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Port details
bbmap BBMap short read aligner, and other bioinformatic tools
39.34 biology on this many watch lists=2 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 39.15Version 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: 2025-08-21 20:31:40
Commit Hash: 5d8f84c
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
Also Listed In: java
License: BSD3CLAUSE
WWW:
https://jgi.doe.gov/data-and-tools/bbtools/
https://sourceforge.net/projects/bbmap/
https://bitbucket.org/berkeleylab/jgi-bbtools/src/master/
Description:
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.
HomepageHomepageHomepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (2729 items)
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  1. /usr/local/share/licenses/bbmap-39.34/catalog.mk
  2. /usr/local/share/licenses/bbmap-39.34/LICENSE
  3. /usr/local/share/licenses/bbmap-39.34/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/Xcalcmem.sh
  13. libexec/bbmap/a_sample_mt.sh
  14. libexec/bbmap/addadapters.sh
  15. libexec/bbmap/addssu.sh
  16. libexec/bbmap/adjusthomopolymers.sh
  17. libexec/bbmap/alignrandom.sh
  18. libexec/bbmap/alltoall.sh
  19. libexec/bbmap/analyzeaccession.sh
  20. libexec/bbmap/analyzegenes.sh
  21. libexec/bbmap/analyzesketchresults.sh
  22. libexec/bbmap/applyvariants.sh
  23. libexec/bbmap/bandedaligner.sh
  24. libexec/bbmap/bandedplusaligner.sh
  25. libexec/bbmap/bbcms.sh
  26. libexec/bbmap/bbcountunique.sh
  27. libexec/bbmap/bbcrisprfinder.sh
  28. libexec/bbmap/bbduk.sh
  29. libexec/bbmap/bbest.sh
  30. libexec/bbmap/bbfakereads.sh
  31. libexec/bbmap/bbmap.sh
  32. libexec/bbmap/bbmapskimmer.sh
  33. libexec/bbmap/bbmask.sh
  34. libexec/bbmap/bbmerge-auto.sh
  35. libexec/bbmap/bbmerge.sh
  36. libexec/bbmap/bbnorm.sh
  37. libexec/bbmap/bbrealign.sh
  38. libexec/bbmap/bbrename.sh
  39. libexec/bbmap/bbsketch.sh
  40. libexec/bbmap/bbsort.sh
  41. libexec/bbmap/bbsplit.sh
  42. libexec/bbmap/bbsplitpairs.sh
  43. libexec/bbmap/bbstats.sh
  44. libexec/bbmap/bbversion.sh
  45. libexec/bbmap/bbwrap.sh
  46. libexec/bbmap/bloomfilter.sh
  47. libexec/bbmap/bloomfilterparser.sh
  48. libexec/bbmap/calcmem.sh
  49. libexec/bbmap/calctruequality.sh
  50. libexec/bbmap/callgenes.sh
  51. libexec/bbmap/callpeaks.sh
  52. libexec/bbmap/callvariants.sh
  53. libexec/bbmap/callvariants2.sh
  54. libexec/bbmap/cat.sh
  55. libexec/bbmap/cg2illumina.sh
  56. libexec/bbmap/checkstrand.sh
  57. libexec/bbmap/cladeloader.sh
  58. libexec/bbmap/clumpify.sh
  59. libexec/bbmap/commonkmers.sh
  60. libexec/bbmap/comparegff.sh
  61. libexec/bbmap/comparelabels.sh
  62. libexec/bbmap/comparesketch.sh
  63. libexec/bbmap/comparessu.sh
  64. libexec/bbmap/comparevcf.sh
  65. libexec/bbmap/consect.sh
  66. libexec/bbmap/consensus.sh
  67. libexec/bbmap/copyfile.sh
  68. libexec/bbmap/countbarcodes.sh
  69. libexec/bbmap/countbarcodes2.sh
  70. libexec/bbmap/countduplicates.sh
  71. libexec/bbmap/countgc.sh
  72. libexec/bbmap/countsharedlines.sh
  73. libexec/bbmap/crossblock.sh
  74. libexec/bbmap/crosscontaminate.sh
  75. libexec/bbmap/crosscutaligner.sh
  76. libexec/bbmap/cutgff.sh
  77. libexec/bbmap/cutprimers.sh
  78. libexec/bbmap/decontaminate.sh
  79. libexec/bbmap/dedupe.sh
  80. libexec/bbmap/dedupe2.sh
  81. libexec/bbmap/dedupebymapping.sh
  82. libexec/bbmap/demuxbyname.sh
  83. libexec/bbmap/demuxserver.sh
  84. libexec/bbmap/diskbench.sh
  85. libexec/bbmap/driftingaligner.sh
  86. libexec/bbmap/driftingplusaligner.sh
  87. libexec/bbmap/estherfilter.sh
  88. libexec/bbmap/explodetree.sh
  89. libexec/bbmap/fetchproks.sh
  90. libexec/bbmap/filterassemblysummary.sh
  91. libexec/bbmap/filterbarcodes.sh
  92. libexec/bbmap/filterbycoverage.sh
  93. libexec/bbmap/filterbyname.sh
  94. libexec/bbmap/filterbysequence.sh
  95. libexec/bbmap/filterbytaxa.sh
  96. libexec/bbmap/filterbytile.sh
  97. libexec/bbmap/filterlines.sh
  98. libexec/bbmap/filterqc.sh
  99. libexec/bbmap/filtersam.sh
  100. libexec/bbmap/filtersilva.sh
  101. libexec/bbmap/filtersubs.sh
  102. libexec/bbmap/filtervcf.sh
  103. libexec/bbmap/findrepeats.sh
  104. libexec/bbmap/fixgaps.sh
  105. libexec/bbmap/fungalrelease.sh
  106. libexec/bbmap/fuse.sh
  107. libexec/bbmap/gbff2gff.sh
  108. libexec/bbmap/getreads.sh
  109. libexec/bbmap/gi2ancestors.sh
  110. libexec/bbmap/gi2taxid.sh
  111. libexec/bbmap/gitable.sh
  112. libexec/bbmap/glocalaligner.sh
  113. libexec/bbmap/gradebins.sh
  114. libexec/bbmap/grademerge.sh
  115. libexec/bbmap/gradesam.sh
  116. libexec/bbmap/icecreamfinder.sh
  117. libexec/bbmap/icecreamgrader.sh
  118. libexec/bbmap/icecreammaker.sh
  119. libexec/bbmap/idmatrix.sh
  120. libexec/bbmap/idtree.sh
  121. libexec/bbmap/indelfree.sh
  122. libexec/bbmap/invertkey.sh
  123. libexec/bbmap/javasetup.sh
  124. libexec/bbmap/kapastats.sh
  125. libexec/bbmap/kcompress.sh
  126. libexec/bbmap/keepbestcopy.sh
  127. libexec/bbmap/khist.sh
  128. libexec/bbmap/kmercountexact.sh
  129. libexec/bbmap/kmercountmulti.sh
  130. libexec/bbmap/kmercoverage.sh
  131. libexec/bbmap/kmerfilterset.sh
  132. libexec/bbmap/kmerlimit.sh
  133. libexec/bbmap/kmerlimit2.sh
  134. libexec/bbmap/kmerposition.sh
  135. libexec/bbmap/kmutate.sh
  136. libexec/bbmap/lilypad.sh
  137. libexec/bbmap/loadreads.sh
  138. libexec/bbmap/loglog.sh
  139. libexec/bbmap/makechimeras.sh
  140. libexec/bbmap/makecontaminatedgenomes.sh
  141. libexec/bbmap/makepolymers.sh
  142. libexec/bbmap/makequickbinvector.sh
  143. libexec/bbmap/mapPacBio.sh
  144. libexec/bbmap/matrixtocolumns.sh
  145. libexec/bbmap/memdetect.sh
  146. libexec/bbmap/mergeOTUs.sh
  147. libexec/bbmap/mergebarcodes.sh
  148. libexec/bbmap/mergepgm.sh
  149. libexec/bbmap/mergeribo.sh
  150. libexec/bbmap/mergesam.sh
  151. libexec/bbmap/mergesketch.sh
  152. libexec/bbmap/mergesorted.sh
  153. libexec/bbmap/microalign.sh
  154. libexec/bbmap/msa.sh
  155. libexec/bbmap/mutate.sh
  156. libexec/bbmap/muxbyname.sh
  157. libexec/bbmap/netfilter.sh
  158. libexec/bbmap/novademux.sh
  159. libexec/bbmap/partition.sh
  160. libexec/bbmap/phylip2fasta.sh
  161. libexec/bbmap/picksubset.sh
  162. libexec/bbmap/pileup.sh
  163. libexec/bbmap/pileup2.sh
  164. libexec/bbmap/plotflowcell.sh
  165. libexec/bbmap/plotgc.sh
  166. libexec/bbmap/plothist.sh
  167. libexec/bbmap/plotreadposition.sh
  168. libexec/bbmap/polyfilter.sh
  169. libexec/bbmap/postfilter.sh
  170. libexec/bbmap/printtime.sh
  171. libexec/bbmap/processfrag.sh
  172. libexec/bbmap/processhi-c.sh
  173. libexec/bbmap/processspeed.sh
  174. libexec/bbmap/quabblealigner.sh
  175. libexec/bbmap/quantumaligner.sh
  176. libexec/bbmap/quickbin.sh
  177. libexec/bbmap/quickclade.sh
  178. libexec/bbmap/randomgenome.sh
  179. libexec/bbmap/randomreads.sh
  180. libexec/bbmap/randomreadsmg.sh
  181. libexec/bbmap/readlength.sh
  182. libexec/bbmap/readqc.sh
