:889897","NC_002945.4:905912","NC_002945.4:917766","NC_002945.4:920753","NC_002945.4:941068","NC_002945.4:942431","NC_002945.4:943719","NC_002945.4:946102","NC_002945.4:948022","NC_002945.4:948811","NC_002945.4:948974","NC_002945.4:960995","NC_002945.4:96244","NC_002945.4:965529","NC_002945.4:967989","NC_002945.4:973459","NC_002945.4:974604","NC_002945.4:976327","NC_002945.4:982301","NC_002945.4:990611","NC_002945.4:997676","NC_002945.4:998183","NC_002945.4:998196"],"data":[60,60,59,60,59,59,60,55,60,60,60,60,59,59,60,60,59,60,59,60,52,55,56,59,59,59,60,59,60,60,59,59,60,60,59,59,59,56,60,60,60,59,59,59,60,59,60,60,60,60,60,59,59,56,56,59,60,60,59,60,59,58,60,59,59,59,60,59,59,59,59,59,60,59,58,57,57,60,59,60,60,59,59,60,59,60,59,59,59,59,60,59,59,60,60,59,60,60,59,59,60,60,60,60,60,59,60,60,59,59,60,60,60,59,59,59,60,59,60,59,60,60,59,60,60,60,59,59,59,59,60,59,60,60,59,59,59,59,59,59,59,59,59,60,60,59,59,60,60,60,59,60,59,59,60,60,59,59,59,59,59,60,60,60,60,59,60,59,59,59,59,59,59,59,60,60,60,60,60,60,60,60,60,59,60,60,59,60,60,60,59,59,60,59,60,60,60,60,59,60,60,59,60,60,59,59,60,60,60,59,60,60,59,59,60,59,60,60,59,59,60,60,60,59,60,59,59,59,59,60,60,59,59,59,60,60,60,59,59,60,60,59,60,60,60,59,59,59,60,59,59,59,60,59,59,60,60,60,59,60,59,60,60,60,59,60,60,59,59,60,60,60,60,60,59,60,60,60,59,59,60,59,60,59,59,59,59,59,60,59,60,59,60,59,60,59,59,59,60,60,60,60,59,59,59,60,60,60,60,60,60,59,59,59,59,59,59,59,59,60,58,60,59,60,59,60,59,59,57,57,57,57,57,60,60,60,59,59,59,59,59,59,60,59,59,60,60,60,59,60,60,59,60,59,60,60,60,60,60,60,60,59,60,59,58,59,59,59,60,59,60,59,59,59,59,59,59,59,59,60,60,60,60,60,59,60,60,59,59,59,59,59,59,59,60,59,60,60,59,60,59,60,60,60,59,60,60,59,59,60,60,60,59,59,59,59,60,59,60,59,59,60,59,59,60,60,59,60,59,60,60,60,59,60,59,59,60,60,60,59,60,59,59,59,59,60,59,59,59,60,60,59,59,60,59,60,60,59,60,60,59,59,59,59,59,60,60,59,59,59,59,59,60,60,60,60,60,59,60,59,60,60,60,60,60,59,60,59,59,60,59,59,59,59,60,59,59,59,60,60,59,58,60,59,60,59,59,60,59,59,59,60,59,59,60,59,59,59,60,59,59,59,59,59,60,60,60,59,59,59,60,60]}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_newick.newick	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+(root,((((SRR1792271_zc,SRR1792272_zc),SRR1791772_zc),SRR8073662_zc),SRR1791698_zc_vcf),SRR1792265_zc);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_snps_json.json	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,1 @@
+{"columns":["NC_002945.4:1005705","NC_002945.4:1348342","NC_002945.4:1382465","NC_002945.4:1463503","NC_002945.4:1704859","NC_002945.4:1723583","NC_002945.4:1911237","NC_002945.4:1961826","NC_002945.4:228109","NC_002945.4:2412437","NC_002945.4:2413021","NC_002945.4:3069493","NC_002945.4:3319244","NC_002945.4:3373966","NC_002945.4:3413486","NC_002945.4:3941254","NC_002945.4:3942270","NC_002945.4:4236320","NC_002945.4:4278315","NC_002945.4:960995","NC_002945.4:997676"],"index":["SRR1792265_zc","SRR1792272_zc","SRR1792271_zc","SRR8073662_zc","SRR1791772_zc","SRR1791698_zc_vcf","root"],"data":[["C","G","G","A","C","G","C","G","C","R","C","A","C","G","A","G","A","G","T","T","C"],["G","A","G","A","C","A","C","C","T","A","T","C","A","A","G","A","A","A","C","G","T"],["G","A","G","A","C","A","C","C","T","A","T","C","A","A","G","A","A","A","C","G","T"],["G","A","G","A","C","G","C","C","T","A","T","C","A","G","G","G","A","G","C","G","T"],["G","A","C","G","T","G","C","C","T","A","T","C","A","G","G","G","A","G","C","G","T"],["G","A","G","A","C","G","T","C","T","A","T","C","A","G","G","G","C","G","C","G","T"],["C","G","G","A","C","G","C","G","C","G","T","C","A","G","G","G","A","G","C","T","C"]]}
