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Port details
bbmap BBMap short read aligner, and other bioinformatic tools
38.92 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 38.92Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-18 16:24:08
Last Update: 2021-08-22 13:59:58
Commit Hash: c5efaea
Also Listed In: java
License: BSD3CLAUSE
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (1994 items)
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  1. /usr/local/share/licenses/bbmap-38.92/catalog.mk
  2. /usr/local/share/licenses/bbmap-38.92/LICENSE
  3. /usr/local/share/licenses/bbmap-38.92/BSD3CLAUSE
  4. bin/bbduk.sh
  5. bin/bbmap.sh
  6. bin/bbmerge.sh
  7. bin/bbnorm.sh
  8. bin/bloomfilter.sh
  9. bin/dedupe.sh
  10. bin/reformat.sh
  11. bin/tadpole.sh
  12. libexec/bbmap/a_sample_mt.sh
  13. libexec/bbmap/addadapters.sh
  14. libexec/bbmap/addssu.sh
  15. libexec/bbmap/adjusthomopolymers.sh
  16. libexec/bbmap/alltoall.sh
  17. libexec/bbmap/analyzeaccession.sh
  18. libexec/bbmap/analyzegenes.sh
  19. libexec/bbmap/analyzesketchresults.sh
  20. libexec/bbmap/applyvariants.sh
  21. libexec/bbmap/bbcms.sh
  22. libexec/bbmap/bbcountunique.sh
  23. libexec/bbmap/bbduk.sh
  24. libexec/bbmap/bbest.sh
  25. libexec/bbmap/bbfakereads.sh
  26. libexec/bbmap/bbmap.sh
  27. libexec/bbmap/bbmapskimmer.sh
  28. libexec/bbmap/bbmask.sh
  29. libexec/bbmap/bbmerge-auto.sh
  30. libexec/bbmap/bbmerge.sh
  31. libexec/bbmap/bbnorm.sh
  32. libexec/bbmap/bbrealign.sh
  33. libexec/bbmap/bbrename.sh
  34. libexec/bbmap/bbsketch.sh
  35. libexec/bbmap/bbsplit.sh
  36. libexec/bbmap/bbsplitpairs.sh
  37. libexec/bbmap/bbstats.sh
  38. libexec/bbmap/bbversion.sh
  39. libexec/bbmap/bbwrap.sh
  40. libexec/bbmap/bloomfilter.sh
  41. libexec/bbmap/calcmem.sh
  42. libexec/bbmap/calctruequality.sh
  43. libexec/bbmap/callgenes.sh
  44. libexec/bbmap/callpeaks.sh
  45. libexec/bbmap/callvariants.sh
  46. libexec/bbmap/callvariants2.sh
  47. libexec/bbmap/clumpify.sh
  48. libexec/bbmap/commonkmers.sh
  49. libexec/bbmap/comparegff.sh
  50. libexec/bbmap/comparesketch.sh
  51. libexec/bbmap/comparessu.sh
  52. libexec/bbmap/comparevcf.sh
  53. libexec/bbmap/consect.sh
  54. libexec/bbmap/consensus.sh
  55. libexec/bbmap/countbarcodes.sh
  56. libexec/bbmap/countgc.sh
  57. libexec/bbmap/countsharedlines.sh
  58. libexec/bbmap/crossblock.sh
  59. libexec/bbmap/crosscontaminate.sh
  60. libexec/bbmap/cutgff.sh
  61. libexec/bbmap/cutprimers.sh
  62. libexec/bbmap/decontaminate.sh
  63. libexec/bbmap/dedupe.sh
  64. libexec/bbmap/dedupe2.sh
  65. libexec/bbmap/dedupebymapping.sh
  66. libexec/bbmap/demuxbyname.sh
  67. libexec/bbmap/diskbench.sh
  68. libexec/bbmap/estherfilter.sh
  69. libexec/bbmap/explodetree.sh
  70. libexec/bbmap/fetchproks.sh
  71. libexec/bbmap/filterassemblysummary.sh
  72. libexec/bbmap/filterbarcodes.sh
  73. libexec/bbmap/filterbycoverage.sh
  74. libexec/bbmap/filterbyname.sh
  75. libexec/bbmap/filterbysequence.sh
  76. libexec/bbmap/filterbytaxa.sh
  77. libexec/bbmap/filterbytile.sh
  78. libexec/bbmap/filterlines.sh
  79. libexec/bbmap/filterqc.sh
  80. libexec/bbmap/filtersam.sh
  81. libexec/bbmap/filtersilva.sh
  82. libexec/bbmap/filtersubs.sh
  83. libexec/bbmap/filtervcf.sh
  84. libexec/bbmap/fixgaps.sh
  85. libexec/bbmap/fungalrelease.sh
  86. libexec/bbmap/fuse.sh
  87. libexec/bbmap/gbff2gff.sh
  88. libexec/bbmap/getreads.sh
  89. libexec/bbmap/gi2ancestors.sh
  90. libexec/bbmap/gi2taxid.sh
  91. libexec/bbmap/gitable.sh
  92. libexec/bbmap/grademerge.sh
  93. libexec/bbmap/gradesam.sh
  94. libexec/bbmap/icecreamfinder.sh
  95. libexec/bbmap/icecreamgrader.sh
  96. libexec/bbmap/icecreammaker.sh
  97. libexec/bbmap/idmatrix.sh
  98. libexec/bbmap/idtree.sh
  99. libexec/bbmap/invertkey.sh
  100. libexec/bbmap/kapastats.sh
  101. libexec/bbmap/kcompress.sh
  102. libexec/bbmap/keepbestcopy.sh
  103. libexec/bbmap/khist.sh
  104. libexec/bbmap/kmercountexact.sh
  105. libexec/bbmap/kmercountmulti.sh
  106. libexec/bbmap/kmercoverage.sh
  107. libexec/bbmap/kmerfilterset.sh
  108. libexec/bbmap/kmerlimit.sh
  109. libexec/bbmap/kmerlimit2.sh
  110. libexec/bbmap/kmerposition.sh
  111. libexec/bbmap/kmutate.sh
  112. libexec/bbmap/lilypad.sh
  113. libexec/bbmap/loadreads.sh
  114. libexec/bbmap/loglog.sh
  115. libexec/bbmap/makechimeras.sh
  116. libexec/bbmap/makecontaminatedgenomes.sh
  117. libexec/bbmap/makepolymers.sh
  118. libexec/bbmap/mapPacBio.sh
  119. libexec/bbmap/matrixtocolumns.sh
  120. libexec/bbmap/mergeOTUs.sh
  121. libexec/bbmap/mergebarcodes.sh
  122. libexec/bbmap/mergepgm.sh
  123. libexec/bbmap/mergeribo.sh
  124. libexec/bbmap/mergesam.sh
  125. libexec/bbmap/mergesketch.sh
  126. libexec/bbmap/mergesorted.sh
  127. libexec/bbmap/msa.sh
  128. libexec/bbmap/mutate.sh
  129. libexec/bbmap/muxbyname.sh
  130. libexec/bbmap/partition.sh
  131. libexec/bbmap/phylip2fasta.sh
  132. libexec/bbmap/pileup.sh
  133. libexec/bbmap/plotflowcell.sh
