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  1. tests/perl_tests/00.compile.t .............. ok
  2. tests/perl_tests/add-json.pl.t ............. ok
  3. # using temp dir /tmp/GoGBhQvdX6
  4. tests/perl_tests/bam-to-json.pl.t .......... ok
  5. # writing output to /tmp/iydqnmsAU6
  6. # writing output to /tmp/00LYFYQllU
  7. tests/perl_tests/biodb-to-json.pl.t ........ ok
  8. tests/perl_tests/conf_format.t ............. ok
  9. # using temp dir /tmp/G_xkqYlNsO
  10. # using temp dir /tmp/YS1Z1cP3SW
  11. tests/perl_tests/draw-basepair-track.pl.t .. ok
  12. tests/perl_tests/fakefasta.t ............... ok
  13. tests/perl_tests/featurestream.t ........... ok
  14.  
  15. # Failed test 'got the right number of classes'
  16. # at tests/perl_tests/flatfile-to-json.pl.t line 339.
  17. # got: '129'
  18. # expected: '5'
  19. # [
  20. # {
  21. # 'attributes' => [
  22. # 'Start',
  23. # 'End',
  24. # 'Strand',
  25. # 'Score',
  26. # 'Id',
  27. # 'Type',
  28. # 'Subfeatures',
  29. # 'Source',
  30. # 'Name',
  31. # 'Seq_id'
  32. # ],
  33. # 'isArrayAttr' => {
  34. # 'Subfeatures' => 1
  35. # }
  36. # },
  37. # {
  38. # 'attributes' => [
  39. # 'Start',
  40. # 'End',
  41. # 'Strand',
  42. # 'Score',
  43. # 'Seq_id',
  44. # 'Type',
  45. # 'Source'
  46. # ],
  47. # 'isArrayAttr' => {}
  48. # },
  49. # {
  50. # 'attributes' => [
  51. # 'Start',
  52. # 'End',
  53. # 'Strand',
  54. # 'Seq_id',
  55. # 'Type',
  56. # 'Source',
  57. # 'Phase'
  58. # ],
  59. # 'isArrayAttr' => {}
  60. # },
  61. # {
  62. # 'attributes' => [
  63. # 'Start',
  64. # 'End',
  65. # 'Strand',
  66. # 'Score',
  67. # 'Source',
  68. # 'Type',
  69. # 'Phase',
  70. # 'Seq_id'
  71. # ],
  72. # 'isArrayAttr' => {}
  73. # },
  74. # {
  75. # 'attributes' => [
  76. # 'Start',
  77. # 'End',
  78. # 'Strand',
  79. # 'Phase',
  80. # 'Seq_id',
  81. # 'Score',
  82. # 'Source',
  83. # 'Type'
  84. # ],
  85. # 'isArrayAttr' => {}
  86. # },
  87. # {
  88. # 'attributes' => [
  89. # 'Start',
  90. # 'End',
  91. # 'Strand',
  92. # 'Seq_id',
  93. # 'Phase',
  94. # 'Score',
  95. # 'Type',
  96. # 'Source'
  97. # ],
  98. # 'isArrayAttr' => {}
  99. # },
  100. # {
  101. # 'attributes' => [
  102. # 'Start',
  103. # 'End',
  104. # 'Strand',
  105. # 'Seq_id',
  106. # 'Phase',
  107. # 'Score',
  108. # 'Type',
  109. # 'Source'
  110. # ],
  111. # 'isArrayAttr' => {}
  112. # },
  113. # {
  114. # 'attributes' => [
  115. # 'Start',
  116. # 'End',
  117. # 'Strand',
  118. # 'Type',
  119. # 'Source',
  120. # 'Score',
  121. # 'Seq_id',
  122. # 'Phase'
  123. # ],
  124. # 'isArrayAttr' => {}
  125. # },
  126. # {
  127. # 'attributes' => [
  128. # 'Start',
  129. # 'End',
  130. # 'Strand',
  131. # 'Phase',
  132. # 'Seq_id',
  133. # 'Source',
  134. # 'Type',
  135. # 'Score'
  136. # ],
  137. # 'isArrayAttr' => {}
  138. # },
  139. # {
  140. # 'attributes' => [
  141. # 'Start',
  142. # 'End',
  143. # 'Strand',
  144. # 'Score',
  145. # 'Type',
  146. # 'Source',
  147. # 'Seq_id',
  148. # 'Phase'
  149. # ],
  150. # 'isArrayAttr' => {}
  151. # },
  152. # {
  153. # 'attributes' => [
  154. # 'Start',
  155. # 'End',
  156. # 'Strand',
  157. # 'Source',
  158. # 'Type',
  159. # 'Score',
  160. # 'Phase',
  161. # 'Seq_id'
  162. # ],
  163. # 'isArrayAttr' => {}
  164. # },
  165. # {
  166. # 'attributes' => [
  167. # 'Start',
  168. # 'End',
  169. # 'Strand',
  170. # 'Phase',