\ No newline at end of file
Binary file test-data/sort_table.xlsx has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/vsnp_genbank.loc.sample	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,4 @@
+## vSNP Genbank files
+#Value	Name	Path	Description
+#AF2122	Mycobacterium_AF2122/NC_002945v4.gbk	vsnp/AF2122/Mycobacterium_AF2122/NC_002945v4.gbk	Genbank file for Mycobacterium bovis AF2122/97
+#NC_006932	Brucella_abortus1/NC_006932-NC_006933.gbk	vsnp/NC_006932/Brucella_abortus1/NC_006932-NC_006933.gbk	Genbank file for Brucella abortus bv. 1 str. 9-941
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <table name="vsnp_genbank" comment_char="#">
+        <columns>value, name, path, description</columns>
+        <file path="tool-data/vsnp_genbank.loc" />
+    </table>
+</tables>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vsnp_build_tables.py	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,381 @@
+#!/usr/bin/env python
+
+import argparse
+import multiprocessing
+import os
+import pandas
+import queue
+import pandas.io.formats.excel
+import re
+from Bio import SeqIO
+
+INPUT_JSON_AVG_MQ_DIR = 'input_json_avg_mq_dir'
+INPUT_JSON_DIR = 'input_json_dir'
+INPUT_NEWICK_DIR = 'input_newick_dir'
+# Maximum columns allowed in a LibreOffice
+# spreadsheet is 1024.  Excel allows for
+# 16,384 columns, but we'll set the lower
+# number as the maximum.  Some browsers
+# (e.g., Firefox on Linux) are configured
+# to use LibreOffice for Excel spreadsheets.
+MAXCOLS = 1024
+OUTPUT_EXCEL_DIR = 'output_excel_dir'
+
+
+def annotate_table(table_df, group, annotation_dict):
+    for gbk_chrome, pro in list(annotation_dict.items()):
+        ref_pos = list(table_df)
+        ref_series = pandas.Series(ref_pos)
+        ref_df = pandas.DataFrame(ref_series.str.split(':', expand=True).values, columns=['reference', 'position'])
+        all_ref = ref_df[ref_df['reference'] == gbk_chrome]
+        positions = all_ref.position.to_frame()
+        # Create an annotation file.
+        annotation_file = "%s_annotations.csv" % group
+        with open(annotation_file, "a") as fh:
+            for index, row in positions.iterrows():
+                pos = row.position
+                try:
+                    aaa = pro.iloc[pro.index.get_loc(int(pos))][['chrom', 'locus', 'product', 'gene']]
+                    try:
+                        chrom, name, locus, tag = aaa.values[0]
+                        print("{}:{}\t{}, {}, {}".format(chrom, pos, locus, tag, name), file=fh)
+                    except ValueError:
+                        # If only one annotation for the entire
+                        # chromosome (e.g., flu) then having [0] fails
+                        chrom, name, locus, tag = aaa.values
+                        print("{}:{}\t{}, {}, {}".format(chrom, pos, locus, tag, name), file=fh)
+                except KeyError:
+                    print("{}:{}\tNo annotated product".format(gbk_chrome, pos), file=fh)
+    # Read the annotation file into a data frame.