  134. libexec/bbmap/plotgc.sh
  135. libexec/bbmap/postfilter.sh
  136. libexec/bbmap/printtime.sh
  137. libexec/bbmap/processfrag.sh
  138. libexec/bbmap/processhi-c.sh
  139. libexec/bbmap/processspeed.sh
  140. libexec/bbmap/randomgenome.sh
  141. libexec/bbmap/randomreads.sh
  142. libexec/bbmap/readlength.sh
  143. libexec/bbmap/readqc.sh
  144. libexec/bbmap/reducesilva.sh
  145. libexec/bbmap/reformat.sh
  146. libexec/bbmap/reformatpb.sh
  147. libexec/bbmap/removebadbarcodes.sh
  148. libexec/bbmap/removecatdogmousehuman.sh
  149. libexec/bbmap/removehuman.sh
  150. libexec/bbmap/removehuman2.sh
  151. libexec/bbmap/removemicrobes.sh
  152. libexec/bbmap/removesmartbell.sh
  153. libexec/bbmap/rename.sh
  154. libexec/bbmap/renameimg.sh
  155. libexec/bbmap/repair.sh
  156. libexec/bbmap/replaceheaders.sh
  157. libexec/bbmap/representative.sh
  158. libexec/bbmap/rqcfilter.sh
  159. libexec/bbmap/rqcfilter2.sh
  160. libexec/bbmap/runhmm.sh
  161. libexec/bbmap/samtoroc.sh
  162. libexec/bbmap/seal.sh
  163. libexec/bbmap/sendsketch.sh
  164. libexec/bbmap/shred.sh
  165. libexec/bbmap/shrinkaccession.sh
  166. libexec/bbmap/shuffle.sh
  167. libexec/bbmap/shuffle2.sh
  168. libexec/bbmap/sketch.sh
  169. libexec/bbmap/sketchblacklist.sh
  170. libexec/bbmap/sketchblacklist2.sh
  171. libexec/bbmap/sortbyname.sh
  172. libexec/bbmap/splitbytaxa.sh
  173. libexec/bbmap/splitnextera.sh
  174. libexec/bbmap/splitribo.sh
  175. libexec/bbmap/splitsam.sh
  176. libexec/bbmap/splitsam4way.sh
  177. libexec/bbmap/splitsam6way.sh
  178. libexec/bbmap/stats.sh
  179. libexec/bbmap/statswrapper.sh
  180. libexec/bbmap/streamsam.sh
  181. libexec/bbmap/subsketch.sh
  182. libexec/bbmap/summarizecontam.sh
  183. libexec/bbmap/summarizecoverage.sh
  184. libexec/bbmap/summarizecrossblock.sh
  185. libexec/bbmap/summarizemerge.sh
  186. libexec/bbmap/summarizequast.sh
  187. libexec/bbmap/summarizescafstats.sh
  188. libexec/bbmap/summarizeseal.sh
  189. libexec/bbmap/summarizesketch.sh
  190. libexec/bbmap/synthmda.sh
  191. libexec/bbmap/tadpipe.sh
  192. libexec/bbmap/tadpole.sh
  193. libexec/bbmap/tadwrapper.sh
  194. libexec/bbmap/taxonomy.sh
  195. libexec/bbmap/taxserver.sh
  196. libexec/bbmap/taxsize.sh
  197. libexec/bbmap/taxtree.sh
  198. libexec/bbmap/testfilesystem.sh
  199. libexec/bbmap/testformat.sh
  200. libexec/bbmap/testformat2.sh
  201. libexec/bbmap/tetramerfreq.sh
  202. libexec/bbmap/textfile.sh
  203. libexec/bbmap/translate6frames.sh
  204. libexec/bbmap/unicode2ascii.sh
  205. libexec/bbmap/unzip.sh
  206. libexec/bbmap/vcf2gff.sh
  207. libexec/bbmap/webcheck.sh
  208. share/java/classes/bbmap/align2/AbstractIndex.class
  209. share/java/classes/bbmap/align2/AbstractIndex.java
  210. share/java/classes/bbmap/align2/AbstractMapThread.class
  211. share/java/classes/bbmap/align2/AbstractMapThread.java
  212. share/java/classes/bbmap/align2/AbstractMapper.class
  213. share/java/classes/bbmap/align2/AbstractMapper.java
  214. share/java/classes/bbmap/align2/BBIndex.class
  215. share/java/classes/bbmap/align2/BBIndex.java
  216. share/java/classes/bbmap/align2/BBIndex5.class
  217. share/java/classes/bbmap/align2/BBIndex5.java
  218. share/java/classes/bbmap/align2/BBIndexAcc.class
  219. share/java/classes/bbmap/align2/BBIndexAcc.java
  220. share/java/classes/bbmap/align2/BBIndexPacBio.class
  221. share/java/classes/bbmap/align2/BBIndexPacBio.java
  222. share/java/classes/bbmap/align2/BBIndexPacBioSkimmer.class
  223. share/java/classes/bbmap/align2/BBIndexPacBioSkimmer.java
  224. share/java/classes/bbmap/align2/BBMap.class
  225. share/java/classes/bbmap/align2/BBMap.java
  226. share/java/classes/bbmap/align2/BBMap5.class
  227. share/java/classes/bbmap/align2/BBMap5.java
  228. share/java/classes/bbmap/align2/BBMapAcc.class
  229. share/java/classes/bbmap/align2/BBMapAcc.java
  230. share/java/classes/bbmap/align2/BBMapPacBio.class
  231. share/java/classes/bbmap/align2/BBMapPacBio.java
  232. share/java/classes/bbmap/align2/BBMapPacBioSkimmer.class
  233. share/java/classes/bbmap/align2/BBMapPacBioSkimmer.java
  234. share/java/classes/bbmap/align2/BBMapThread$1.class
  235. share/java/classes/bbmap/align2/BBMapThread.class
  236. share/java/classes/bbmap/align2/BBMapThread.java
  237. share/java/classes/bbmap/align2/BBMapThread5$1.class
  238. share/java/classes/bbmap/align2/BBMapThread5.class
  239. share/java/classes/bbmap/align2/BBMapThread5.java
  240. share/java/classes/bbmap/align2/BBMapThreadAcc$1.class
  241. share/java/classes/bbmap/align2/BBMapThreadAcc.class
  242. share/java/classes/bbmap/align2/BBMapThreadAcc.java
  243. share/java/classes/bbmap/align2/BBMapThreadPacBio$1.class
  244. share/java/classes/bbmap/align2/BBMapThreadPacBio.class
  245. share/java/classes/bbmap/align2/BBMapThreadPacBio.java
  246. share/java/classes/bbmap/align2/BBMapThreadPacBioSkimmer.class
  247. share/java/classes/bbmap/align2/BBMapThreadPacBioSkimmer.java