  171. # 'Source',
  172. # 'Seq_id',
  173. # 'Type'
  174. # ],
  175. # 'isArrayAttr' => {}
  176. # },
  177. # {
  178. # 'attributes' => [
  179. # 'Start',
  180. # 'End',
  181. # 'Strand',
  182. # 'Source',
  183. # 'Seq_id',
  184. # 'Type',
  185. # 'Score'
  186. # ],
  187. # 'isArrayAttr' => {}
  188. # },
  189. # {
  190. # 'attributes' => [
  191. # 'Start',
  192. # 'End',
  193. # 'Strand',
  194. # 'Score',
  195. # 'Name',
  196. # 'Subfeatures',
  197. # 'Source',
  198. # 'Type',
  199. # 'Id',
  200. # 'Seq_id'
  201. # ],
  202. # 'isArrayAttr' => {
  203. # 'Subfeatures' => 1
  204. # }
  205. # },
  206. # {
  207. # 'attributes' => [
  208. # 'Start',
  209. # 'End',
  210. # 'Strand',
  211. # 'Score',
  212. # 'Seq_id',
  213. # 'Type',
  214. # 'Source'
  215. # ],
  216. # 'isArrayAttr' => {}
  217. # },
  218. # {
  219. # 'attributes' => [
  220. # 'Start',
  221. # 'End',
  222. # 'Strand',
  223. # 'Seq_id',
  224. # 'Type',
  225. # 'Phase',
  226. # 'Source'
  227. # ],
  228. # 'isArrayAttr' => {}
  229. # },
  230. # {
  231. # 'attributes' => [
  232. # 'Start',
  233. # 'End',
  234. # 'Strand',
  235. # 'Score',
  236. # 'Source',
  237. # 'Type',
  238. # 'Phase',
  239. # 'Seq_id'
  240. # ],
  241. # 'isArrayAttr' => {}
  242. # },
  243. # {
  244. # 'attributes' => [
  245. # 'Start',
  246. # 'End',
  247. # 'Strand',
  248. # 'Type',
  249. # 'Seq_id',
  250. # 'Source',
  251. # 'Phase'
  252. # ],
  253. # 'isArrayAttr' => {}
  254. # },
  255. # {
  256. # 'attributes' => [
  257. # 'Start',
  258. # 'End',
  259. # 'Strand',
  260. # 'Source',
  261. # 'Type',
  262. # 'Seq_id',
  263. # 'Score'
  264. # ],
  265. # 'isArrayAttr' => {}
  266. # },
  267. # {
  268. # 'attributes' => [
  269. # 'Start',
  270. # 'End',
  271. # 'Strand',
  272. # 'Seq_id',
  273. # 'Name',
  274. # 'Subfeatures',
  275. # 'Source',
  276. # 'Type',
  277. # 'Id',
  278. # 'Score'
  279. # ],
  280. # 'isArrayAttr' => {
  281. # 'Subfeatures' => 1
  282. # }
  283. # },
  284. # {
  285. # 'attributes' => [
  286. # 'Start',
  287. # 'End',
  288. # 'Strand',
  289. # 'Source',
  290. # 'Type',
  291. # 'Seq_id',
  292. # 'Score'
  293. # ],
  294. # 'isArrayAttr' => {}
  295. # },
  296. # {
  297. # 'attributes' => [
  298. # 'Start',
  299. # 'End',
  300. # 'Strand',
  301. # 'Score',
  302. # 'Type',
  303. # 'Seq_id',
  304. # 'Source'
  305. # ],
  306. # 'isArrayAttr' => {}
  307. # },
  308. # {
  309. # 'attributes' => [
  310. # 'Start',
  311. # 'End',
  312. # 'Strand',
  313. # 'Seq_id',
  314. # 'Type',
  315. # 'Source',
  316. # 'Score'
  317. # ],
  318. # 'isArrayAttr' => {}
  319. # },
  320. # {
  321. # 'attributes' => [
  322. # 'Start',
  323. # 'End',
  324. # 'Strand',
  325. # 'Source',
  326. # 'Phase',
  327. # 'Type',
  328. # 'Seq_id'
  329. # ],
  330. # 'isArrayAttr' => {}
  331. # },
  332. # {
  333. # 'attributes' => [
  334. # 'Start',
  335. # 'End',
  336. # 'Strand',
  337. # 'Seq_id',
  338. # 'Phase',
  339. # 'Type',
  340. # 'Source',
  341. # 'Score'
  342. # ],
  343. # 'isArrayAttr' => {}
  344. # },
  345. # {
  346. # 'attributes' => [
  347. # 'Start',
  348. # 'End',
  349. # 'Strand',
  350. # 'Seq_id',
  351. # 'Phase',
  352. # 'Type',
  353. # 'Source',
  354. # 'Score'
  355. # ],
  356. # 'isArrayAttr' => {}
  357. # },
  358. # {
  359. # 'attributes' => [
  360. # 'Start',
  361. # 'End',
  362. # 'Strand',
  363. # 'Type',
  364. # 'Source',