  183. libexec/bbmap/reducecolumns.sh
  184. libexec/bbmap/reducesilva.sh
  185. libexec/bbmap/reformat.sh
  186. libexec/bbmap/reformatpb.sh
  187. libexec/bbmap/removebadbarcodes.sh
  188. libexec/bbmap/removecatdogmousehuman.sh
  189. libexec/bbmap/removehuman.sh
  190. libexec/bbmap/removehuman2.sh
  191. libexec/bbmap/removemicrobes.sh
  192. libexec/bbmap/removesmartbell.sh
  193. libexec/bbmap/rename.sh
  194. libexec/bbmap/renamebymapping.sh
  195. libexec/bbmap/renamebysketch.sh
  196. libexec/bbmap/renameimg.sh
  197. libexec/bbmap/renameref.sh
  198. libexec/bbmap/repair.sh
  199. libexec/bbmap/replaceheaders.sh
  200. libexec/bbmap/representative.sh
  201. libexec/bbmap/rqcfilter.sh
  202. libexec/bbmap/rqcfilter2.sh
  203. libexec/bbmap/runhmm.sh
  204. libexec/bbmap/samtoroc.sh
  205. libexec/bbmap/scoresequence.sh
  206. libexec/bbmap/seal.sh
  207. libexec/bbmap/sendsketch.sh
  208. libexec/bbmap/seqtovec.sh
  209. libexec/bbmap/shred.sh
  210. libexec/bbmap/shrinkaccession.sh
  211. libexec/bbmap/shuffle.sh
  212. libexec/bbmap/shuffle2.sh
  213. libexec/bbmap/sketch.sh
  214. libexec/bbmap/sketchblacklist.sh
  215. libexec/bbmap/sketchblacklist2.sh
  216. libexec/bbmap/sortbyname.sh
  217. libexec/bbmap/splitbytaxa.sh
  218. libexec/bbmap/splitnextera.sh
  219. libexec/bbmap/splitribo.sh
  220. libexec/bbmap/splitsam.sh
  221. libexec/bbmap/splitsam4way.sh
  222. libexec/bbmap/splitsam6way.sh
  223. libexec/bbmap/stats.sh
  224. libexec/bbmap/stats3.sh
  225. libexec/bbmap/statswrapper.sh
  226. libexec/bbmap/streamsam.sh
  227. libexec/bbmap/subsketch.sh
  228. libexec/bbmap/summarizecontam.sh
  229. libexec/bbmap/summarizecoverage.sh
  230. libexec/bbmap/summarizecrossblock.sh
  231. libexec/bbmap/summarizemerge.sh
  232. libexec/bbmap/summarizequast.sh
  233. libexec/bbmap/summarizescafstats.sh
  234. libexec/bbmap/summarizeseal.sh
  235. libexec/bbmap/summarizesketch.sh
  236. libexec/bbmap/synthmda.sh
  237. libexec/bbmap/tadpipe.sh
  238. libexec/bbmap/tadpole.sh
  239. libexec/bbmap/tadwrapper.sh
  240. libexec/bbmap/tagandmerge.sh
  241. libexec/bbmap/taxonomy.sh
  242. libexec/bbmap/taxserver.sh
  243. libexec/bbmap/taxsize.sh
  244. libexec/bbmap/taxtree.sh
  245. libexec/bbmap/testaligners.sh
  246. libexec/bbmap/testaligners2.sh
  247. libexec/bbmap/testfilesystem.sh
  248. libexec/bbmap/testformat.sh
  249. libexec/bbmap/testformat2.sh
  250. libexec/bbmap/tetramerfreq.sh
  251. libexec/bbmap/textfile.sh
  252. libexec/bbmap/tiledump.sh
  253. libexec/bbmap/train.sh
  254. libexec/bbmap/translate6frames.sh
  255. libexec/bbmap/trimcontigs.sh
  256. libexec/bbmap/unicode2ascii.sh
  257. libexec/bbmap/unzip.sh
  258. libexec/bbmap/vcf2gff.sh
  259. libexec/bbmap/visualizealignment.sh
  260. libexec/bbmap/wavefrontaligner.sh
  261. libexec/bbmap/webcheck.sh
  262. libexec/bbmap/wobblealigner.sh
  263. libexec/bbmap/wobbleplusaligner.sh
  264. share/java/classes/bbmap/align2/AbstractIndex.class
  265. share/java/classes/bbmap/align2/AbstractIndex.java
  266. share/java/classes/bbmap/align2/AbstractMapThread.class
  267. share/java/classes/bbmap/align2/AbstractMapThread.java
  268. share/java/classes/bbmap/align2/AbstractMapper.class
  269. share/java/classes/bbmap/align2/AbstractMapper.java
  270. share/java/classes/bbmap/align2/BBIndex.class
  271. share/java/classes/bbmap/align2/BBIndex.java
  272. share/java/classes/bbmap/align2/BBIndex5.class
  273. share/java/classes/bbmap/align2/BBIndex5.java
  274. share/java/classes/bbmap/align2/BBIndexAcc.class
  275. share/java/classes/bbmap/align2/BBIndexAcc.java
  276. share/java/classes/bbmap/align2/BBIndexPacBio.class
  277. share/java/classes/bbmap/align2/BBIndexPacBio.java
  278. share/java/classes/bbmap/align2/BBIndexPacBioSkimmer.class
  279. share/java/classes/bbmap/align2/BBIndexPacBioSkimmer.java
  280. share/java/classes/bbmap/align2/BBMap.class
  281. share/java/classes/bbmap/align2/BBMap.java
  282. share/java/classes/bbmap/align2/BBMap5.class
  283. share/java/classes/bbmap/align2/BBMap5.java
  284. share/java/classes/bbmap/align2/BBMapAcc.class
  285. share/java/classes/bbmap/align2/BBMapAcc.java
  286. share/java/classes/bbmap/align2/BBMapPacBio.class
  287. share/java/classes/bbmap/align2/BBMapPacBio.java
  288. share/java/classes/bbmap/align2/BBMapPacBioSkimmer.class
  289. share/java/classes/bbmap/align2/BBMapPacBioSkimmer.java
  290. share/java/classes/bbmap/align2/BBMapThread$1.class
  291. share/java/classes/bbmap/align2/BBMapThread.class
  292. share/java/classes/bbmap/align2/BBMapThread.java
  293. share/java/classes/bbmap/align2/BBMapThread5$1.class
  294. share/java/classes/bbmap/align2/BBMapThread5.class
  295. share/java/classes/bbmap/align2/BBMapThread5.java
  296. share/java/classes/bbmap/align2/BBMapThreadAcc$1.class
  297. share/java/classes/bbmap/align2/BBMapThreadAcc.class
  298. share/java/classes/bbmap/align2/BBMapThreadAcc.java
  299. share/java/classes/bbmap/align2/BBMapThreadPacBio$1.class
  300. share/java/classes/bbmap/align2/BBMapThreadPacBio.class
  301. share/java/classes/bbmap/align2/BBMapThreadPacBio.java
  302. share/java/classes/bbmap/align2/BBMapThreadPacBioSkimmer.class
  303. share/java/classes/bbmap/align2/BBMapThreadPacBioSkimmer.java
  304. share/java/classes/bbmap/align2/BBSplitter$1.class
  305. share/java/classes/bbmap/align2/BBSplitter$SetCount.class
  306. share/java/classes/bbmap/align2/BBSplitter.class
  307. share/java/classes/bbmap/align2/BBSplitter.java
  308. share/java/classes/bbmap/align2/BBWrap.class
  309. share/java/classes/bbmap/align2/BBWrap.java
  310. share/java/classes/bbmap/align2/BandedAligner.class
  311. share/java/classes/bbmap/align2/BandedAligner.java
  312. share/java/classes/bbmap/align2/BandedAlignerConcrete.class
  313. share/java/classes/bbmap/align2/BandedAlignerConcrete.java
  314. share/java/classes/bbmap/align2/BandedAlignerJNI.class
  315. share/java/classes/bbmap/align2/BandedAlignerJNI.java
  316. share/java/classes/bbmap/align2/Blacklist.class
  317. share/java/classes/bbmap/align2/Blacklist.java
  318. share/java/classes/bbmap/align2/Block.class
  319. share/java/classes/bbmap/align2/Block.java
  320. share/java/classes/bbmap/align2/ChromLoadThread.class
  321. share/java/classes/bbmap/align2/ChromLoadThread.java
  322. share/java/classes/bbmap/align2/CompareSamFiles$1.class
  323. share/java/classes/bbmap/align2/CompareSamFiles.class
  324. share/java/classes/bbmap/align2/CompareSamFiles.java
  325. share/java/classes/bbmap/align2/CompressString.class
  326. share/java/classes/bbmap/align2/CompressString.java
  327. share/java/classes/bbmap/align2/GapTools$Range.class
  328. share/java/classes/bbmap/align2/GapTools.class
  329. share/java/classes/bbmap/align2/GapTools.java
  330. share/java/classes/bbmap/align2/GradeSamFile$1.class
  331. share/java/classes/bbmap/align2/GradeSamFile.class
  332. share/java/classes/bbmap/align2/GradeSamFile.java