+    annotations_df = pandas.read_csv(annotation_file, sep='\t', header=None, names=['index', 'annotations'], index_col='index')
+    # Remove the annotation_file from disk since both
+    # cascade and sort tables are built using the file,
+    # and it is opened for writing in append mode.
+    os.remove(annotation_file)
+    # Process the data.
+    table_df_transposed = table_df.T
+    table_df_transposed.index = table_df_transposed.index.rename('index')
+    table_df_transposed = table_df_transposed.merge(annotations_df, left_index=True, right_index=True)
+    table_df = table_df_transposed.T
+    return table_df
+
+
+def excel_formatter(json_file_name, excel_file_name, group, annotation_dict):
+    pandas.io.formats.excel.header_style = None
+    table_df = pandas.read_json(json_file_name, orient='split')
+    if annotation_dict is not None:
+        table_df = annotate_table(table_df, group, annotation_dict)
+    else:
+        table_df = table_df.append(pandas.Series(name='no annotations'))
+    writer = pandas.ExcelWriter(excel_file_name, engine='xlsxwriter')
+    table_df.to_excel(writer, sheet_name='Sheet1')
+    writer_book = writer.book
+    ws = writer.sheets['Sheet1']
+    format_a = writer_book.add_format({'bg_color': '#58FA82'})
+    format_g = writer_book.add_format({'bg_color': '#F7FE2E'})
+    format_c = writer_book.add_format({'bg_color': '#0000FF'})
+    format_t = writer_book.add_format({'bg_color': '#FF0000'})
+    format_normal = writer_book.add_format({'bg_color': '#FDFEFE'})
+    formatlowqual = writer_book.add_format({'font_color': '#C70039', 'bg_color': '#E2CFDD'})
+    format_ambigous = writer_book.add_format({'font_color': '#C70039', 'bg_color': '#E2CFDD'})
+    format_n = writer_book.add_format({'bg_color': '#E2CFDD'})
+    rows, cols = table_df.shape
+    ws.set_column(0, 0, 30)
+    ws.set_column(1, cols, 2.1)
+    ws.freeze_panes(2, 1)
+    format_annotation = writer_book.add_format({'font_color': '#0A028C', 'rotation': '-90', 'align': 'top'})
+    # Set last row.
+    ws.set_row(rows + 1, cols + 1, format_annotation)
+    # Make sure that row/column locations don't overlap.
+    ws.conditional_format(rows - 2, 1, rows - 1, cols, {'type': 'cell', 'criteria': '<', 'value': 55, 'format': formatlowqual})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'cell', 'criteria': '==', 'value': 'B$2', 'format': format_normal})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': 'A', 'format': format_a})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': 'G', 'format': format_g})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': 'C', 'format': format_c})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': 'T', 'format': format_t})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': 'S', 'format': format_ambigous})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': 'Y', 'format': format_ambigous})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': 'R', 'format': format_ambigous})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': 'W', 'format': format_ambigous})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': 'K', 'format': format_ambigous})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': 'M', 'format': format_ambigous})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': 'N', 'format': format_n})
+    ws.conditional_format(2, 1, rows - 2, cols, {'type': 'text', 'criteria': 'containing', 'value': '-', 'format': format_n})
+    format_rotation = writer_book.add_format({})
+    format_rotation.set_rotation(90)
+    for column_num, column_name in enumerate(list(table_df.columns)):
+        ws.write(0, column_num + 1, column_name, format_rotation)
+    format_annotation = writer_book.add_format({'font_color': '#0A028C', 'rotation': '-90', 'align': 'top'})
+    # Set last row.
+    ws.set_row(rows, 400, format_annotation)
+    writer.save()
+
+
+def get_annotation_dict(gbk_file):
+    gbk_dict = SeqIO.to_dict(SeqIO.parse(gbk_file, "genbank"))
+    annotation_dict = {}
+    tmp_file = "features.csv"
+    # Create a file of chromosomes and features.