  365. # 'Score',
  366. # 'Seq_id',
  367. # 'Phase'
  368. # ],
  369. # 'isArrayAttr' => {}
  370. # },
  371. # {
  372. # 'attributes' => [
  373. # 'Start',
  374. # 'End',
  375. # 'Strand',
  376. # 'Seq_id',
  377. # 'Type',
  378. # 'Source',
  379. # 'Phase'
  380. # ],
  381. # 'isArrayAttr' => {}
  382. # },
  383. # {
  384. # 'attributes' => [
  385. # 'Start',
  386. # 'End',
  387. # 'Strand',
  388. # 'Seq_id',
  389. # 'Subfeatures',
  390. # 'Source',
  391. # 'Name',
  392. # 'Id',
  393. # 'Type',
  394. # 'Score'
  395. # ],
  396. # 'isArrayAttr' => {
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  399. # },
  400. # {
  401. # 'attributes' => [
  402. # 'Start',
  403. # 'End',
  404. # 'Strand',
  405. # 'Source',
  406. # 'Seq_id',
  407. # 'Type',
  408. # 'Score'
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  410. # 'isArrayAttr' => {}
  411. # },
  412. # {
  413. # 'attributes' => [
  414. # 'Start',
  415. # 'End',
  416. # 'Strand',
  417. # 'Score',
  418. # 'Source',
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  424. # {
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  429. # 'Score',
  430. # 'Source',
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  434. # 'isArrayAttr' => {}
  435. # },
  436. # {
  437. # 'attributes' => [
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  442. # 'Type',
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  446. # 'isArrayAttr' => {}
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  448. # {
  449. # 'attributes' => [
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  454. # 'Seq_id',
  455. # 'Phase',
  456. # 'Source'
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  458. # 'isArrayAttr' => {}
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  460. # {
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  466. # 'Seq_id',
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  1660. # 'Source',
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  1808. # 'attributes' => [
  1809. # 'Start',
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  1811. # 'Strand',
  1812. # 'Seq_id',
  1813. # 'Id',
  1814. # 'Type',
  1815. # 'Source',
  1816. # 'Subfeatures',
  1817. # 'Name',
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  1820. # 'isArrayAttr' => {
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  1826. # 'Start',
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  1828. # 'Strand',
  1829. # 'Seq_id',
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  1837. # 'isArrayAttr' => {
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  1841. # {
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  1860. # 'Start',
  1861. # 'End',
  1862. # 'Strand',
  1863. # 'Seq_id',
  1864. # 'Subfeatures',
  1865. # 'Source',
  1866. # 'Name',
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  1871. # 'isArrayAttr' => {
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  1874. # },
  1875. # {
  1876. # 'attributes' => [
  1877. # 'Start',
  1878. # 'End',
  1879. # 'Strand',
  1880. # 'Name',
  1881. # 'Subfeatures',
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  1883. # 'Type',
  1884. # 'Id',
  1885. # 'Score',
  1886. # 'Seq_id'
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  1888. # 'isArrayAttr' => {
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  1898. # 'isArrayAttr' => {
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  1901. # }
  1902. # ]
  1903.  