  333. share/java/classes/bbmap/align2/Index.class
  334. share/java/classes/bbmap/align2/Index.java
  335. share/java/classes/bbmap/align2/IndexMaker4$BlockMaker$CountThread.class
  336. share/java/classes/bbmap/align2/IndexMaker4$BlockMaker.class
  337. share/java/classes/bbmap/align2/IndexMaker4.class
  338. share/java/classes/bbmap/align2/IndexMaker4.java
  339. share/java/classes/bbmap/align2/IndexMaker5$BlockMaker$CountThread.class
  340. share/java/classes/bbmap/align2/IndexMaker5$BlockMaker.class
  341. share/java/classes/bbmap/align2/IndexMaker5.class
  342. share/java/classes/bbmap/align2/IndexMaker5.java
  343. share/java/classes/bbmap/align2/KeyRing.class
  344. share/java/classes/bbmap/align2/KeyRing.java
  345. share/java/classes/bbmap/align2/MSA.class
  346. share/java/classes/bbmap/align2/MSA.java
  347. share/java/classes/bbmap/align2/MakeQualityHistogram.class
  348. share/java/classes/bbmap/align2/MakeQualityHistogram.java
  349. share/java/classes/bbmap/align2/MakeRocCurve$1.class
  350. share/java/classes/bbmap/align2/MakeRocCurve.class
  351. share/java/classes/bbmap/align2/MakeRocCurve.java
  352. share/java/classes/bbmap/align2/MultiStateAligner10ts.class
  353. share/java/classes/bbmap/align2/MultiStateAligner10ts.java
  354. share/java/classes/bbmap/align2/MultiStateAligner11ts.class
  355. share/java/classes/bbmap/align2/MultiStateAligner11ts.java
  356. share/java/classes/bbmap/align2/MultiStateAligner11tsJNI.class
  357. share/java/classes/bbmap/align2/MultiStateAligner11tsJNI.java
  358. share/java/classes/bbmap/align2/MultiStateAligner9Flat.class
  359. share/java/classes/bbmap/align2/MultiStateAligner9Flat.java
  360. share/java/classes/bbmap/align2/MultiStateAligner9PacBio.class
  361. share/java/classes/bbmap/align2/MultiStateAligner9PacBio.java
  362. share/java/classes/bbmap/align2/MultiStateAligner9XFlat.class
  363. share/java/classes/bbmap/align2/MultiStateAligner9XFlat.java
  364. share/java/classes/bbmap/align2/MultiStateAligner9ts.class
  365. share/java/classes/bbmap/align2/MultiStateAligner9ts.java
  366. share/java/classes/bbmap/align2/NeedlemanWunsch.class
  367. share/java/classes/bbmap/align2/NeedlemanWunsch.java
  368. share/java/classes/bbmap/align2/PackedHeap.class
  369. share/java/classes/bbmap/align2/PackedHeap.java
  370. share/java/classes/bbmap/align2/Pointer.class
  371. share/java/classes/bbmap/align2/Pointer.java
  372. share/java/classes/bbmap/align2/PrintTime.class
  373. share/java/classes/bbmap/align2/PrintTime.java
  374. share/java/classes/bbmap/align2/Quad.class
  375. share/java/classes/bbmap/align2/Quad.java
  376. share/java/classes/bbmap/align2/Quad64.class
  377. share/java/classes/bbmap/align2/Quad64.java
  378. share/java/classes/bbmap/align2/Quad64Heap.class
  379. share/java/classes/bbmap/align2/Quad64Heap.java
  380. share/java/classes/bbmap/align2/QuadHeap.class
  381. share/java/classes/bbmap/align2/QuadHeap.java
  382. share/java/classes/bbmap/align2/QualityTools.class
  383. share/java/classes/bbmap/align2/QualityTools.java
  384. share/java/classes/bbmap/align2/README.md
  385. share/java/classes/bbmap/align2/RefToIndex.class
  386. share/java/classes/bbmap/align2/RefToIndex.java
  387. share/java/classes/bbmap/align2/ReformatBatchOutput.class
  388. share/java/classes/bbmap/align2/ReformatBatchOutput.java
  389. share/java/classes/bbmap/align2/ReformatBatchOutput2.class
  390. share/java/classes/bbmap/align2/ReformatBatchOutput2.java
  391. share/java/classes/bbmap/align2/Solver.class
  392. share/java/classes/bbmap/align2/Solver.java
  393. share/java/classes/bbmap/align2/SplitMappedReads.class
  394. share/java/classes/bbmap/align2/SplitMappedReads.java
  395. share/java/classes/bbmap/align2/TranslateColorspaceRead.class
  396. share/java/classes/bbmap/align2/TranslateColorspaceRead.java
  397. share/java/classes/bbmap/aligner/AlignRandom$1.class
  398. share/java/classes/bbmap/aligner/AlignRandom.class
  399. share/java/classes/bbmap/aligner/AlignRandom.java
  400. share/java/classes/bbmap/aligner/Aligner.class
  401. share/java/classes/bbmap/aligner/Aligner.java
  402. share/java/classes/bbmap/aligner/Alignment.class
  403. share/java/classes/bbmap/aligner/Alignment.java
  404. share/java/classes/bbmap/aligner/AlignmentResult.class
  405. share/java/classes/bbmap/aligner/AlignmentResult.java
  406. share/java/classes/bbmap/aligner/AllToAll$ProcessThread.class
  407. share/java/classes/bbmap/aligner/AllToAll.class
  408. share/java/classes/bbmap/aligner/AllToAll.java
  409. share/java/classes/bbmap/aligner/BandedAligner.class
  410. share/java/classes/bbmap/aligner/BandedAligner.java
  411. share/java/classes/bbmap/aligner/BandedAlignerConcise.class
  412. share/java/classes/bbmap/aligner/BandedAlignerConcise.java
  413. share/java/classes/bbmap/aligner/BandedAlignerInt.class
  414. share/java/classes/bbmap/aligner/BandedAlignerInt.java
  415. share/java/classes/bbmap/aligner/BandedAlignerM.class
  416. share/java/classes/bbmap/aligner/BandedAlignerM.java
  417. share/java/classes/bbmap/aligner/BandedByteAligner.class
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  419. share/java/classes/bbmap/aligner/BandedPlusAligner.class
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  421. share/java/classes/bbmap/aligner/BandedPlusAligner2.class
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  423. share/java/classes/bbmap/aligner/BandedPlusAligner3.class
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  425. share/java/classes/bbmap/aligner/BandedPlusAlignerInt.class
  426. share/java/classes/bbmap/aligner/BandedPlusAlignerInt.java
  427. share/java/classes/bbmap/aligner/ClippingTest.class
  428. share/java/classes/bbmap/aligner/ClippingTest.java
  429. share/java/classes/bbmap/aligner/CrossCutAligner.class
  430. share/java/classes/bbmap/aligner/CrossCutAligner.java
  431. share/java/classes/bbmap/aligner/DiagonalAligner$ExtzResult.class
  432. share/java/classes/bbmap/aligner/DiagonalAligner.class
  433. share/java/classes/bbmap/aligner/DiagonalAligner.java
  434. share/java/classes/bbmap/aligner/DriftingAligner.class
  435. share/java/classes/bbmap/aligner/DriftingAligner.java
  436. share/java/classes/bbmap/aligner/DriftingAlignerConcise.class
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  438. share/java/classes/bbmap/aligner/DriftingAlignerM.class
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  440. share/java/classes/bbmap/aligner/DriftingPlusAligner.class
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  442. share/java/classes/bbmap/aligner/DriftingPlusAligner2.class
  443. share/java/classes/bbmap/aligner/DriftingPlusAligner2.java
  444. share/java/classes/bbmap/aligner/DriftingPlusAligner3.class
  445. share/java/classes/bbmap/aligner/DriftingPlusAligner3.java
  446. share/java/classes/bbmap/aligner/Eh.class
  447. share/java/classes/bbmap/aligner/Factory.class