  248. share/java/classes/bbmap/align2/BBSplitter$1.class
  249. share/java/classes/bbmap/align2/BBSplitter$SetCount.class
  250. share/java/classes/bbmap/align2/BBSplitter.class
  251. share/java/classes/bbmap/align2/BBSplitter.java
  252. share/java/classes/bbmap/align2/BBWrap.class
  253. share/java/classes/bbmap/align2/BBWrap.java
  254. share/java/classes/bbmap/align2/BandedAligner.class
  255. share/java/classes/bbmap/align2/BandedAligner.java
  256. share/java/classes/bbmap/align2/BandedAlignerConcrete.class
  257. share/java/classes/bbmap/align2/BandedAlignerConcrete.java
  258. share/java/classes/bbmap/align2/BandedAlignerJNI.class
  259. share/java/classes/bbmap/align2/BandedAlignerJNI.java
  260. share/java/classes/bbmap/align2/Blacklist.class
  261. share/java/classes/bbmap/align2/Blacklist.java
  262. share/java/classes/bbmap/align2/Block.class
  263. share/java/classes/bbmap/align2/Block.java
  264. share/java/classes/bbmap/align2/ChromLoadThread.class
  265. share/java/classes/bbmap/align2/ChromLoadThread.java
  266. share/java/classes/bbmap/align2/CompareSamFiles$1.class
  267. share/java/classes/bbmap/align2/CompareSamFiles.class
  268. share/java/classes/bbmap/align2/CompareSamFiles.java
  269. share/java/classes/bbmap/align2/CompressString.class
  270. share/java/classes/bbmap/align2/CompressString.java
  271. share/java/classes/bbmap/align2/GapTools$Range.class
  272. share/java/classes/bbmap/align2/GapTools.class
  273. share/java/classes/bbmap/align2/GapTools.java
  274. share/java/classes/bbmap/align2/GradeSamFile$1.class
  275. share/java/classes/bbmap/align2/GradeSamFile.class
  276. share/java/classes/bbmap/align2/GradeSamFile.java
  277. share/java/classes/bbmap/align2/Index.class
  278. share/java/classes/bbmap/align2/Index.java
  279. share/java/classes/bbmap/align2/IndexMaker4$BlockMaker$CountThread.class
  280. share/java/classes/bbmap/align2/IndexMaker4$BlockMaker.class
  281. share/java/classes/bbmap/align2/IndexMaker4.class
  282. share/java/classes/bbmap/align2/IndexMaker4.java
  283. share/java/classes/bbmap/align2/IndexMaker5$BlockMaker$CountThread.class
  284. share/java/classes/bbmap/align2/IndexMaker5$BlockMaker.class
  285. share/java/classes/bbmap/align2/IndexMaker5.class
  286. share/java/classes/bbmap/align2/IndexMaker5.java
  287. share/java/classes/bbmap/align2/KeyRing.class
  288. share/java/classes/bbmap/align2/KeyRing.java
  289. share/java/classes/bbmap/align2/MSA.class
  290. share/java/classes/bbmap/align2/MSA.java
  291. share/java/classes/bbmap/align2/MakeQualityHistogram.class
  292. share/java/classes/bbmap/align2/MakeQualityHistogram.java
  293. share/java/classes/bbmap/align2/MakeRocCurve$1.class
  294. share/java/classes/bbmap/align2/MakeRocCurve.class
  295. share/java/classes/bbmap/align2/MakeRocCurve.java
  296. share/java/classes/bbmap/align2/MultiStateAligner10ts.class
  297. share/java/classes/bbmap/align2/MultiStateAligner10ts.java
  298. share/java/classes/bbmap/align2/MultiStateAligner11ts.class
  299. share/java/classes/bbmap/align2/MultiStateAligner11ts.java
  300. share/java/classes/bbmap/align2/MultiStateAligner11tsJNI.class
  301. share/java/classes/bbmap/align2/MultiStateAligner11tsJNI.java
  302. share/java/classes/bbmap/align2/MultiStateAligner9Flat.class
  303. share/java/classes/bbmap/align2/MultiStateAligner9Flat.java
  304. share/java/classes/bbmap/align2/MultiStateAligner9PacBio.class
  305. share/java/classes/bbmap/align2/MultiStateAligner9PacBio.java
  306. share/java/classes/bbmap/align2/MultiStateAligner9XFlat.class
  307. share/java/classes/bbmap/align2/MultiStateAligner9XFlat.java
  308. share/java/classes/bbmap/align2/MultiStateAligner9ts.class
  309. share/java/classes/bbmap/align2/MultiStateAligner9ts.java
  310. share/java/classes/bbmap/align2/NeedlemanWunsch.class
  311. share/java/classes/bbmap/align2/NeedlemanWunsch.java
  312. share/java/classes/bbmap/align2/PackedHeap.class
  313. share/java/classes/bbmap/align2/PackedHeap.java
  314. share/java/classes/bbmap/align2/Pointer.class
  315. share/java/classes/bbmap/align2/Pointer.java
  316. share/java/classes/bbmap/align2/PrintTime.class
  317. share/java/classes/bbmap/align2/PrintTime.java
  318. share/java/classes/bbmap/align2/Quad.class
  319. share/java/classes/bbmap/align2/Quad.java
  320. share/java/classes/bbmap/align2/Quad64.class
  321. share/java/classes/bbmap/align2/Quad64.java
  322. share/java/classes/bbmap/align2/Quad64Heap.class
  323. share/java/classes/bbmap/align2/Quad64Heap.java
  324. share/java/classes/bbmap/align2/QuadHeap.class
  325. share/java/classes/bbmap/align2/QuadHeap.java
  326. share/java/classes/bbmap/align2/QualityTools.class
  327. share/java/classes/bbmap/align2/QualityTools.java
  328. share/java/classes/bbmap/align2/RandomReads3$1.class
  329. share/java/classes/bbmap/align2/RandomReads3.class
  330. share/java/classes/bbmap/align2/RandomReads3.java
  331. share/java/classes/bbmap/align2/RefToIndex.class