+    for chromosome in list(gbk_dict.keys()):
+        with open(tmp_file, 'w+') as fh:
+            for feature in gbk_dict[chromosome].features:
+                if "CDS" in feature.type or "rRNA" in feature.type:
+                    try:
+                        product = feature.qualifiers['product'][0]
+                    except KeyError:
+                        product = None
+                    try:
+                        locus = feature.qualifiers['locus_tag'][0]
+                    except KeyError:
+                        locus = None
+                    try:
+                        gene = feature.qualifiers['gene'][0]
+                    except KeyError:
+                        gene = None
+                    fh.write("%s\t%d\t%d\t%s\t%s\t%s\n" % (chromosome, int(feature.location.start), int(feature.location.end), locus, product, gene))
+        # Read the chromosomes and features file into a data frame.
+        df = pandas.read_csv(tmp_file, sep='\t', names=["chrom", "start", "stop", "locus", "product", "gene"])
+        # Process the data.
+        df = df.sort_values(['start', 'gene'], ascending=[True, False])
+        df = df.drop_duplicates('start')
+        pro = df.reset_index(drop=True)
+        pro.index = pandas.IntervalIndex.from_arrays(pro['start'], pro['stop'], closed='both')
+        annotation_dict[chromosome] = pro
+    return annotation_dict
+
+
+def get_base_file_name(file_path):
+    base_file_name = os.path.basename(file_path)
+    if base_file_name.find(".") > 0:
+        # Eliminate the extension.
+        return os.path.splitext(base_file_name)[0]
+    elif base_file_name.find("_") > 0:
+        # The dot extension was likely changed to
+        # the " character.
+        items = base_file_name.split("_")
+        return "_".join(items[0:-1])
+    else:
+        return base_file_name
+
+
+def output_cascade_table(cascade_order, mqdf, group, annotation_dict):
+    cascade_order_mq = pandas.concat([cascade_order, mqdf], join='inner')
+    output_table(cascade_order_mq, "cascade", group, annotation_dict)
+
+
+def output_excel(df, type_str, group, annotation_dict, count=None):
+    # Output the temporary json file that
+    # is used by the excel_formatter.
+    if count is None:
+        if group is None:
+            json_file_name = "%s_order_mq.json" % type_str
+            excel_file_name = os.path.join(OUTPUT_EXCEL_DIR, "%s_table.xlsx" % type_str)
+        else:
+            json_file_name = "%s_%s_order_mq.json" % (group, type_str)
+            excel_file_name = os.path.join(OUTPUT_EXCEL_DIR, "%s_%s_table.xlsx" % (group, type_str))
+    else:
+        if group is None:
+            json_file_name = "%s_order_mq_%d.json" % (type_str, count)
+            excel_file_name = os.path.join(OUTPUT_EXCEL_DIR, "%s_table_%d.xlsx" % (type_str, count))
+        else:
+            json_file_name = "%s_%s_order_mq_%d.json" % (group, type_str, count)
+            excel_file_name = os.path.join(OUTPUT_EXCEL_DIR, "%s_%s_table_%d.xlsx" % (group, type_str, count))
+    df.to_json(json_file_name, orient='split')
+    # Output the Excel file.
+    excel_formatter(json_file_name, excel_file_name, group, annotation_dict)
+
+
+def output_sort_table(cascade_order, mqdf, group, annotation_dict):
+    sort_df = cascade_order.T
+    sort_df['abs_value'] = sort_df.index
+    sort_df[['chrom', 'pos']] = sort_df['abs_value'].str.split(':', expand=True)
+    sort_df = sort_df.drop(['abs_value', 'chrom'], axis=1)
+    sort_df.pos = sort_df.pos.astype(int)
+    sort_df = sort_df.sort_values(by=['pos'])
+    sort_df = sort_df.drop(['pos'], axis=1)
+    sort_df = sort_df.T
+    sort_order_mq = pandas.concat([sort_df, mqdf], join='inner')
+    output_table(sort_order_mq, "sort", group, annotation_dict)
+
+
+def output_table(df, type_str, group, annotation_dict):
+    if isinstance(group, str) and group.startswith("dataset"):
+        # Inputs are single files, not collections,
+        # so input file names are not useful for naming
+        # output files.
+        group_str = None
+    else:
+        group_str = group
+    count = 0
+    chunk_start = 0
+    chunk_end = 0
+    column_count = df.shape[1]
+    if column_count >= MAXCOLS:
+        # Here the number of columns is greater than
+        # the maximum allowed by Excel, so multiple
+        # outputs will be produced.