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  449. share/java/classes/bbmap/aligner/FlatAligner.class
  450. share/java/classes/bbmap/aligner/FlatAligner.java
  451. share/java/classes/bbmap/aligner/FlatAligner2.class
  452. share/java/classes/bbmap/aligner/FlatAligner2.java
  453. share/java/classes/bbmap/aligner/GlocalAligner.class
  454. share/java/classes/bbmap/aligner/GlocalAligner.java
  455. share/java/classes/bbmap/aligner/GlocalAlignerConcise.class
  456. share/java/classes/bbmap/aligner/GlocalAlignerConcise.java
  457. share/java/classes/bbmap/aligner/GlocalAlignerInt.class
  458. share/java/classes/bbmap/aligner/GlocalAlignerInt.java
  459. share/java/classes/bbmap/aligner/GlocalAlignerOld.class
  460. share/java/classes/bbmap/aligner/GlocalAlignerOld.java
  461. share/java/classes/bbmap/aligner/GlocalPlusAligner.class
  462. share/java/classes/bbmap/aligner/GlocalPlusAligner.java
  463. share/java/classes/bbmap/aligner/GlocalPlusAligner2.class
  464. share/java/classes/bbmap/aligner/GlocalPlusAligner2.java
  465. share/java/classes/bbmap/aligner/GlocalPlusAligner3.class
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  467. share/java/classes/bbmap/aligner/GlocalPlusAligner4.class
  468. share/java/classes/bbmap/aligner/GlocalPlusAligner4.java
  469. share/java/classes/bbmap/aligner/GlocalPlusAligner5.class
  470. share/java/classes/bbmap/aligner/GlocalPlusAligner5.java
  471. share/java/classes/bbmap/aligner/IDAligner.class
  472. share/java/classes/bbmap/aligner/IDAligner.java
  473. share/java/classes/bbmap/aligner/IndelFreeAligner$ProcessThread.class
  474. share/java/classes/bbmap/aligner/IndelFreeAligner.class
  475. share/java/classes/bbmap/aligner/IndelFreeAligner.java
  476. share/java/classes/bbmap/aligner/IntIndex.class
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  478. share/java/classes/bbmap/aligner/IntListAligner.class
  479. share/java/classes/bbmap/aligner/IntListAligner.java
  480. share/java/classes/bbmap/aligner/Ksw2gg$Cell.class
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  483. share/java/classes/bbmap/aligner/KswGgJava.class
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  485. share/java/classes/bbmap/aligner/MSAViz.class
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  487. share/java/classes/bbmap/aligner/MicroAligner.class
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  489. share/java/classes/bbmap/aligner/MicroAligner2.class
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  491. share/java/classes/bbmap/aligner/MicroAligner3.class
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  495. share/java/classes/bbmap/aligner/MicroWrapper$ProcessThread.class
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  498. share/java/classes/bbmap/aligner/MinHitsCalculator.class
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  500. share/java/classes/bbmap/aligner/MinHitsCalculatorOld.class
  501. share/java/classes/bbmap/aligner/MinHitsCalculatorOld.java
  502. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter.class
  503. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter.java
  504. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter2.class
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  506. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter3.class
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  508. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.class
  509. share/java/classes/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.java
  510. share/java/classes/bbmap/aligner/Parallelogram.class
  511. share/java/classes/bbmap/aligner/Parallelogram.java
  512. share/java/classes/bbmap/aligner/QuabbleAligner.class
  513. share/java/classes/bbmap/aligner/QuabbleAligner.java
  514. share/java/classes/bbmap/aligner/QuantumAligner.class
  515. share/java/classes/bbmap/aligner/QuantumAligner.java
  516. share/java/classes/bbmap/aligner/QuantumAlignerConcise.class
  517. share/java/classes/bbmap/aligner/QuantumAlignerConcise.java
  518. share/java/classes/bbmap/aligner/QuantumAlignerConcise2.class
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  520. share/java/classes/bbmap/aligner/QuantumAlignerM.class
  521. share/java/classes/bbmap/aligner/QuantumAlignerM.java
  522. share/java/classes/bbmap/aligner/QuantumAlignerQC.class
  523. share/java/classes/bbmap/aligner/QuantumAlignerQC.java
  524. share/java/classes/bbmap/aligner/QuantumPlusAligner.class
  525. share/java/classes/bbmap/aligner/QuantumPlusAligner.java
  526. share/java/classes/bbmap/aligner/QuantumPlusAligner2.class
  527. share/java/classes/bbmap/aligner/QuantumPlusAligner2.java
  528. share/java/classes/bbmap/aligner/QuantumPlusAligner3.class
  529. share/java/classes/bbmap/aligner/QuantumPlusAligner3.java
  530. share/java/classes/bbmap/aligner/QuantumPlusAligner4.class
  531. share/java/classes/bbmap/aligner/QuantumPlusAligner4.java
  532. share/java/classes/bbmap/aligner/Query.class
  533. share/java/classes/bbmap/aligner/Query.java
  534. share/java/classes/bbmap/aligner/README.md
  535. share/java/classes/bbmap/aligner/RelativeAligner.class
  536. share/java/classes/bbmap/aligner/RelativeAligner.java
  537. share/java/classes/bbmap/aligner/ScrabbleAligner.class
  538. share/java/classes/bbmap/aligner/ScrabbleAligner.java
  539. share/java/classes/bbmap/aligner/SideChannel3.class
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  541. share/java/classes/bbmap/aligner/SingleStateAlignerFlat.class
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  543. share/java/classes/bbmap/aligner/SingleStateAlignerFlat2.class
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  545. share/java/classes/bbmap/aligner/SingleStateAlignerFlat2Amino.class
  546. share/java/classes/bbmap/aligner/SingleStateAlignerFlat2Amino.java
  547. share/java/classes/bbmap/aligner/SingleStateAlignerFlat2_1D.class
  548. share/java/classes/bbmap/aligner/SingleStateAlignerFlat2_1D.java
  549. share/java/classes/bbmap/aligner/SingleStateAlignerFlat3.class
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  551. share/java/classes/bbmap/aligner/SingleStateAlignerFlatFloat.class
  552. share/java/classes/bbmap/aligner/SingleStateAlignerFlatFloat.java
  553. share/java/classes/bbmap/aligner/SingleStateAlignerPacBioAdapter.class
  554. share/java/classes/bbmap/aligner/SingleStateAlignerPacBioAdapter.java
  555. share/java/classes/bbmap/aligner/Test$Runner.class
  556. share/java/classes/bbmap/aligner/Test.class
  557. share/java/classes/bbmap/aligner/Test.java
  558. share/java/classes/bbmap/aligner/TestAlignerSuite$Job.class
  559. share/java/classes/bbmap/aligner/TestAlignerSuite$Worker.class
  560. share/java/classes/bbmap/aligner/TestAlignerSuite.class
  561. share/java/classes/bbmap/aligner/TestAlignerSuite.java
  562. share/java/classes/bbmap/aligner/VisualizationConverter.class
  563. share/java/classes/bbmap/aligner/VisualizationConverter.java
  564. share/java/classes/bbmap/aligner/Visualizer.class