  332. share/java/classes/bbmap/align2/RefToIndex.java
  333. share/java/classes/bbmap/align2/ReformatBatchOutput.class
  334. share/java/classes/bbmap/align2/ReformatBatchOutput.java
  335. share/java/classes/bbmap/align2/ReformatBatchOutput2.class
  336. share/java/classes/bbmap/align2/ReformatBatchOutput2.java
  337. share/java/classes/bbmap/align2/Solver.class
  338. share/java/classes/bbmap/align2/Solver.java
  339. share/java/classes/bbmap/align2/SplitMappedReads.class
  340. share/java/classes/bbmap/align2/SplitMappedReads.java
  341. share/java/classes/bbmap/align2/TranslateColorspaceRead.class
  342. share/java/classes/bbmap/align2/TranslateColorspaceRead.java
  343. share/java/classes/bbmap/aligner/Aligner.class
  344. share/java/classes/bbmap/aligner/Aligner.java
  345. share/java/classes/bbmap/aligner/Alignment.class
  346. share/java/classes/bbmap/aligner/Alignment.java
  347. share/java/classes/bbmap/aligner/AlignmentResult.class
  348. share/java/classes/bbmap/aligner/AlignmentResult.java
  349. share/java/classes/bbmap/aligner/AllToAll$ProcessThread.class
  350. share/java/classes/bbmap/aligner/AllToAll.class
  351. share/java/classes/bbmap/aligner/AllToAll.java
  352. share/java/classes/bbmap/aligner/FlatAligner.class
  353. share/java/classes/bbmap/aligner/FlatAligner.java
  354. share/java/classes/bbmap/aligner/FlatAligner2.class
  355. share/java/classes/bbmap/aligner/FlatAligner2.java
  356. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter.class
  357. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter.java
  358. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter2.class
  359. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter2.java
  360. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter3.class
  361. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter3.java
  362. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.class
  363. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.java
  364. share/java/classes/bbmap/aligner/SingleStateAlignerFlat.class
  365. share/java/classes/bbmap/aligner/SingleStateAlignerFlat.java
  366. share/java/classes/bbmap/aligner/SingleStateAlignerFlat2.class
  367. share/java/classes/bbmap/aligner/SingleStateAlignerFlat2.java
  368. share/java/classes/bbmap/aligner/SingleStateAlignerFlat2Amino.class
  369. share/java/classes/bbmap/aligner/SingleStateAlignerFlat2Amino.java
  370. share/java/classes/bbmap/aligner/SingleStateAlignerFlat2_1D.class
  371. share/java/classes/bbmap/aligner/SingleStateAlignerFlat2_1D.java
  372. share/java/classes/bbmap/aligner/SingleStateAlignerFlat3.class
  373. share/java/classes/bbmap/aligner/SingleStateAlignerFlat3.java
  374. share/java/classes/bbmap/aligner/SingleStateAlignerFlatFloat.class
  375. share/java/classes/bbmap/aligner/SingleStateAlignerFlatFloat.java
  376. share/java/classes/bbmap/aligner/SingleStateAlignerPacBioAdapter.class
  377. share/java/classes/bbmap/aligner/SingleStateAlignerPacBioAdapter.java
  378. share/java/classes/bbmap/assemble/AbstractBuildThread.class
  379. share/java/classes/bbmap/assemble/AbstractBuildThread.java
  380. share/java/classes/bbmap/assemble/AbstractExploreThread.class
  381. share/java/classes/bbmap/assemble/AbstractExploreThread.java
  382. share/java/classes/bbmap/assemble/AbstractProcessContigThread.class
  383. share/java/classes/bbmap/assemble/AbstractProcessContigThread.java
  384. share/java/classes/bbmap/assemble/AbstractRemoveThread$RemoveThread1.class
  385. share/java/classes/bbmap/assemble/AbstractRemoveThread$RemoveThread2.class
  386. share/java/classes/bbmap/assemble/AbstractRemoveThread.class
  387. share/java/classes/bbmap/assemble/AbstractRemoveThread.java
  388. share/java/classes/bbmap/assemble/AbstractShaveThread.class
  389. share/java/classes/bbmap/assemble/AbstractShaveThread.java
  390. share/java/classes/bbmap/assemble/BubblePopper.class
  391. share/java/classes/bbmap/assemble/BubblePopper.java
  392. share/java/classes/bbmap/assemble/Contig.class
  393. share/java/classes/bbmap/assemble/Contig.java
  394. share/java/classes/bbmap/assemble/Edge.class
  395. share/java/classes/bbmap/assemble/Edge.java
  396. share/java/classes/bbmap/assemble/ErrorTracker.class
  397. share/java/classes/bbmap/assemble/ErrorTracker.java
  398. share/java/classes/bbmap/assemble/KmerCompressor$BuildThread.class
  399. share/java/classes/bbmap/assemble/KmerCompressor.class
  400. share/java/classes/bbmap/assemble/KmerCompressor.java
  401. share/java/classes/bbmap/assemble/Postfilter.class
  402. share/java/classes/bbmap/assemble/Postfilter.java
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  1022. share/java/classes/bbmap/jgi/CovStatsLine.class
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  1024. share/java/classes/bbmap/jgi/CoveragePileup.class
  1025. share/java/classes/bbmap/jgi/CoveragePileup.java
  1026. share/java/classes/bbmap/jgi/CrossContaminate$Vessel.class
  1027. share/java/classes/bbmap/jgi/CrossContaminate.class