+        while column_count >= MAXCOLS:
+            count += 1
+            chunk_end += MAXCOLS
+            df_of_type = df.iloc[:, chunk_start:chunk_end]
+            output_excel(df_of_type, type_str, group_str, annotation_dict, count=count)
+            chunk_start += MAXCOLS
+            column_count -= MAXCOLS
+        count += 1
+        df_of_type = df.iloc[:, chunk_start:]
+        output_excel(df_of_type, type_str, group_str, annotation_dict, count=count)
+    else:
+        output_excel(df, type_str, group_str, annotation_dict)
+
+
+def preprocess_tables(task_queue, annotation_dict, timeout):
+    while True:
+        try:
+            tup = task_queue.get(block=True, timeout=timeout)
+        except queue.Empty:
+            break
+        newick_file, json_file, json_avg_mq_file = tup
+        avg_mq_series = pandas.read_json(json_avg_mq_file, typ='series', orient='split')
+        # Map quality to dataframe.
+        mqdf = avg_mq_series.to_frame(name='MQ')
+        mqdf = mqdf.T
+        # Get the group.
+        group = get_base_file_name(newick_file)
+        snps_df = pandas.read_json(json_file, orient='split')
+        with open(newick_file, 'r') as fh:
+            for line in fh:
+                line = re.sub('[:,]', '\n', line)
+                line = re.sub('[)(]', '', line)
+                line = re.sub(r'[0-9].*\.[0-9].*\n', '', line)
+                line = re.sub('root\n', '', line)
+        sample_order = line.split('\n')
+        sample_order = list([_f for _f in sample_order if _f])
+        sample_order.insert(0, 'root')
+        tree_order = snps_df.loc[sample_order]
+        # Count number of SNPs in each column.
+        snp_per_column = []
+        for column_header in tree_order:
+            count = 0
+            column = tree_order[column_header]
+            for element in column:
+                if element != column[0]:
+                    count = count + 1
+            snp_per_column.append(count)
+        row1 = pandas.Series(snp_per_column, tree_order.columns, name="snp_per_column")
+        # Count number of SNPS from the
+        # top of each column in the table.
+        snp_from_top = []
+        for column_header in tree_order:
+            count = 0
+            column = tree_order[column_header]
+            # for each element in the column
+            # skip the first element
+            for element in column[1:]:
+                if element == column[0]:
+                    count = count + 1
+                else:
+                    break
+            snp_from_top.append(count)
+        row2 = pandas.Series(snp_from_top, tree_order.columns, name="snp_from_top")
+        tree_order = tree_order.append([row1])
+        tree_order = tree_order.append([row2])
+        # In pandas=0.18.1 even this does not work:
+        # abc = row1.to_frame()
+        # abc = abc.T --> tree_order.shape (5, 18), abc.shape (1, 18)
+        # tree_order.append(abc)
+        # Continue to get error: "*** ValueError: all the input arrays must have same number of dimensions"
+        tree_order = tree_order.T
+        tree_order = tree_order.sort_values(['snp_from_top', 'snp_per_column'], ascending=[True, False])
+        tree_order = tree_order.T
+        # Remove snp_per_column and snp_from_top rows.
+        cascade_order = tree_order[:-2]
+        # Output the cascade table.
+        output_cascade_table(cascade_order, mqdf, group, annotation_dict)
+        # Output the sorted table.
+        output_sort_table(cascade_order, mqdf, group, annotation_dict)
+        task_queue.task_done()
+
+
+def set_num_cpus(num_files, processes):
+    num_cpus = int(multiprocessing.cpu_count())
+    if num_files < num_cpus and num_files < processes:
+        return num_files
+    if num_cpus < processes:
+        half_cpus = int(num_cpus / 2)
+        if num_files < half_cpus:
+            return num_files
+        return half_cpus
+    return processes
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument('--input_avg_mq_json', action='store', dest='input_avg_mq_json', required=False, default=None, help='Average MQ json file')
+    parser.add_argument('--input_newick', action='store', dest='input_newick', required=False, default=None, help='Newick file')
+    parser.add_argument('--input_snps_json', action='store', dest='input_snps_json', required=False, default=None, help='SNPs json file')
+    parser.add_argument('--gbk_file', action='store', dest='gbk_file', required=False, default=None, help='Optional gbk file'),
+    parser.add_argument('--processes', action='store', dest='processes', type=int, help='User-selected number of processes to use for job splitting')
+
+    args = parser.parse_args()
+
+    if args.gbk_file is not None:
+        # Create the annotation_dict for annotating
+        # the Excel tables.