  565. share/java/classes/bbmap/aligner/Visualizer.java
  566. share/java/classes/bbmap/aligner/WaveFrontAligner.class
  567. share/java/classes/bbmap/aligner/WaveFrontAligner.java
  568. share/java/classes/bbmap/aligner/WaveFrontAligner2.class
  569. share/java/classes/bbmap/aligner/WaveFrontAligner2.java
  570. share/java/classes/bbmap/aligner/WaveFrontAlignerViz.class
  571. share/java/classes/bbmap/aligner/WaveFrontAlignerViz.java
  572. share/java/classes/bbmap/aligner/WobbleAligner.class
  573. share/java/classes/bbmap/aligner/WobbleAligner.java
  574. share/java/classes/bbmap/aligner/WobbleAlignerConcise.class
  575. share/java/classes/bbmap/aligner/WobbleAlignerConcise.java
  576. share/java/classes/bbmap/aligner/WobblePlusAligner.class
  577. share/java/classes/bbmap/aligner/WobblePlusAligner.java
  578. share/java/classes/bbmap/aligner/WobblePlusAligner2.class
  579. share/java/classes/bbmap/aligner/WobblePlusAligner2.java
  580. share/java/classes/bbmap/aligner/WobblePlusAligner3.class
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  582. share/java/classes/bbmap/aligner/WobblePlusAligner4.class
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  584. share/java/classes/bbmap/aligner/WobblePlusAligner5.class
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  586. share/java/classes/bbmap/aligner/XDropHAligner.class
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  588. share/java/classes/bbmap/assemble/AbstractBuildThread.class
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  592. share/java/classes/bbmap/assemble/AbstractProcessContigThread.class
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  594. share/java/classes/bbmap/assemble/AbstractRemoveThread$RemoveThread1.class
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  611. share/java/classes/bbmap/assemble/Postfilter.class
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  614. share/java/classes/bbmap/assemble/Rollback.class
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  616. share/java/classes/bbmap/assemble/ShaveObject.class
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  678. share/java/classes/bbmap/barcode/LegacyFileWriter$QTag.class
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  681. share/java/classes/bbmap/barcode/NovaDemux.class
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  689. share/java/classes/bbmap/barcode/README.md
  690. share/java/classes/bbmap/barcode/TagAndMerge.class
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  694. share/java/classes/bbmap/barcode/stub/PCRMatrixProb.class
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  700. share/java/classes/bbmap/bbmin/Minimizer.class
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  1469. share/java/classes/bbmap/jgi/CovStatsLine.class
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  1506. share/java/classes/bbmap/jgi/DedupeProtein$ClusterLengthComparator.class
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  1515. share/java/classes/bbmap/jgi/DemuxByName.class
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  1528. share/java/classes/bbmap/jgi/FilterReadsWithSubs.class
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  1530. share/java/classes/bbmap/jgi/FindHiCJunctions.class
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  1532. share/java/classes/bbmap/jgi/FindPrimers$ProcessThread.class
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  1539. share/java/classes/bbmap/jgi/FungalRelease.class
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  1541. share/java/classes/bbmap/jgi/GatherKapaStats$KapaEntry.class
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  1547. share/java/classes/bbmap/jgi/GetReads.class
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  1549. share/java/classes/bbmap/jgi/GradeMergedReads.class
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  1551. share/java/classes/bbmap/jgi/GreedyBarCodeFinder.class
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  1553. share/java/classes/bbmap/jgi/IdentityMatrix$ProcessThread.class
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  1562. share/java/classes/bbmap/jgi/KmerCountExact$DumpKmersThread.class
  1563. share/java/classes/bbmap/jgi/KmerCountExact$MakeKhistThread.class
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  1566. share/java/classes/bbmap/jgi/KmerCountMulti$ProcessThread.class
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  1569. share/java/classes/bbmap/jgi/KmerCoverage$1.class
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  1573. share/java/classes/bbmap/jgi/KmerFilterSetMaker.class
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  1575. share/java/classes/bbmap/jgi/KmerNormalize$1.class
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  1579. share/java/classes/bbmap/jgi/KmerSample.class
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  1581. share/java/classes/bbmap/jgi/MakeLengthHistogram$1.class
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  1584. share/java/classes/bbmap/jgi/MakePolymers.class
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  1586. share/java/classes/bbmap/jgi/MergeBarcodes.class
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  1588. share/java/classes/bbmap/jgi/MergeSam.class
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  1590. share/java/classes/bbmap/jgi/Orf.class
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  1595. share/java/classes/bbmap/jgi/PhylipToFasta.class
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  1597. share/java/classes/bbmap/jgi/PickSubset$Edge.class
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  1599. share/java/classes/bbmap/jgi/PickSubset.class
  1600. share/java/classes/bbmap/jgi/PickSubset.java
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  1606. share/java/classes/bbmap/jgi/ReadKmerDepthDistribution$1.class
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  1609. share/java/classes/bbmap/jgi/ReadKmerDepthDistribution.java
  1610. share/java/classes/bbmap/jgi/RedirectTest.class
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  1612. share/java/classes/bbmap/jgi/RefRenamer.class
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  1614. share/java/classes/bbmap/jgi/ReformatReads.class
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  1616. share/java/classes/bbmap/jgi/RemapQuality.class
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  1618. share/java/classes/bbmap/jgi/RemoveBadBarcodes.class
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  1620. share/java/classes/bbmap/jgi/RenameReads.class
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  1624. share/java/classes/bbmap/jgi/RepresentativeSet$Edge.class
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  1628. share/java/classes/bbmap/jgi/SamToEst$1.class
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  1632. share/java/classes/bbmap/jgi/Seal$LoadThread.class