  1028. share/java/classes/bbmap/jgi/CrossContaminate.java
  1029. share/java/classes/bbmap/jgi/CutPrimers.class
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  1036. share/java/classes/bbmap/jgi/Dedupe$MstThread.class
  1037. share/java/classes/bbmap/jgi/Dedupe$Overlap.class
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  1039. share/java/classes/bbmap/jgi/Dedupe$UnitOffsetComparator.class
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  1042. share/java/classes/bbmap/jgi/Dedupe2$ClusterLengthComparator.class
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  1051. share/java/classes/bbmap/jgi/DedupeByMapping$Quad.class
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  1054. share/java/classes/bbmap/jgi/DedupeProtein$ClusterLengthComparator.class
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  1063. share/java/classes/bbmap/jgi/DemuxByName.class
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  1078. share/java/classes/bbmap/jgi/FilterReadsWithSubs.class
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  1089. share/java/classes/bbmap/jgi/FungalRelease.class
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  1093. share/java/classes/bbmap/jgi/GatherKapaStats$KapaEntry.class
  1094. share/java/classes/bbmap/jgi/GatherKapaStats$Plate.class
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  1099. share/java/classes/bbmap/jgi/GetReads.class
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  1114. share/java/classes/bbmap/jgi/KmerCountExact$DumpKmersThread.class
  1115. share/java/classes/bbmap/jgi/KmerCountExact$MakeKhistThread.class
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  1125. share/java/classes/bbmap/jgi/KmerFilterSetMaker.class
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  1137. share/java/classes/bbmap/jgi/MakeLengthHistogram$1.class
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  1140. share/java/classes/bbmap/jgi/MakePolymers.class
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  1152. share/java/classes/bbmap/jgi/Orf.class
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  1156. share/java/classes/bbmap/jgi/PhylipToFasta.class
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  1162. share/java/classes/bbmap/jgi/RandomGenome.class
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  1168. share/java/classes/bbmap/jgi/RedirectTest.class
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  1170. share/java/classes/bbmap/jgi/ReformatReads.class
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  1172. share/java/classes/bbmap/jgi/RemapQuality.class
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  1196. share/java/classes/bbmap/jgi/SmallKmerFrequency$CountComparator.class
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  1198. share/java/classes/bbmap/jgi/SmallKmerFrequency$NumComparator.class
  1199. share/java/classes/bbmap/jgi/SmallKmerFrequency.class
  1200. share/java/classes/bbmap/jgi/SmallKmerFrequency.java
  1201. share/java/classes/bbmap/jgi/SplitNexteraLMP.class
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  1205. share/java/classes/bbmap/jgi/SplitSam4Way.class
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  1207. share/java/classes/bbmap/jgi/SplitSam6Way.class
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  1218. share/java/classes/bbmap/jgi/TestFormat$Barcode.class
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  1223. share/java/classes/bbmap/jgi/TetramerFrequencies$PrintThread.class
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  1230. share/java/classes/bbmap/jgi/Unzip.class
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  1279. share/java/classes/bbmap/kmer/OwnershipThread.class
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  1281. share/java/classes/bbmap/kmer/ScheduleMaker.class
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  1342. share/java/classes/bbmap/prok/CallGenes$ProcessThread.class
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  1362. share/java/classes/bbmap/prok/MergeRibo$ListComparator.class
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  1364. share/java/classes/bbmap/prok/MergeRibo$Ribo.class
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  1367. share/java/classes/bbmap/prok/MergeRibo_Fast$ProcessThread.class
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  1378. share/java/classes/bbmap/prok/RiboMaker$ProcessThread.class
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  1381. share/java/classes/bbmap/prok/ScafData.class
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  1385. share/java/classes/bbmap/prok/SplitRibo$ProcessThread.class
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  1789. share/java/classes/bbmap/tax/IDNode.java
  1790. share/java/classes/bbmap/tax/IDTree.class
  1791. share/java/classes/bbmap/tax/IDTree.java
  1792. share/java/classes/bbmap/tax/ImgRecord.class
  1793. share/java/classes/bbmap/tax/ImgRecord.java