+        annotation_dict = get_annotation_dict(args.gbk_file)
+    else:
+        annotation_dict = None
+
+    # The assumption here is that the list of files
+    # in both INPUT_NEWICK_DIR and INPUT_JSON_DIR are
+    # named such that they are properly matched if
+    # the directories contain more than 1 file (i.e.,
+    # hopefully the newick file names and json file names
+    # will be something like Mbovis-01D6_* so they can be
+    # sorted and properly associated with each other).
+    if args.input_newick is not None:
+        newick_files = [args.input_newick]
+    else:
+        newick_files = []
+        for file_name in sorted(os.listdir(INPUT_NEWICK_DIR)):
+            file_path = os.path.abspath(os.path.join(INPUT_NEWICK_DIR, file_name))
+            newick_files.append(file_path)
+    if args.input_snps_json is not None:
+        json_files = [args.input_snps_json]
+    else:
+        json_files = []
+        for file_name in sorted(os.listdir(INPUT_JSON_DIR)):
+            file_path = os.path.abspath(os.path.join(INPUT_JSON_DIR, file_name))
+            json_files.append(file_path)
+    if args.input_avg_mq_json is not None:
+        json_avg_mq_files = [args.input_avg_mq_json]
+    else:
+        json_avg_mq_files = []
+        for file_name in sorted(os.listdir(INPUT_JSON_AVG_MQ_DIR)):
+            file_path = os.path.abspath(os.path.join(INPUT_JSON_AVG_MQ_DIR, file_name))
+            json_avg_mq_files.append(file_path)
+
+    multiprocessing.set_start_method('spawn')
+    queue1 = multiprocessing.JoinableQueue()
+    queue2 = multiprocessing.JoinableQueue()
+    num_files = len(newick_files)
+    cpus = set_num_cpus(num_files, args.processes)
+    # Set a timeout for get()s in the queue.
+    timeout = 0.05
+
+    for i, newick_file in enumerate(newick_files):
+        json_file = json_files[i]
+        json_avg_mq_file = json_avg_mq_files[i]
+        queue1.put((newick_file, json_file, json_avg_mq_file))
+
+    # Complete the preprocess_tables task.
+    processes = [multiprocessing.Process(target=preprocess_tables, args=(queue1, annotation_dict, timeout, )) for _ in range(cpus)]
+    for p in processes:
+        p.start()
+    for p in processes:
+        p.join()
+    queue1.join()
+
+    if queue1.empty():
+        queue1.close()
+        queue1.join_thread()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vsnp_build_tables.xml	Fri May 08 12:59:27 2020 -0400
@@ -0,0 +1,206 @@
+<tool id="vsnp_build_tables" name="vSNP: build tables" version="1.0.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="1.76">biopython</requirement>
+        <requirement type="package" version="0.25.3">pandas</requirement>
+        <requirement type="package" version="1.2.8">xlsxwriter</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+#set output_excel_dir = 'output_excel_dir'
+#set input_type = $input_type_cond.input_type
+mkdir $output_excel_dir &&
+#if $input_type == "collection":
+    #set input_newick_dir = 'input_newick_dir'
+    mkdir $input_newick_dir &&
+    #set input_json_avg_mq_dir = 'input_json_avg_mq_dir'
+    mkdir $input_json_avg_mq_dir &&
+    #set input_json_dir = 'input_json_dir'
+    mkdir $input_json_dir &&
+    #for $i in $input_type_cond.input_avg_mq_json_collection:
+        #set file_name = $i.file_name
+        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
+        ln -s '$file_name' '$input_json_avg_mq_dir/$identifier' &&
+    #end for
+    #for $i in $input_type_cond.input_snps_json_collection:
+        #set file_name = $i.file_name
+        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
+        ln -s '$file_name' '$input_json_dir/$identifier' &&
+    #end for
+    #for $i in $input_type_cond.input_newick_collection:
+        #set file_name = $i.file_name
+        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
+        ln -s '$file_name' '$input_newick_dir/$identifier' &&
+    #end for
+#end if
+python '$__tool_directory__/vsnp_build_tables.py'
+--processes \${GALAXY_SLOTS:-4}
+#if $input_type == "single":
+    --input_avg_mq_json '$input_avg_mq_json'
+    --input_snps_json '$input_snps_json'
+    --input_newick '$input_newick'
+#end if:
+#if str($gbk_cond.gbk_param) == "yes":
+    #set gbk_source_cond = $gbk_cond.gbk_source_cond
+    #set gbk_source = $gbk_source_cond.gbk_source
+    #if str($gbk_source) == "cached":
+        --gbk_file '$gbk_source_cond.gbk_file.fields.path'
+    #else:
+        --gbk_file '$gbk_source_cond.gbk_file'
+    #end if
+#end if
+]]></command>
+    <inputs>
+        <conditional name="input_type_cond">
+            <param name="input_type" type="select" label="Choose the category for the files to be analyzed">
+                <option value="single" selected="true">Single files</option>
+                <option value="collection">Collection of files</option>
+            </param>
+            <when value="single">
+                <param name="input_snps_json" type="data" format="json" label="SNPs json file">
+                    <validator type="unspecified_build"/>
+                </param>
+                <param name="input_avg_mq_json" type="data" format="json" label="Average MQ json file">
+                    <validator type="unspecified_build"/>
+                </param>
+                <param name="input_newick" type="data" format="newick" label="Best-scoring ML tree file">
+                    <validator type="unspecified_build"/>
+                </param>
+            </when>
+            <when value="collection">
+                <param name="input_snps_json_collection" format="json" type="data_collection" collection_type="list" label="Collection of SNPs json files">
+                    <validator type="unspecified_build"/>
+                </param>
+                <param name="input_avg_mq_json_collection" format="json" type="data_collection" collection_type="list" label="Collection of average MQ json files">
+                    <validator type="unspecified_build"/>
+                </param>
+                <param name="input_newick_collection" format="newick" type="data_collection" collection_type="list" label="Collection of best-scoring ML tree files">
+                    <validator type="unspecified_build"/>
+                </param>
+            </when>
+        </conditional>
+        <conditional name="gbk_cond">
+            <param name="gbk_param" type="select" label="Use Genbank file?">
+                <option value="yes" selected="true">yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <conditional name="gbk_source_cond">
+                    <param name="gbk_source" type="select" label="Choose the source for the Genbank file">
+                        <option value="cached" selected="true">locally cached</option>
+                        <option value="history">from history</option>
+                    </param>
+                    <when value="cached">
+                        <param name="gbk_file" type="select" label="Genbank file">
+                            <options from_data_table="vsnp_genbank">
+                                <!-- No filter here! -->
+                            </options>
+                            <validator type="no_options" message="A cached Genbank file is not available for the build associated with the selected average MQ json file"/>
+                        </param>
+                    </when>
+                    <when value="history">
+                        <param name="gbk_file" type="data" format="genbank" label="Genbank file">
+                            <validator type="no_options" message="The current history does not include a genbank dataset"/>
+                        </param>
+                    </when>
+                </conditional>
+            </when>
+            <when value="no"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <collection name="excel" type="list">
+            <discover_datasets pattern="__name__" directory="output_excel_dir" format="xlsx" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_snps_json" value="input_snps_json.json" ftype="json" dbkey="89"/>
+            <param name="input_newick" value="input_newick.newick" ftype="newick" dbkey="89"/>
+            <param name="input_avg_mq_json" value="input_avg_mq_json.json" ftype="json" dbkey="89"/>
+            <param name="gbk_param" value="no"/>
+            <output_collection name="excel" type="list">
+                <element name="cascade_table.xlsx" file="cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="sort_table.xlsx" file="sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_type" value="collection"/>
+            <param name="input_snps_json_collection">
+                <collection type="list">
+                    <element name="Mbovis-01_snps.json" value="Mbovis-01_snps.json" dbkey="89"/>
+                    <element name="Mbovis-01D_snps.json" value="Mbovis-01D_snps.json" dbkey="89"/>