  1904. # Failed test 'got the right number of classes'
  1905. # at tests/perl_tests/flatfile-to-json.pl.t line 339.
  1906. # got: '129'
  1907. # expected: '5'
  1908. # [
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  1912. # 'End',
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  1962. # },
  1963. # {
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  1970. # 'Type',
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  1972. # 'Seq_id'
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  1974. # 'isArrayAttr' => {}
  1975. # },
  1976. # {
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  3792.  
  3793. # Failed test at tests/perl_tests/flatfile-to-json.pl.t line 386.
  3794. # Structures begin differing at:
  3795. # $got->{attributes}[3] = 'Score'
  3796. # $expected->{attributes}[3] = 'Seq_id'
  3797. # {
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  3808. # 'Start',
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  3883. # {
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  3900. # 'Name',
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  3903. # 'isArrayAttr' => {}
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  3905. # {
  3906. # 'attributes' => [
  3907. # 'Start',
  3908. # 'End',
  3909. # 'Strand',
  3910. # 'Name',
  3911. # 'Seq_id',
  3912. # 'Score'
  3913. # ],
  3914. # 'isArrayAttr' => {}
  3915. # },
  3916. # {
  3917. # 'attributes' => [
  3918. # 'Start',
  3919. # 'End',
  3920. # 'Strand',
  3921. # 'Seq_id',
  3922. # 'Name',
  3923. # 'Score'
  3924. # ],
  3925. # 'isArrayAttr' => {}
  3926. # },
  3927. # {
  3928. # 'attributes' => [
  3929. # 'Start',
  3930. # 'End',
  3931. # 'Strand',
  3932. # 'Score',
  3933. # 'Name',
  3934. # 'Seq_id'
  3935. # ],
  3936. # 'isArrayAttr' => {}
  3937. # },
  3938. # {
  3939. # 'attributes' => [
  3940. # 'Start',
  3941. # 'End',
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  3944. # 'isArrayAttr' => {
  3945. # 'Sublist' => 1
  3946. # }
  3947. # }
  3948. # ],
  3949. # 'count' => 20,
  3950. # 'lazyClass' => 12,
  3951. # 'maxEnd' => 102906693,
  3952. # 'minStart' => 102746607,
  3953. # 'nclist' => [
  3954. # [
  3955. # 0,
  3956. # 102746607,
  3957. # 102747330,
  3958. # 1,
  3959. # '1',
  3960. # 'chr10',
  3961. # 'chr10_100010101'
  3962. # ],
  3963. # [
  3964. # 1,
  3965. # 102756707,
  3966. # 102757063,
  3967. # 1,
  3968. # 'chr10_100020212',
  3969. # 'chr10',
  3970. # '1'
  3971. # ],
  3972. # [
  3973. # 2,
  3974. # 102757103,
  3975. # 102757628,
  3976. # 1,
  3977. # '1',
  3978. # 'chr10_100020608',
  3979. # 'chr10'
  3980. # ],
  3981. # [
  3982. # 3,
  3983. # 102758816,
  3984. # 102759393,
  3985. # 1,