  1794. share/java/classes/bbmap/tax/ImgRecord2.class
  1795. share/java/classes/bbmap/tax/ImgRecord2.java
  1796. share/java/classes/bbmap/tax/PrintTaxonomy.class
  1797. share/java/classes/bbmap/tax/PrintTaxonomy.java
  1798. share/java/classes/bbmap/tax/Query.class
  1799. share/java/classes/bbmap/tax/Query.java
  1800. share/java/classes/bbmap/tax/RenameGiToTaxid.class
  1801. share/java/classes/bbmap/tax/RenameGiToTaxid.java
  1802. share/java/classes/bbmap/tax/RenameIMG.class
  1803. share/java/classes/bbmap/tax/RenameIMG.java
  1804. share/java/classes/bbmap/tax/ShrinkAccession.class
  1805. share/java/classes/bbmap/tax/ShrinkAccession.java
  1806. share/java/classes/bbmap/tax/SplitByTaxa.class
  1807. share/java/classes/bbmap/tax/SplitByTaxa.java
  1808. share/java/classes/bbmap/tax/TaxApp$1.class
  1809. share/java/classes/bbmap/tax/TaxApp.class
  1810. share/java/classes/bbmap/tax/TaxApp.java
  1811. share/java/classes/bbmap/tax/TaxClient.class
  1812. share/java/classes/bbmap/tax/TaxClient.java
  1813. share/java/classes/bbmap/tax/TaxFilter$1.class
  1814. share/java/classes/bbmap/tax/TaxFilter.class
  1815. share/java/classes/bbmap/tax/TaxFilter.java
  1816. share/java/classes/bbmap/tax/TaxNode$CountComparator.class
  1817. share/java/classes/bbmap/tax/TaxNode.class
  1818. share/java/classes/bbmap/tax/TaxNode.java
  1819. share/java/classes/bbmap/tax/TaxServer$CompareThread.class
  1820. share/java/classes/bbmap/tax/TaxServer$HelpHandler.class
  1821. share/java/classes/bbmap/tax/TaxServer$IconHandler.class
  1822. share/java/classes/bbmap/tax/TaxServer$KillHandler.class
  1823. share/java/classes/bbmap/tax/TaxServer$SketchHandler$SketchInstance.class
  1824. share/java/classes/bbmap/tax/TaxServer$SketchHandler.class
  1825. share/java/classes/bbmap/tax/TaxServer$StatsHandler.class
  1826. share/java/classes/bbmap/tax/TaxServer$TaxHandler.class
  1827. share/java/classes/bbmap/tax/TaxServer.class
  1828. share/java/classes/bbmap/tax/TaxServer.java
  1829. share/java/classes/bbmap/tax/TaxSize.class
  1830. share/java/classes/bbmap/tax/TaxSize.java
  1831. share/java/classes/bbmap/tax/TaxTree.class
  1832. share/java/classes/bbmap/tax/TaxTree.java
  1833. share/java/classes/bbmap/template/A_Sample.class
  1834. share/java/classes/bbmap/template/A_Sample.java
  1835. share/java/classes/bbmap/template/A_Sample2.class
  1836. share/java/classes/bbmap/template/A_Sample2.java
  1837. share/java/classes/bbmap/template/A_SampleBasic.class
  1838. share/java/classes/bbmap/template/A_SampleBasic.java
  1839. share/java/classes/bbmap/template/A_SampleBasic2.class
  1840. share/java/classes/bbmap/template/A_SampleBasic2.java
  1841. share/java/classes/bbmap/template/A_SampleByteFile.class
  1842. share/java/classes/bbmap/template/A_SampleByteFile.java
  1843. share/java/classes/bbmap/template/A_SampleD.class
  1844. share/java/classes/bbmap/template/A_SampleD.java
  1845. share/java/classes/bbmap/template/A_SampleMT$ProcessThread.class
  1846. share/java/classes/bbmap/template/A_SampleMT.class
  1847. share/java/classes/bbmap/template/A_SampleMT.java
  1848. share/java/classes/bbmap/template/A_SampleSamStreamer$ProcessThread.class
  1849. share/java/classes/bbmap/template/A_SampleSamStreamer.class
  1850. share/java/classes/bbmap/template/A_SampleSamStreamer.java
  1851. share/java/classes/bbmap/template/A_SampleSummary.class
  1852. share/java/classes/bbmap/template/A_SampleSummary.java
  1853. share/java/classes/bbmap/template/A_Sample_Generator$ProcessThread.class
  1854. share/java/classes/bbmap/template/A_Sample_Generator.class
  1855. share/java/classes/bbmap/template/A_Sample_Generator.java
  1856. share/java/classes/bbmap/template/A_Sample_Unpaired.class
  1857. share/java/classes/bbmap/template/A_Sample_Unpaired.java
  1858. share/java/classes/bbmap/template/Accumulator.class
  1859. share/java/classes/bbmap/template/Accumulator.java
  1860. share/java/classes/bbmap/template/BBTool_ST.class
  1861. share/java/classes/bbmap/template/BBTool_ST.java
  1862. share/java/classes/bbmap/template/DoWorker.class
  1863. share/java/classes/bbmap/template/DoWorker.java
  1864. share/java/classes/bbmap/template/ThreadPoolJob.class
  1865. share/java/classes/bbmap/template/ThreadPoolJob.java
  1866. share/java/classes/bbmap/template/ThreadWaiter.class
  1867. share/java/classes/bbmap/template/ThreadWaiter.java
  1868. share/java/classes/bbmap/ukmer/AbstractKmerTableU$AllocThread.class
  1869. share/java/classes/bbmap/ukmer/AbstractKmerTableU.class
  1870. share/java/classes/bbmap/ukmer/AbstractKmerTableU.java
  1871. share/java/classes/bbmap/ukmer/DumpThreadU.class
  1872. share/java/classes/bbmap/ukmer/DumpThreadU.java
  1873. share/java/classes/bbmap/ukmer/HashArrayU.class
  1874. share/java/classes/bbmap/ukmer/HashArrayU.java
  1875. share/java/classes/bbmap/ukmer/HashArrayU1D$WalkerU1D.class
  1876. share/java/classes/bbmap/ukmer/HashArrayU1D.class
  1877. share/java/classes/bbmap/ukmer/HashArrayU1D.java