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  1634. share/java/classes/bbmap/jgi/Seal.class
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  1636. share/java/classes/bbmap/jgi/SealRefInfo.class
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  1638. share/java/classes/bbmap/jgi/SmallKmerFrequency$CountComparator.class
  1639. share/java/classes/bbmap/jgi/SmallKmerFrequency$Kmer.class
  1640. share/java/classes/bbmap/jgi/SmallKmerFrequency$NumComparator.class
  1641. share/java/classes/bbmap/jgi/SmallKmerFrequency.class
  1642. share/java/classes/bbmap/jgi/SmallKmerFrequency.java
  1643. share/java/classes/bbmap/jgi/SplitNexteraLMP.class
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  1645. share/java/classes/bbmap/jgi/SplitPairsAndSingles.class
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  1647. share/java/classes/bbmap/jgi/SplitSam4Way.class
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  1649. share/java/classes/bbmap/jgi/SplitSam6Way.class
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  1651. share/java/classes/bbmap/jgi/SplitSamFile.class
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  1653. share/java/classes/bbmap/jgi/TestFilesystem$WriteThread.class
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  1656. share/java/classes/bbmap/jgi/TestFormat$TestThread.class
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  1659. share/java/classes/bbmap/jgi/TetramerFrequencies$Line.class
  1660. share/java/classes/bbmap/jgi/TetramerFrequencies$PrintThread.class
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  1663. share/java/classes/bbmap/jgi/TetramerFrequencies_old$Line.class
  1664. share/java/classes/bbmap/jgi/TetramerFrequencies_old$PrintThread.class
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  1667. share/java/classes/bbmap/jgi/TranslateSixFrames.class
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  1669. share/java/classes/bbmap/jgi/TrimContigs$Range.class
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  1672. share/java/classes/bbmap/jgi/UnicodeToAscii.class
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  1674. share/java/classes/bbmap/jgi/Unzip.class
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  1680. share/java/classes/bbmap/json/JsonParser.class
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  1682. share/java/classes/bbmap/json/README.md
  1683. share/java/classes/bbmap/kmer/AbstractKmerTable$AllocThread.class
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  1688. share/java/classes/bbmap/kmer/DumpThread.class
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  1705. share/java/classes/bbmap/kmer/HistogramMaker$FillThread.class
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  1708. share/java/classes/bbmap/kmer/KmerBuffer.class
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  1710. share/java/classes/bbmap/kmer/KmerLink.class
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  1718. share/java/classes/bbmap/kmer/KmerTable.class
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  1720. share/java/classes/bbmap/kmer/KmerTableSet$LoadThread.class
  1721. share/java/classes/bbmap/kmer/KmerTableSet$WalkerKST.class
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  1724. share/java/classes/bbmap/kmer/OwnershipThread.class
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  1726. share/java/classes/bbmap/kmer/README.md
  1727. share/java/classes/bbmap/kmer/ScheduleMaker.class
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  1729. share/java/classes/bbmap/kmer/SimpleKmerTable.class
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  1731. share/java/classes/bbmap/kmer/TableLoaderLockFree$LoadThread.class
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  1734. share/java/classes/bbmap/kmer/TableReader.class
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  1736. share/java/classes/bbmap/kmer/Walker.class
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  1738. share/java/classes/bbmap/ml/Bell.class
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  1748. share/java/classes/bbmap/ml/DataLoader$Triple.class
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  1763. share/java/classes/bbmap/ml/MSig.class
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  1770. share/java/classes/bbmap/ml/ProcessBBMergeHeaders$Header.class
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  1773. share/java/classes/bbmap/ml/Profiler.class
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  1778. share/java/classes/bbmap/ml/ReduceColumns.class
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  1780. share/java/classes/bbmap/ml/Sample.class
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  2078. share/java/classes/bbmap/sketch/SketchIndex$IndexThread.class
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  2498. share/java/classes/bbmap/tax/SplitByTaxa.java
  2499. share/java/classes/bbmap/tax/TaxApp$1.class
  2500. share/java/classes/bbmap/tax/TaxApp.class
  2501. share/java/classes/bbmap/tax/TaxApp.java
  2502. share/java/classes/bbmap/tax/TaxClient.class
  2503. share/java/classes/bbmap/tax/TaxClient.java
  2504. share/java/classes/bbmap/tax/TaxFilter$1.class
  2505. share/java/classes/bbmap/tax/TaxFilter.class
  2506. share/java/classes/bbmap/tax/TaxFilter.java
  2507. share/java/classes/bbmap/tax/TaxNode$CountComparator.class
  2508. share/java/classes/bbmap/tax/TaxNode.class
  2509. share/java/classes/bbmap/tax/TaxNode.java
  2510. share/java/classes/bbmap/tax/TaxServer$CompareThread.class
  2511. share/java/classes/bbmap/tax/TaxServer$HelpHandler.class
  2512. share/java/classes/bbmap/tax/TaxServer$IconHandler.class
  2513. share/java/classes/bbmap/tax/TaxServer$KillHandler.class
  2514. share/java/classes/bbmap/tax/TaxServer$SketchHandler$SketchInstance.class
  2515. share/java/classes/bbmap/tax/TaxServer$SketchHandler.class
  2516. share/java/classes/bbmap/tax/TaxServer$StatsHandler.class
  2517. share/java/classes/bbmap/tax/TaxServer$TaxHandler.class
  2518. share/java/classes/bbmap/tax/TaxServer.class
  2519. share/java/classes/bbmap/tax/TaxServer.java
  2520. share/java/classes/bbmap/tax/TaxSize.class
  2521. share/java/classes/bbmap/tax/TaxSize.java
  2522. share/java/classes/bbmap/tax/TaxTree.class
  2523. share/java/classes/bbmap/tax/TaxTree.java
  2524. share/java/classes/bbmap/template/A_Sample.class
  2525. share/java/classes/bbmap/template/A_Sample.java
  2526. share/java/classes/bbmap/template/A_Sample2.class
  2527. share/java/classes/bbmap/template/A_Sample2.java
  2528. share/java/classes/bbmap/template/A_SampleBasic.class
  2529. share/java/classes/bbmap/template/A_SampleBasic.java
  2530. share/java/classes/bbmap/template/A_SampleBasic2.class
  2531. share/java/classes/bbmap/template/A_SampleBasic2.java
  2532. share/java/classes/bbmap/template/A_SampleByteFile.class