  3986. # '1',
  3987. # 'chr10_100022332',
  3988. # 'chr10'
  3989. # ],
  3990. # [
  3991. # 2,
  3992. # 102759402,
  3993. # 102759798,
  3994. # 1,
  3995. # '1',
  3996. # 'chr10_100023087',
  3997. # 'chr10'
  3998. # ],
  3999. # [
  4000. # 4,
  4001. # 102763502,
  4002. # 102763900,
  4003. # 1,
  4004. # '1',
  4005. # 'chr10',
  4006. # 'chr10_100027151'
  4007. # ],
  4008. # [
  4009. # 5,
  4010. # 102778574,
  4011. # 102779028,
  4012. # 1,
  4013. # '1',
  4014. # 'chr10',
  4015. # 'chr10_100042744'
  4016. # ],
  4017. # [
  4018. # 6,
  4019. # 102790835,
  4020. # 102791548,
  4021. # 1,
  4022. # 'chr10_100059467',
  4023. # 'chr10',
  4024. # '1'
  4025. # ],
  4026. # [
  4027. # 4,
  4028. # 102807700,
  4029. # 102808458,
  4030. # 1,
  4031. # '1',
  4032. # 'chr10',
  4033. # 'chr10_100076094'
  4034. # ],
  4035. # [
  4036. # 7,
  4037. # 102809834,
  4038. # 102810339,
  4039. # 1,
  4040. # 'chr10_100078435',
  4041. # 'chr10',
  4042. # '1'
  4043. # ],
  4044. # [
  4045. # 8,
  4046. # 102820652,
  4047. # 102821466,
  4048. # 1,
  4049. # 'chr10',
  4050. # 'chr10_100089212',
  4051. # '1'
  4052. # ],
  4053. # [
  4054. # 7,
  4055. # 102821565,
  4056. # 102821902,
  4057. # 1,
  4058. # 'chr10_100090127',
  4059. # 'chr10',
  4060. # '1'
  4061. # ],
  4062. # [
  4063. # 7,
  4064. # 102822305,
  4065. # 102822874,
  4066. # 1,
  4067. # 'chr10_100090866',
  4068. # 'chr10',
  4069. # '1'
  4070. # ],
  4071. # [
  4072. # 9,
  4073. # 102825930,
  4074. # 102826474,
  4075. # 1,
  4076. # 'chr10_100094501',
  4077. # 'chr10',
  4078. # '1'
  4079. # ],
  4080. # [
  4081. # 4,
  4082. # 102826938,
  4083. # 102827286,
  4084. # 1,
  4085. # '1',
  4086. # 'chr10',
  4087. # 'chr10_100095501'
  4088. # ],
  4089. # [
  4090. # 5,
  4091. # 102827366,
  4092. # 102827778,
  4093. # 1,
  4094. # '1',
  4095. # 'chr10',
  4096. # 'chr10_100095928'
  4097. # ],
  4098. # [
  4099. # 10,
  4100. # 102883063,
  4101. # 102883551,
  4102. # 1,
  4103. # 'chr10',
  4104. # 'chr10_100154436',
  4105. # '1'
  4106. # ],
  4107. # [
  4108. # 11,
  4109. # 102891173,
  4110. # 102891794,
  4111. # 1,
  4112. # '1',
  4113. # 'chr10_100162617',
  4114. # 'chr10'
  4115. # ],
  4116. # [
  4117. # 10,
  4118. # 102893599,
  4119. # 102894301,
  4120. # 1,
  4121. # 'chr10',
  4122. # 'chr10_100165069',
  4123. # '1'
  4124. # ],
  4125. # [
  4126. # 3,
  4127. # 102905801,
  4128. # 102906693,
  4129. # 1,
  4130. # '1',
  4131. # 'chr10_100177356',
  4132. # 'chr10'
  4133. # ]
  4134. # ],
  4135. # 'urlTemplate' => 'lf-{Chunk}.jsonz'
  4136. # }
  4137. # }
  4138.  
  4139. # Failed test at tests/perl_tests/flatfile-to-json.pl.t line 424.