  1878. share/java/classes/bbmap/ukmer/HashArrayU2D.class
  1879. share/java/classes/bbmap/ukmer/HashArrayU2D.java
  1880. share/java/classes/bbmap/ukmer/HashArrayUHybrid.class
  1881. share/java/classes/bbmap/ukmer/HashArrayUHybrid.java
  1882. share/java/classes/bbmap/ukmer/HashBufferU.class
  1883. share/java/classes/bbmap/ukmer/HashBufferU.java
  1884. share/java/classes/bbmap/ukmer/HashForestU.class
  1885. share/java/classes/bbmap/ukmer/HashForestU.java
  1886. share/java/classes/bbmap/ukmer/HistogramMakerU$FillThread.class
  1887. share/java/classes/bbmap/ukmer/HistogramMakerU.class
  1888. share/java/classes/bbmap/ukmer/HistogramMakerU.java
  1889. share/java/classes/bbmap/ukmer/Kmer.class
  1890. share/java/classes/bbmap/ukmer/Kmer.java
  1891. share/java/classes/bbmap/ukmer/KmerBufferU.class
  1892. share/java/classes/bbmap/ukmer/KmerBufferU.java
  1893. share/java/classes/bbmap/ukmer/KmerNodeU.class
  1894. share/java/classes/bbmap/ukmer/KmerNodeU.java
  1895. share/java/classes/bbmap/ukmer/KmerNodeU1D.class
  1896. share/java/classes/bbmap/ukmer/KmerNodeU1D.java
  1897. share/java/classes/bbmap/ukmer/KmerNodeU2D.class
  1898. share/java/classes/bbmap/ukmer/KmerNodeU2D.java
  1899. share/java/classes/bbmap/ukmer/KmerTableSetU$LoadThread.class
  1900. share/java/classes/bbmap/ukmer/KmerTableSetU$WalkerKSTU.class
  1901. share/java/classes/bbmap/ukmer/KmerTableSetU.class
  1902. share/java/classes/bbmap/ukmer/KmerTableSetU.java
  1903. share/java/classes/bbmap/ukmer/OwnershipThread.class
  1904. share/java/classes/bbmap/ukmer/OwnershipThread.java
  1905. share/java/classes/bbmap/ukmer/WalkerU.class
  1906. share/java/classes/bbmap/ukmer/WalkerU.java
  1907. share/java/classes/bbmap/var/ApplyVarsToReference$1.class
  1908. share/java/classes/bbmap/var/ApplyVarsToReference.class
  1909. share/java/classes/bbmap/var/ApplyVarsToReference.java
  1910. share/java/classes/bbmap/var/GenerateConsensusVariations$1.class
  1911. share/java/classes/bbmap/var/GenerateConsensusVariations.class
  1912. share/java/classes/bbmap/var/GenerateConsensusVariations.java
  1913. share/java/classes/bbmap/var/GenerateVarlets$ProcessThread.class
  1914. share/java/classes/bbmap/var/GenerateVarlets.class
  1915. share/java/classes/bbmap/var/GenerateVarlets.java
  1916. share/java/classes/bbmap/var/GenerateVarlets2$1.class
  1917. share/java/classes/bbmap/var/GenerateVarlets2$ProcessThread.class
  1918. share/java/classes/bbmap/var/GenerateVarlets2.class
  1919. share/java/classes/bbmap/var/GenerateVarlets2.java
  1920. share/java/classes/bbmap/var/GenerateVarlets3$1.class
  1921. share/java/classes/bbmap/var/GenerateVarlets3$ProcessThread.class
  1922. share/java/classes/bbmap/var/GenerateVarlets3.class
  1923. share/java/classes/bbmap/var/GenerateVarlets3.java
  1924. share/java/classes/bbmap/var/StackVariations$1.class
  1925. share/java/classes/bbmap/var/StackVariations$SVThread.class
  1926. share/java/classes/bbmap/var/StackVariations.class
  1927. share/java/classes/bbmap/var/StackVariations.java
  1928. share/java/classes/bbmap/var/StackVariations2$1.class
  1929. share/java/classes/bbmap/var/StackVariations2$SVThread.class
  1930. share/java/classes/bbmap/var/StackVariations2.class
  1931. share/java/classes/bbmap/var/StackVariations2.java
  1932. share/java/classes/bbmap/var/VarLine.class
  1933. share/java/classes/bbmap/var/VarLine.java
  1934. share/java/classes/bbmap/var/Variation.class
  1935. share/java/classes/bbmap/var/Variation.java
  1936. share/java/classes/bbmap/var/Varlet.class
  1937. share/java/classes/bbmap/var/Varlet.java
  1938. share/java/classes/bbmap/var2/ApplyVariants.class
  1939. share/java/classes/bbmap/var2/ApplyVariants.java
  1940. share/java/classes/bbmap/var2/CallVariants$ProcessThread.class
  1941. share/java/classes/bbmap/var2/CallVariants.class
  1942. share/java/classes/bbmap/var2/CallVariants.java
  1943. share/java/classes/bbmap/var2/CallVariants2$Sample$ProcessThread.class
  1944. share/java/classes/bbmap/var2/CallVariants2$Sample.class
  1945. share/java/classes/bbmap/var2/CallVariants2.class
  1946. share/java/classes/bbmap/var2/CallVariants2.java
  1947. share/java/classes/bbmap/var2/CompareVCF.class
  1948. share/java/classes/bbmap/var2/CompareVCF.java
  1949. share/java/classes/bbmap/var2/FilterSam$ProcessThread.class
  1950. share/java/classes/bbmap/var2/FilterSam.class
  1951. share/java/classes/bbmap/var2/FilterSam.java
  1952. share/java/classes/bbmap/var2/FilterVCF$ProcessThread.class
  1953. share/java/classes/bbmap/var2/FilterVCF.class
  1954. share/java/classes/bbmap/var2/FilterVCF.java
  1955. share/java/classes/bbmap/var2/MergeSamples$MergeThread.class
  1956. share/java/classes/bbmap/var2/MergeSamples.class
  1957. share/java/classes/bbmap/var2/MergeSamples.java
  1958. share/java/classes/bbmap/var2/Realign$ProcessThread.class
  1959. share/java/classes/bbmap/var2/Realign.class
  1960. share/java/classes/bbmap/var2/Realign.java
  1961. share/java/classes/bbmap/var2/Realigner.class
