fixed some tests

data/PF16593.testspan.fa

@@ -5,7 +5,7 @@ RRSFRTSRRRLDR---RQQRVKLVQEIFAPVISPID
 >R6E3D1_9BACT/67-102
 RTRMRGMRHLLERSLLRRERLHRVLDIMDFLPPHYS
 >D6E761_9ACTN/55-86
-R-VHRGQRRRYDR---RRQRIDLLQRFFADEVAKVD
+-RVHRGQRRRYDR---RRQRIDLLQRFFADEVAKVD
 >R5Z6B4_9FIRM/50-82
 RRTHRTSRRRLDR---EKARIACLKEMFAEEINKID
 >R6P3Z6_9FIRM/51-83
@@ -17,7 +17,7 @@ RTGYRGVRRLRERHLLRRERLHRVLNILGFLPNHYA
 >Q73QW6_TREDE/53-85
 RRLHRGARRRIER---RKKRIKLLQELFSQEIAKTD
 >E1QW44_OLSUV/56-87
-R-IHRSQRRRYVR---RRWRLDLLQSLFQDEVSKVD
+-RIHRSQRRRYVR---RRWRLDLLQSLFQDEVSKVD
 >D4J3S7_9FIRM/50-82
 RRMFRTARRRLDR---RNWRIQVLQEIFSEEISKVD
 >R5FLM1_9ACTN/58-90

data/PF16593.testspan.testnj.nh

@@ -1 +1 @@
-((R5Z6B4_9FIRM/50-82:0.135045,((((R6P3Z6_9FIRM/51-83:0.103652,D6GRK4_FILAD/50-82:0.0781834):0.0451682,(R5ZG15_9CLOT/70-102:0.148578,(Q73QW6_TREDE/53-85:0.0740277,(CAS9_STRP1/62-94:0.169154,R7KD29_9FIRM/54-85:0.176458):0.0497483):0.0211):0.0208769):0.0207905,(R6ET93_9FIRM/56-88:0.0806945,((R7KBA0_9CLOT/53-85:0.0765842,(D6E761_9ACTN/55-86:0.142657,((R5FLM1_9ACTN/58-90:0.0446524,(F2NB82_CORGP/56-87:0.146582,F7UWL3_EEGSY/55-86:0.0730434):0.0576378):0.0231315,(E1QW44_OLSUV/56-87:0.0828336,R7D1C6_9ACTN/56-87:0.0760403):0.00830604):0.0228878):0.1026):0.0267413,(R5J5B2_9FIRM/85-117:0.114975,(R6U7U5_9CLOT/49-81:0.131966,R6QHH1_9FIRM/50-82:0.0344826):0.114332):0.0102414):0.00765481):0.0119626):0.0163622,(R6ZAM8_9CLOT/50-82:0.147951,((G2KVM6_LACSM/51-83:0.0836572,(J9W3C2_LACBU/51-83:0.133998,D6S374_9LACO/52-84:0.0567985):0.0315726):0.0606467,(R7K435_9FIRM/50-82:0.154058,(G4Q6A5_ACIIR/50-82:0.170649,(R7I2K1_9CLOT/56-88:0.0929321,(R5CLM1_9BACT/64-99:0.10474,(K4I9M9_PSYTT/60-95:0.0409738,(G8X9H3_FLACA/61-96:0.0458767,(H1Z4Q9_MYROD/60-95:0.00271042,(R7D4J2_9BACE/64-99:0.0670185,(I4A2W8_ORNRL/62-97:0.0392829,(R6E3D1_9BACT/67-102:1e-09,C9RJP1_FIBSS/68-102:0.386939):0.104995):0.108293):0.0408077):0.0753735):0.0647164):0.0698542):0.865217):0.142336):0.086133):0.0199944):0.0352117):0.0101702):0.00652163):0.00126384,((D4J3S7_9FIRM/50-82:0.100016,R5BQB0_9FIRM/56-88:0.143668):0.