  4140. # Structures begin differing at:
  4141. # $got->{attributes}[3] = 'Name'
  4142. # $expected->{attributes}[3] = 'Source'
  4143. # {
  4144. # 'featureCount' => 7,
  4145. # 'formatVersion' => 1,
  4146. # 'histograms' => {
  4147. # 'meta' => [
  4148. # {
  4149. # 'arrayParams' => {
  4150. # 'chunkSize' => 10000,
  4151. # 'length' => 3,
  4152. # 'urlTemplate' => 'hist-500-{Chunk}.jsonz'
  4153. # },
  4154. # 'basesPerBin' => '500'
  4155. # }
  4156. # ],
  4157. # 'stats' => [
  4158. # {
  4159. # 'basesPerBin' => '500',
  4160. # 'max' => 4,
  4161. # 'mean' => '2.33333333333333'
  4162. # }
  4163. # ]
  4164. # },
  4165. # 'intervals' => {
  4166. # 'classes' => [
  4167. # {
  4168. # 'attributes' => [
  4169. # 'Start',
  4170. # 'End',
  4171. # 'Strand',
  4172. # 'Name',
  4173. # 'Source',
  4174. # 'Type',
  4175. # 'Seq_id',
  4176. # 'Score'
  4177. # ],
  4178. # 'isArrayAttr' => {}
  4179. # },
  4180. # {
  4181. # 'attributes' => [
  4182. # 'Start',
  4183. # 'End',
  4184. # 'Strand',
  4185. # 'Type',
  4186. # 'Seq_id',
  4187. # 'Name',
  4188. # 'Source',
  4189. # 'Score'
  4190. # ],
  4191. # 'isArrayAttr' => {}
  4192. # },
  4193. # {
  4194. # 'attributes' => [
  4195. # 'Start',
  4196. # 'End',
  4197. # 'Strand',
  4198. # 'Seq_id',
  4199. # 'Type',
  4200. # 'Source',
  4201. # 'Name',
  4202. # 'Score'
  4203. # ],
  4204. # 'isArrayAttr' => {}
  4205. # },
  4206. # {
  4207. # 'attributes' => [
  4208. # 'Start',
  4209. # 'End',
  4210. # 'Strand',
  4211. # 'Source',
  4212. # 'Name',
  4213. # 'Seq_id',
  4214. # 'Type',
  4215. # 'Score'
  4216. # ],
  4217. # 'isArrayAttr' => {}
  4218. # },
  4219. # {
  4220. # 'attributes' => [
  4221. # 'Start',
  4222. # 'End',
  4223. # 'Strand',
  4224. # 'Score',
  4225. # 'Seq_id',
  4226. # 'Type',
  4227. # 'Source',
  4228. # 'Name'
  4229. # ],
  4230. # 'isArrayAttr' => {}
  4231. # },
  4232. # {
  4233. # 'attributes' => [
  4234. # 'Start',
  4235. # 'End',
  4236. # 'Chunk'
  4237. # ],
  4238. # 'isArrayAttr' => {
  4239. # 'Sublist' => 1
  4240. # }
  4241. # }
  4242. # ],
  4243. # 'count' => 7,
  4244. # 'lazyClass' => 5,
  4245. # 'maxEnd' => 1262,
  4246. # 'minStart' => 792,
  4247. # 'nclist' => [
  4248. # [
  4249. # 0,
  4250. # 792,
  4251. # 842,
  4252. # 0,
  4253. # 'FakeName',
  4254. # 'zonk',
  4255. # 'micro_array_oligo',
  4256. # 'ctgA',
  4257. # '41.32'
  4258. # ],
  4259. # [
  4260. # 0,
  4261. # 852,
  4262. # 902,
  4263. # 0,
  4264. # 'FakeName',
  4265. # 'zonk',
  4266. # 'micro_array_oligo',
  4267. # 'ctgA',
  4268. # '21.2'
  4269. # ],
  4270. # [
  4271. # 1,
  4272. # 912,
  4273. # 962,
  4274. # 0,
  4275. # 'micro_array_oligo',
  4276. # 'ctgA',
  4277. # 'FakeName',
  4278. # 'zonk',
  4279. # '20.8'
  4280. # ],
  4281. # [
  4282. # 2,
  4283. # 1032,
  4284. # 1082,
  4285. # 0,
  4286. # 'ctgA',
  4287. # 'micro_array_oligo',
  4288. # 'zonk',
  4289. # 'FakeName',
  4290. # '17.08'
  4291. # ],
  4292. # [
  4293. # 3,
  4294. # 1092,
  4295. # 1142,
  4296. # 0,
  4297. # 'zonk',
  4298. # 'FakeName',
  4299. # 'ctgA',
  4300. # 'micro_array_oligo',
  4301. # '9.76'
  4302. # ],
  4303. # [
  4304. # 4,
  4305. # 1152,
  4306. # 1202,
  4307. # 0,
  4308. # '3.81',
  4309. # 'ctgA',
  4310. # 'micro_array_oligo',
  4311. # 'zonk',
  4312. # 'FakeName'
  4313. # ],
  4314. # [
  4315. # 2,
  4316. # 1212,
  4317. # 1262,
  4318. # 0,
  4319. # 'ctgA',
  4320. # 'micro_array_oligo',
  4321. # 'zonk',
  4322. # 'FakeName',
  4323. # '3.3'
  4324. # ]
  4325. # ],
  4326. # 'urlTemplate' => 'lf-{Chunk}.jsonz'
  4327. # }
  4328. # }
  4329. # Looks like you failed 4 tests of 37.