  1962. share/java/classes/bbmap/var2/Realigner.java
  1963. share/java/classes/bbmap/var2/SamFilter.class
  1964. share/java/classes/bbmap/var2/SamFilter.java
  1965. share/java/classes/bbmap/var2/ScafMap.class
  1966. share/java/classes/bbmap/var2/ScafMap.java
  1967. share/java/classes/bbmap/var2/Scaffold.class
  1968. share/java/classes/bbmap/var2/Scaffold.java
  1969. share/java/classes/bbmap/var2/SoftClipper.class
  1970. share/java/classes/bbmap/var2/SoftClipper.java
  1971. share/java/classes/bbmap/var2/VCFFile$1.class
  1972. share/java/classes/bbmap/var2/VCFFile.class
  1973. share/java/classes/bbmap/var2/VCFFile.java
  1974. share/java/classes/bbmap/var2/VCFLine.class
  1975. share/java/classes/bbmap/var2/VCFLine.java
  1976. share/java/classes/bbmap/var2/Var.class
  1977. share/java/classes/bbmap/var2/Var.java
  1978. share/java/classes/bbmap/var2/VarFilter.class
  1979. share/java/classes/bbmap/var2/VarFilter.java
  1980. share/java/classes/bbmap/var2/VarKey.class
  1981. share/java/classes/bbmap/var2/VarKey.java
  1982. share/java/classes/bbmap/var2/VarMap$ProcessThread.class
  1983. share/java/classes/bbmap/var2/VarMap$VarMapIterator.class
  1984. share/java/classes/bbmap/var2/VarMap.class
  1985. share/java/classes/bbmap/var2/VarMap.java
  1986. share/java/classes/bbmap/var2/VcfLoader$ProcessThread.class
  1987. share/java/classes/bbmap/var2/VcfLoader.class
  1988. share/java/classes/bbmap/var2/VcfLoader.java
  1989. share/java/classes/bbmap/var2/VcfWriter$ProcessThread.class
  1990. share/java/classes/bbmap/var2/VcfWriter.class
  1991. share/java/classes/bbmap/var2/VcfWriter.java
  1992. @owner
  1993. @group
  1994. @mode
Collapse this list.
Dependency lines:
  • bbmap>0:biology/bbmap
To install the port: cd /usr/ports/biology/bbmap/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/bbmap
  • pkg install bbmap
PKGNAME: bbmap
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
bbmap
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd6438.9238.90
FreeBSD:11:armv6--
FreeBSD:11:i38638.9238.90
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-38.92
FreeBSD:12:amd6438.9238.92
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i38638.9238.92
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64-38.92
FreeBSD:13:amd6438.9238.92
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i38638.9238.92
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64-38.90
FreeBSD:14:aarch6438.92-
FreeBSD:14:amd6438.92-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i38638.92-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Runtime dependencies:
  1. bash : shells/bash
  2. pigz : archivers/pigz
  3. pbzip2 : archivers/pbzip2
  4. java : java/openjdk8
This port is required by:
for Run
  1. biology/biostar-tools

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (22 items)
Collapse this list.
  1. http://downloads.sourceforge.net/project/bbmap/
  2. http://excellmedia.dl.sourceforge.net/project/bbmap/
  3. http://freefr.dl.sourceforge.net/project/bbmap/
  4. http://jaist.dl.sourceforge.net/project/bbmap/
  5. http://nchc.dl.sourceforge.net/project/bbmap/
  6. http://netcologne.dl.sourceforge.net/project/bbmap/
  7. http://netix.dl.sourceforge.net/project/bbmap/
  8. http://superb-dca2.dl.sourceforge.net/project/bbmap/
  9. http://superb-sea2.dl.sourceforge.net/project/bbmap/
  10. http://ufpr.dl.sourceforge.net/project/bbmap/
  11. http://vorboss.dl.sourceforge.net/project/bbmap/
  12. https://downloads.sourceforge.net/project/bbmap/
  13. https://excellmedia.dl.sourceforge.net/project/bbmap/
  14. https://freefr.dl.sourceforge.net/project/bbmap/
  15. https://jaist.dl.sourceforge.net/project/bbmap/
  16. https://nchc.dl.sourceforge.net/project/bbmap/
  17. https://netcologne.dl.sourceforge.net/project/bbmap/
  18. https://netix.dl.sourceforge.net/project/bbmap/
  19. https://superb-dca2.dl.sourceforge.net/project/bbmap/
  20. https://superb-sea2.dl.sourceforge.net/project/bbmap/
  21. https://ufpr.dl.sourceforge.net/project/bbmap/
  22. https://vorboss.dl.sourceforge.net/project/bbmap/
Collapse this list.

Number of commits found: 2

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
22 Aug 2021 13:59:58
 files touched by this commit commit hash:c5efaea23b875a30e9a7652734d2c992d44f9fbc  38.92
jwb search for other commits by this committer
biology/bbmap: Update to 38.92

Numerous small fixes and enhancements

Reported by:    portscout
18 Apr 2021 16:21:29
 files touched by this commit commit hash:15458dfbacb842d71a41dcfdb6be83301ef0b7b6  38.90
jwb search for other commits by this committer
biology/bbmap: BBMap short read aligner, and other bioinformatic tools

This package includes BBMap, a short read aligner, as well as various other
bioinformatic tools. It is written in pure Java, can run on any platform, and
has no dependencies other than Java being installed (compiled for Java 6 and
higher). All tools are efficient and multithreaded.

Number of commits found: 2