0157838,(((R6TGA0_9STAP/49-81:0.182597,B0RZQ7_FINM2/52-84:0.172103):0.0879157,(R5V4T4_9FIRM/50-82:0.206075,(R7FJU9_9CLOT/50-82:0.0590525,R6XMN7_9FIRM/50-82:0.0678313):0.0282864):0.0647951):0.0233574,(R5SXF4_9CLOT/52-84:0.0754567,(I6T669_ENTHA/62-94:0.114539,V5XLV7_ENTMU/62-94:0.138781):0.0603162):0.0189135):0.00806006):0.00126384);
+((((R6TGA0_9STAP/49-81:0.182776,B0RZQ7_FINM2/52-84:0.171923):0.0889587,(R5V4T4_9FIRM/50-82:0.205064,(R7FJU9_9CLOT/50-82:0.0590525,R6XMN7_9FIRM/50-82:0.0678313):0.0292973):0.0637521):0.0270811,(R5BQB0_9FIRM/56-88:0.14091,((I6T669_ENTHA/62-94:0.114539,V5XLV7_ENTMU/62-94:0.138781):0.0714209,((R5J5B2_9FIRM/85-117:0.114201,(R6U7U5_9CLOT/49-81:0.131966,R6QHH1_9FIRM/50-82:0.0344826):0.115105):0.0188653,(R5SXF4_9CLOT/52-84:0.0757383,((G2KVM6_LACSM/51-83:0.0838069,(J9W3C2_LACBU/51-83:0.133998,D6S374_9LACO/52-84:0.0567985):0.0314228):0.0580789,(R7K435_9FIRM/50-82:0.153707,(G4Q6A5_ACIIR/50-82:0.167859,(R7I2K1_9CLOT/56-88:0.0876802,(R5CLM1_9BACT/64-99:0.104685,(K4I9M9_PSYTT/60-95:0.0392853,(G8X9H3_FLACA/61-96:0.0452438,(H1Z4Q9_MYROD/60-95:0.00356905,(R7D4J2_9BACE/64-99:0.0654308,(I4A2W8_ORNRL/62-97:0.0350065,(R6E3D1_9BACT/67-102:1e-09,C9RJP1_FIBSS/68-102:0.381979):0.109272):0.10988):0.039949):0.0760064):0.066405):0.0699089):0.870468):0.145127):0.0864832):0.0225622):0.0250679):0.00829601):0.0134623):0.00853147):0.00802017):0.00197259,((D4J3S7_9FIRM/50-82:0.0988263,R6ZAM8_9CLOT/50-82:0.150999):0.0209996,(R5Z6B4_9FIRM/50-82:0.129134,(R6ET93_9FIRM/56-88:0.0881345,((R7KBA0_9CLOT/53-85:0.0710526,((D6E761_9ACTN/55-86:0.134129,((R5FLM1_9ACTN/58-90:0.043173,(F2NB82_CORGP/56-87:0.147341,F7UWL3_EEGSY/55-86:0.072285):0.0591173):0.0211125,(E1QW44_OLSUV/56-87:0.0775554,R7D1C6_9ACTN/56-87:0.0783538):0.00451843):0.0254042):0.0784491,(CAS9_STRP1/62-94:0.171573,R7KD29_9FIRM/54-85:0.174039):0.044912):0.0240118):0.0277527,(R5ZG15_9CLOT/70-102:0.16549,(Q73QW6_TREDE/53-85:0.0899189,(R6P3Z6_9FIRM/51-83:0.103081,D6GRK4_FILAD/50-82:0.0787538):0.0232984):0.0253115):0.00618097):0.0213449):0.013982):0.00551327):0.00197259);