  4330. tests/perl_tests/flatfile-to-json.pl.t .....
  4331. Dubious, test returned 4 (wstat 1024, 0x400)
  4332. Failed 4/37 subtests
  4333. tests/perl_tests/genbank.t ................. ok
  4334.  
  4335. # Failed test 'got right data from volvox test data run'
  4336. # at tests/perl_tests/generate-names.pl.t line 39.
  4337. # Structures begin differing at:
  4338. # $got->{e8b/f.json}{rs17878802}{exact}[0][1] = '12'
  4339. # $expected->{e8b/f.json}{rs17878802}{exact}[0][1] = '11'
  4340.  
  4341. # Failed test 'same data after incremental run'
  4342. # at tests/perl_tests/generate-names.pl.t line 58.
  4343. # Structures begin differing at:
  4344. # $got->{f4d/1.json}{rs4998557}{exact}[0][1] = '12'
  4345. # $expected->{f4d/1.json}{rs4998557}{exact}[0][1] = '11'
  4346.  
  4347. # Failed test 'same data after incremental run with --safeMode'
  4348. # at tests/perl_tests/generate-names.pl.t line 74.
  4349. # Structures begin differing at:
  4350. # $got->{262/f.json}{rs80265967}{exact}[0][1] = '12'
  4351. # $expected->{262/f.json}{rs80265967}{exact}[0][1] = '11'
  4352. # Looks like you failed 3 tests of 4.
  4353. tests/perl_tests/generate-names.pl.t .......
  4354. Dubious, test returned 3 (wstat 768, 0x300)
  4355. Failed 3/4 subtests
  4356. tests/perl_tests/json.t .................... ok
  4357. # loaded 2559 test features
  4358. tests/perl_tests/lazy_nclist.t ............. ok
  4359. tests/perl_tests/maker2jbrowse.t ........... ok
  4360. tests/perl_tests/nclist.t .................. ok
  4361. WARNING: multiple reference sequences found named 'NC_001133', using only the first one.
  4362. WARNING: multiple reference sequences found named 'NC_001133', using only the first one.
  4363. # /tmp/vAvvKy5uR9
  4364. tests/perl_tests/prepare-refseqs.pl.t ...... ok
  4365. tests/perl_tests/remove-track.pl.t ......... ok
  4366. # writing output to /tmp/JAnibomp9z
  4367. # Track nonExistentTrack not found in the UCSC track database (trackDb.txt.gz) file. Is it a real UCSC track? at bin/ucsc-to-json.pl line 194.
  4368. # To format the jaxQtlAsIs track, you must have both files tests/data/hg19/database//jaxQtlAsIs.sql and tests/data/hg19/database//jaxQtlAsIs.txt.gz
  4369. tests/perl_tests/ucsc-to-json.pl.t ......... ok
  4370. # using temp dir /tmp/l1RmHY1m73
  4371. tests/perl_tests/wig-to-json.pl.t .......... ok
  4372.  
  4373. Test Summary Report
  4374. -------------------
  4375. tests/perl_tests/flatfile-to-json.pl.t (Wstat: 1024 Tests: 37 Failed: 4)
  4376. Failed tests: 30, 32, 35, 37
  4377. Non-zero exit status: 4
  4378. tests/perl_tests/generate-names.pl.t (Wstat: 768 Tests: 4 Failed: 3)
  4379. Failed tests: 1-3
  4380. Non-zero exit status: 3
  4381. Files=19, Tests=231, 16 wallclock secs ( 0.09 usr 0.03 sys + 12.12 cusr 1.82 csys = 14.06 CPU)
  4382. Result: FAIL
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