  2533. share/java/classes/bbmap/template/A_SampleByteFile.java
  2534. share/java/classes/bbmap/template/A_SampleByteFileMT$ProcessThread.class
  2535. share/java/classes/bbmap/template/A_SampleByteFileMT.class
  2536. share/java/classes/bbmap/template/A_SampleByteFileMT.java
  2537. share/java/classes/bbmap/template/A_SampleD.class
  2538. share/java/classes/bbmap/template/A_SampleD.java
  2539. share/java/classes/bbmap/template/A_SampleMT$ProcessThread.class
  2540. share/java/classes/bbmap/template/A_SampleMT.class
  2541. share/java/classes/bbmap/template/A_SampleMT.java
  2542. share/java/classes/bbmap/template/A_SampleMultipleInput.class
  2543. share/java/classes/bbmap/template/A_SampleMultipleInput.java
  2544. share/java/classes/bbmap/template/A_SampleSamStreamer$ProcessThread.class
  2545. share/java/classes/bbmap/template/A_SampleSamStreamer.class
  2546. share/java/classes/bbmap/template/A_SampleSamStreamer.java
  2547. share/java/classes/bbmap/template/A_SampleSummary.class
  2548. share/java/classes/bbmap/template/A_SampleSummary.java
  2549. share/java/classes/bbmap/template/A_Sample_Generator$ProcessThread.class
  2550. share/java/classes/bbmap/template/A_Sample_Generator.class
  2551. share/java/classes/bbmap/template/A_Sample_Generator.java
  2552. share/java/classes/bbmap/template/A_Sample_Unpaired.class
  2553. share/java/classes/bbmap/template/A_Sample_Unpaired.java
  2554. share/java/classes/bbmap/template/Accumulator.class
  2555. share/java/classes/bbmap/template/Accumulator.java
  2556. share/java/classes/bbmap/template/BBTool_ST.class
  2557. share/java/classes/bbmap/template/BBTool_ST.java
  2558. share/java/classes/bbmap/template/DoWorker.class
  2559. share/java/classes/bbmap/template/DoWorker.java
  2560. share/java/classes/bbmap/template/README.md
  2561. share/java/classes/bbmap/template/ThreadPoolJob.class
  2562. share/java/classes/bbmap/template/ThreadPoolJob.java
  2563. share/java/classes/bbmap/template/ThreadWaiter.class
  2564. share/java/classes/bbmap/template/ThreadWaiter.java
  2565. share/java/classes/bbmap/tracker/AdapterTracker.class
  2566. share/java/classes/bbmap/tracker/AdapterTracker.java
  2567. share/java/classes/bbmap/tracker/CrisprTracker.class
  2568. share/java/classes/bbmap/tracker/CrisprTracker.java
  2569. share/java/classes/bbmap/tracker/EntropyTracker.class
  2570. share/java/classes/bbmap/tracker/EntropyTracker.java
  2571. share/java/classes/bbmap/tracker/PalindromeTracker.class
  2572. share/java/classes/bbmap/tracker/PalindromeTracker.java
  2573. share/java/classes/bbmap/tracker/PolymerTracker.class
  2574. share/java/classes/bbmap/tracker/PolymerTracker.java
  2575. share/java/classes/bbmap/tracker/QualityTracker.class
  2576. share/java/classes/bbmap/tracker/QualityTracker.java
  2577. share/java/classes/bbmap/tracker/ReadStats.class
  2578. share/java/classes/bbmap/tracker/ReadStats.java
  2579. share/java/classes/bbmap/tracker/SealStats$SealStatsLine.class
  2580. share/java/classes/bbmap/tracker/SealStats.class
  2581. share/java/classes/bbmap/tracker/SealStats.java
  2582. share/java/classes/bbmap/ukmer/AbstractKmerTableU$AllocThread.class
  2583. share/java/classes/bbmap/ukmer/AbstractKmerTableU.class
  2584. share/java/classes/bbmap/ukmer/AbstractKmerTableU.java
  2585. share/java/classes/bbmap/ukmer/DumpThreadU.class
  2586. share/java/classes/bbmap/ukmer/DumpThreadU.java
  2587. share/java/classes/bbmap/ukmer/HashArrayU.class
  2588. share/java/classes/bbmap/ukmer/HashArrayU.java
  2589. share/java/classes/bbmap/ukmer/HashArrayU1D$WalkerU1D.class
  2590. share/java/classes/bbmap/ukmer/HashArrayU1D.class
  2591. share/java/classes/bbmap/ukmer/HashArrayU1D.java
  2592. share/java/classes/bbmap/ukmer/HashArrayU2D.class
  2593. share/java/classes/bbmap/ukmer/HashArrayU2D.java
  2594. share/java/classes/bbmap/ukmer/HashArrayUHybrid.class
  2595. share/java/classes/bbmap/ukmer/HashArrayUHybrid.java
  2596. share/java/classes/bbmap/ukmer/HashBufferU.class
  2597. share/java/classes/bbmap/ukmer/HashBufferU.java
  2598. share/java/classes/bbmap/ukmer/HashForestU.class
  2599. share/java/classes/bbmap/ukmer/HashForestU.java
  2600. share/java/classes/bbmap/ukmer/HistogramMakerU$FillThread.class
  2601. share/java/classes/bbmap/ukmer/HistogramMakerU.class
  2602. share/java/classes/bbmap/ukmer/HistogramMakerU.java
  2603. share/java/classes/bbmap/ukmer/Kmer.class
  2604. share/java/classes/bbmap/ukmer/Kmer.java
  2605. share/java/classes/bbmap/ukmer/KmerBufferU.class
  2606. share/java/classes/bbmap/ukmer/KmerBufferU.java
  2607. share/java/classes/bbmap/ukmer/KmerNodeU.class
  2608. share/java/classes/bbmap/ukmer/KmerNodeU.java
  2609. share/java/classes/bbmap/ukmer/KmerNodeU1D.class
  2610. share/java/classes/bbmap/ukmer/KmerNodeU1D.java
  2611. share/java/classes/bbmap/ukmer/KmerNodeU2D.class
  2612. share/java/classes/bbmap/ukmer/KmerNodeU2D.java
  2613. share/java/classes/bbmap/ukmer/KmerTableSetU$LoadThread.class
  2614. share/java/classes/bbmap/ukmer/KmerTableSetU$WalkerKSTU.class
  2615. share/java/classes/bbmap/ukmer/KmerTableSetU.class
  2616. share/java/classes/bbmap/ukmer/KmerTableSetU.java
  2617. share/java/classes/bbmap/ukmer/OwnershipThread.class
  2618. share/java/classes/bbmap/ukmer/OwnershipThread.java
  2619. share/java/classes/bbmap/ukmer/README.md
  2620. share/java/classes/bbmap/ukmer/WalkerU.class
  2621. share/java/classes/bbmap/ukmer/WalkerU.java
  2622. share/java/classes/bbmap/var/ApplyVarsToReference$1.class
  2623. share/java/classes/bbmap/var/ApplyVarsToReference.class
  2624. share/java/classes/bbmap/var/ApplyVarsToReference.java
  2625. share/java/classes/bbmap/var/GenerateConsensusVariations$1.class
  2626. share/java/classes/bbmap/var/GenerateConsensusVariations.class
  2627. share/java/classes/bbmap/var/GenerateConsensusVariations.java
  2628. share/java/classes/bbmap/var/GenerateVarlets$ProcessThread.class
  2629. share/java/classes/bbmap/var/GenerateVarlets.class
  2630. share/java/classes/bbmap/var/GenerateVarlets.java
  2631. share/java/classes/bbmap/var/GenerateVarlets2$1.class
  2632. share/java/classes/bbmap/var/GenerateVarlets2$ProcessThread.class
  2633. share/java/classes/bbmap/var/GenerateVarlets2.class
  2634. share/java/classes/bbmap/var/GenerateVarlets2.java
  2635. share/java/classes/bbmap/var/GenerateVarlets3$1.class
  2636. share/java/classes/bbmap/var/GenerateVarlets3$ProcessThread.class
  2637. share/java/classes/bbmap/var/GenerateVarlets3.class
  2638. share/java/classes/bbmap/var/GenerateVarlets3.java
  2639. share/java/classes/bbmap/var/README.md
  2640. share/java/classes/bbmap/var/StackVariations$1.class
  2641. share/java/classes/bbmap/var/StackVariations$SVThread.class
  2642. share/java/classes/bbmap/var/StackVariations.class
  2643. share/java/classes/bbmap/var/StackVariations.java
  2644. share/java/classes/bbmap/var/StackVariations2$1.class
  2645. share/java/classes/bbmap/var/StackVariations2$SVThread.class