data/PF16593.testspan.testupgma.nh

@@ -1 +1 @@
-((R7D4J2_9BACE/64-99:0.25453,(R5CLM1_9BACT/64-99:0.246672,((I4A2W8_ORNRL/62-97:0.0842244,K4I9M9_PSYTT/60-95:0.0842244):0.157166,((R6E3D1_9BACT/67-102:0.0772295,C9RJP1_FIBSS/68-102:0.0772295):0.107412,(H1Z4Q9_MYROD/60-95:0.0878458,G8X9H3_FLACA/61-96:0.0878458):0.0967959):0.0567484):0.00528193):0.00785831):1.20612,((G4Q6A5_ACIIR/50-82:0.606596,((R6U7U5_9CLOT/49-81:0.0832241,R6QHH1_9FIRM/50-82:0.0832241):0.523371,(((G2KVM6_LACSM/51-83:0.153013,(J9W3C2_LACBU/51-83:0.0953984,D6S374_9LACO/52-84:0.0953984):0.0576149):0.170288,(R5ZG15_9CLOT/70-102:0.159914,R7K435_9FIRM/50-82:0.159914):0.163387):0.283295,((R6ZAM8_9CLOT/50-82:0.407548,(((Q73QW6_TREDE/53-85:0.147526,(R6P3Z6_9FIRM/51-83:0.0909175,D6GRK4_FILAD/50-82:0.0909175):0.0566086):0.136645,(R5J5B2_9FIRM/85-117:0.153008,(R6ET93_9FIRM/56-88:0.0891042,R7KBA0_9CLOT/53-85:0.0891042):0.0639038):0.131163):0.123377,(R5BQB0_9FIRM/56-88:0.226457,(R5Z6B4_9FIRM/50-82:0.17646,(D4J3S7_9FIRM/50-82:0.0996152,R5SXF4_9CLOT/52-84:0.0996152):0.0768449):0.0499964):0.181092):1e-09):0.0923764,(V5XLV7_ENTMU/62-94:0.228777,(I6T669_ENTHA/62-94:0.139908,(R7FJU9_9CLOT/50-82:0.0634419,R6XMN7_9FIRM/50-82:0.0634419):0.0764659):0.0888688):0.271148):0.106671):1e-09):1e-09):0.364001,(((D6E761_9ACTN/55-86:0.26485,((R5FLM1_9ACTN/58-90:0.13307,(E1QW44_OLSUV/56-87:0.0794369,R7D1C6_9ACTN/56-87:0.0794369):0.0536335):0.103184,(F2NB82_CORGP/56-87:0.109813,F7UWL3_EEGSY/55-86:0.109813):0.126442):0.0285959):0.274185,(CAS9_STRP1/62-94:0.289636,(R7I2K1_9CLOT/56-88:0.155777,R7KD29_9FIRM/54-85:0.155777):0.133859):0.249399):0.188575,(R5V4T4_9FIRM/50-82:0.351263,(R6TGA0_9STAP/49-81:0.17735,B0RZQ7_FINM2/52-84:0.17735):0.173913):0.376347):0.242986):0.490051);
+((R7D4J2_9BACE/64-99:0.25453,(R5CLM1_9BACT/64-99:0.246672,((I4A2W8_ORNRL/62-97:0.0842244,K4I9M9_PSYTT/60-95:0.0842244):0.157166,((R6E3D1_9BACT/67-102:0.0772295,C9RJP1_FIBSS/68-102:0.0772295):0.107412,(H1Z4Q9_MYROD/60-95:0.0878458,G8X9H3_FLACA/61-96:0.0878458):0.0967959):0.0567484):0.00528193):0.00785831):1.15855,((G4Q6A5_ACIIR/50-82:0.606596,((R6U7U5_9CLOT/49-81:0.0832241,R6QHH1_9FIRM/50-82:0.0832241):0.523371,(((G2KVM6_LACSM/51-83:0.153013,(J9W3C2_LACBU/51-83:0.0953984,D6S374_9LACO/52-84:0.0953984):0.0576149):0.170288,(R5ZG15_9CLOT/70-102:0.159914,R7K435_9FIRM/50-82:0.159914):0.163387):0.283295,((R6ZAM8_9CLOT/50-82:0.407548,(((Q73QW6_TREDE/53-85:0.147526,(R6P3Z6_9FIRM/51-83:0.0909175,D6GRK4_FILAD/50-82:0.0909175):0.0566086):0.136645,(R5J5B2_9FIRM/85-117:0.153008,(R6ET93_9FIRM/56-88:0.0891042,R7KBA0_9CLOT/53-85:0.0891042):0.0639038):0.131163):0.123377,(R5BQB0_9FIRM/56-88:0.226457,(R5Z6B4_9FIRM/50-82:0.17646,(D4J3S7_9FIRM/50-82:0.0996152,R5SXF4_9CLOT/52-84:0.0996152):0.0768449):0.0499964):0.181092):1e-09):0.0923764,(V5XLV7_ENTMU/62-94:0.228777,(I6T669_ENTHA/62-94:0.139908,(R7FJU9_9CLOT/50-82:0.0634419,R6XMN7_9FIRM/50-82:0.0634419):0.0764659):0.0888688):0.271148):0.106671):1e-09):1e-09):0.311436,((R6TGA0_9STAP/49-81:0.17735,B0RZQ7_FINM2/52-84:0.17735):0.447584,(R5V4T4_9FIRM/50-82:0.526099,((D6E761_9ACTN/55-86:0.259345,((R5FLM1_9ACTN/58-90:0.123819,(E1QW44_OLSUV/56-87:0.0779546,R7D1C6_9ACTN/56-87:0.0779546):0.0458644):0.10842,(F2NB82_CORGP/56-87:0.109813,F7UWL3_EEGSY/55-86:0.109813):0.122427):0.0271054):0.266754,(CAS9_STRP1/62-94:0.289636,(R7I2K1_9CLOT/56-88:0.155777,R7KD29_9FIRM/54-85:0.155777):0.133859):0.236462):1e-09):0.0988349):0.293098):0.495049);

data/testrates.out.json

@@ -6,8 +6,8 @@
  "delextprob": 0.4,
  "rootprob":
  {
-  "A": 6.40988e-17,
-  "C": 1.98932e-18,
+  "A": 0,
+  "C": 0,
   "G": 0,
   "T": 1
  },

data/testrates.probs.json

@@ -5,8 +5,8 @@
  "delBegin": 0.181269,
  "delExtend": 0.4,
  "insVec": {
-  "A": 6.40988e-17,
-  "C": 1.98932e-18,
+  "A": 0,
+  "C": 0,
   "G": 0,
   "T": 1
  },