+                    <element name="Mbovis-01D6_snps.json" value="Mbovis-01D6_snps.json" dbkey="89"/>
+                </collection>
+            </param>
+            <param name="input_newick_collection">
+                <collection type="list">
+                    <element name="Mbovis-01_snps.newick" value="Mbovis-01_snps.newick" dbkey="89"/>
+                    <element name="Mbovis-01D_snps.newick" value="Mbovis-01D_snps.newick" dbkey="89"/>
+                    <element name="Mbovis-01D6_snps.newick" value="Mbovis-01D6_snps.newick" dbkey="89"/>
+                </collection>
+            </param>
+            <param name="input_avg_mq_json_collection">
+                <collection type="list">
+                    <element name="Mbovis-01_snps.json" value="Mbovis-01_avg_mq.json" dbkey="89"/>
+                    <element name="Mbovis-01D_snps.json" value="Mbovis-01D_avg_mq.json" dbkey="89"/>
+                    <element name="Mbovis-01D6_snps.json" value="Mbovis-01D6_avg_mq.json" dbkey="89"/>
+                </collection>
+            </param>
+            <param name="gbk_param" value="no"/>
+            <output_collection name="excel" type="list">
+                <element name="Mbovis-01D6_snps_cascade_table.xlsx" file="Mbovis-01D6_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01D6_snps_sort_table.xlsx" file="Mbovis-01D6_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01D_snps_cascade_table.xlsx" file="Mbovis-01D_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01D_snps_sort_table.xlsx" file="Mbovis-01D_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01_snps_cascade_table.xlsx" file="Mbovis-01_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01_snps_sort_table.xlsx" file="Mbovis-01_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Accepts a combination of single SNPs json, average MQ json and newick files (or associated collections of
+each) to produce annotated SNPs tables in the form of Excel spreadsheets.  The SNPs json and average MQ json
+files are typically produced by the **vSNP: get SNPs** tool and the newick files are typically produced by
+the **Phyogenetic reconstruction with RaXML** tool.
+
+The SNPs tables display closely related isolates and enables identification of mixed SNPs when multiple
+bacterial strains are infecting an organism.  The table structure is shown below.  The columns identify the
+genome location of the SNP calls and the isolates are contained within the rows.  The reference (or ancestral
+strain if the reference is an outgroup) is listed across the top, identified as the "reference call".  SNPs
+that are not highlighted will match the reference.  The map-quality row values are the average of the map
+quality scores of each isolate  in that position.  These scores measure the confidence that the read has been
+mapped to the correct location on the genome.  The maximum score possible is 60, and lower scores lessen the
+confidence that the SNP was correctly identified.  The annotation of the position is provided at the bottom
+of the table.
+
+.. image:: table_description.png
+
+SNPs are sorted according to their evolutionary age within the table.  The oldest SNPs (encompassing the most
+isolates) are furthest to the left.  This sorting is somewhat crude - the intent is to improve readibility or
+more easily match a related tree.
+
+For a more detailed discussion, see the **Validating and correcting SNP calls** section of
+the `vSNP documentation`_.
+
+.. _vSNP documentation: https://github.com/USDA-VS/vSNP/blob/master/docs/detailed_usage.md
+
+**Required Options**
+
+ * **Choose the category for the files to be analyzed** -  select "Single files" or "Collections of files", then select the appropriate history items (single SNPs json, average MQ json and newick files, or collections of each) based on the selected option.
+ * **Use Genbank file** - Select "yes" to annotate the tables using the information in the Genbank file.  Locally cached files, if available, provide the most widely used annotations, but more custom Genbank files can be chosen from the current history.
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @misc{None,
+            journal = {None},
+            author = {1. Stuber T},
+            title = {Manuscript in preparation},
+            year = {None},
+            url = {https://github.com/USDA-VS/vSNP},}
+        </citation>
+    </citations>
+</tool>
+