  2646. share/java/classes/bbmap/var/StackVariations2.class
  2647. share/java/classes/bbmap/var/StackVariations2.java
  2648. share/java/classes/bbmap/var/VarLine.class
  2649. share/java/classes/bbmap/var/VarLine.java
  2650. share/java/classes/bbmap/var/Variation.class
  2651. share/java/classes/bbmap/var/Variation.java
  2652. share/java/classes/bbmap/var/Varlet.class
  2653. share/java/classes/bbmap/var/Varlet.java
  2654. share/java/classes/bbmap/var2/AnalyzeVars.class
  2655. share/java/classes/bbmap/var2/AnalyzeVars.java
  2656. share/java/classes/bbmap/var2/ApplyVariants.class
  2657. share/java/classes/bbmap/var2/ApplyVariants.java
  2658. share/java/classes/bbmap/var2/CVOutputWriter.class
  2659. share/java/classes/bbmap/var2/CVOutputWriter.java
  2660. share/java/classes/bbmap/var2/CallVariants$ProcessThread.class
  2661. share/java/classes/bbmap/var2/CallVariants.class
  2662. share/java/classes/bbmap/var2/CallVariants.java
  2663. share/java/classes/bbmap/var2/CallVariants2$Sample$ProcessThread.class
  2664. share/java/classes/bbmap/var2/CallVariants2$Sample.class
  2665. share/java/classes/bbmap/var2/CallVariants2.class
  2666. share/java/classes/bbmap/var2/CallVariants2.java
  2667. share/java/classes/bbmap/var2/CompareVCF.class
  2668. share/java/classes/bbmap/var2/CompareVCF.java
  2669. share/java/classes/bbmap/var2/FeatureVectorMaker.class
  2670. share/java/classes/bbmap/var2/FeatureVectorMaker.java
  2671. share/java/classes/bbmap/var2/FilterSam$ProcessThread.class
  2672. share/java/classes/bbmap/var2/FilterSam.class
  2673. share/java/classes/bbmap/var2/FilterSam.java
  2674. share/java/classes/bbmap/var2/FilterVCF$ProcessThread.class
  2675. share/java/classes/bbmap/var2/FilterVCF.class
  2676. share/java/classes/bbmap/var2/FilterVCF.java
  2677. share/java/classes/bbmap/var2/MergeSamples$MergeThread.class
  2678. share/java/classes/bbmap/var2/MergeSamples.class
  2679. share/java/classes/bbmap/var2/MergeSamples.java
  2680. share/java/classes/bbmap/var2/README.md
  2681. share/java/classes/bbmap/var2/Realign$ProcessThread.class
  2682. share/java/classes/bbmap/var2/Realign.class
  2683. share/java/classes/bbmap/var2/Realign.java
  2684. share/java/classes/bbmap/var2/Realigner.class
  2685. share/java/classes/bbmap/var2/Realigner.java
  2686. share/java/classes/bbmap/var2/SamFilter.class
  2687. share/java/classes/bbmap/var2/SamFilter.java
  2688. share/java/classes/bbmap/var2/ScafMap.class
  2689. share/java/classes/bbmap/var2/ScafMap.java
  2690. share/java/classes/bbmap/var2/Scaffold.class
  2691. share/java/classes/bbmap/var2/Scaffold.java
  2692. share/java/classes/bbmap/var2/SoftClipper.class
  2693. share/java/classes/bbmap/var2/SoftClipper.java
  2694. share/java/classes/bbmap/var2/VCFFile$1.class
  2695. share/java/classes/bbmap/var2/VCFFile.class
  2696. share/java/classes/bbmap/var2/VCFFile.java
  2697. share/java/classes/bbmap/var2/VCFLine.class
  2698. share/java/classes/bbmap/var2/VCFLine.java
  2699. share/java/classes/bbmap/var2/Var.class
  2700. share/java/classes/bbmap/var2/Var.java
  2701. share/java/classes/bbmap/var2/VarFilter.class
  2702. share/java/classes/bbmap/var2/VarFilter.java
  2703. share/java/classes/bbmap/var2/VarHelper.class
  2704. share/java/classes/bbmap/var2/VarHelper.java
  2705. share/java/classes/bbmap/var2/VarKey.class
  2706. share/java/classes/bbmap/var2/VarKey.java
  2707. share/java/classes/bbmap/var2/VarMap$ProcessThread.class
  2708. share/java/classes/bbmap/var2/VarMap$VarMapIterator.class
  2709. share/java/classes/bbmap/var2/VarMap.class
  2710. share/java/classes/bbmap/var2/VarMap.java
  2711. share/java/classes/bbmap/var2/VarProb.class
  2712. share/java/classes/bbmap/var2/VarProb.java
  2713. share/java/classes/bbmap/var2/VcfLoader$ProcessThread.class
  2714. share/java/classes/bbmap/var2/VcfLoader.class
  2715. share/java/classes/bbmap/var2/VcfLoader.java
  2716. share/java/classes/bbmap/var2/VcfToVar.class
  2717. share/java/classes/bbmap/var2/VcfToVar.java
  2718. share/java/classes/bbmap/var2/VcfWriter$ProcessThread.class
  2719. share/java/classes/bbmap/var2/VcfWriter.class
  2720. share/java/classes/bbmap/var2/VcfWriter.java
  2721. share/java/classes/bbmap/var2/VectorDonovan$QuantileTransformer.class
  2722. share/java/classes/bbmap/var2/VectorDonovan.class
  2723. share/java/classes/bbmap/var2/VectorDonovan.java
  2724. share/java/classes/bbmap/var2/VectorElba$ElbaMinMaxValues.class
  2725. share/java/classes/bbmap/var2/VectorElba.class
  2726. share/java/classes/bbmap/var2/VectorElba.java
  2727. @owner
  2728. @group
  2729. @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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: bbmap
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1755776772 SHA256 (BBMap_39.34.tar.gz) = c9c096c6ce3cc87da5607b731532bb9ac0aaebea2bd8fbf0a56e235968c4fbf4 SIZE (BBMap_39.34.tar.gz) = 13743574

Packages (timestamps in pop-ups are UTC):
bbmap
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest39.3439.34-39.3439.34---
FreeBSD:13:quarterly39.1539.1538.9239.1539.15-38.9238.92
FreeBSD:14:latest39.3439.3438.9239.3439.34--38.92
FreeBSD:14:quarterly39.1539.15-39.1539.15-38.9238.92
FreeBSD:15:latest--n/a39.15n/a-38.9238.92
FreeBSD:15:quarterly--n/a-n/a---
FreeBSD:16:latest--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Runtime dependencies:
  1. bash : shells/bash
  2. pbzip2 : archivers/pbzip2
  3. pigz : archivers/pigz
  4. java : java/openjdk8
This port is required by:
for Run
  1. biology/biostar-tools

Configuration Options:
No options to configure
Options name:
biology_bbmap
USES:
java shebangfix
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (48 items)
Collapse this list.
  1. http://cfhcable.dl.sourceforge.net/project/bbmap/
  2. http://cytranet.dl.sourceforge.net/project/bbmap/
  3. http://deac-ams.dl.sourceforge.net/project/bbmap/
  4. http://deac-fra.dl.sourceforge.net/project/bbmap/
  5. http://deac-riga.dl.sourceforge.net/project/bbmap/
  6. http://downloads.sourceforge.net/project/bbmap/
  7. http://excellmedia.dl.sourceforge.net/project/bbmap/
  8. http://freefr.dl.sourceforge.net/project/bbmap/
  9. http://gigenet.dl.sourceforge.net/project/bbmap/
  10. http://ixpeering.dl.sourceforge.net/project/bbmap/
  11. http://jaist.dl.sourceforge.net/project/bbmap/
  12. http://kumisystems.dl.sourceforge.net/project/bbmap/
  13. http://liquidtelecom.dl.sourceforge.net/project/bbmap/
  14. http://nchc.dl.sourceforge.net/project/bbmap/
  15. http://netactuate.dl.sourceforge.net/project/bbmap/
  16. http://netcologne.dl.sourceforge.net/project/bbmap/
  17. http://onboardcloud.dl.sourceforge.net/project/bbmap/
  18. http://phoenixnap.dl.sourceforge.net/project/bbmap/
  19. http://razaoinfo.dl.sourceforge.net/project/bbmap/
  20. http://sinalbr.dl.sourceforge.net/project/bbmap/
  21. http://sitsa.dl.sourceforge.net/project/bbmap/
  22. http://tenet.dl.sourceforge.net/project/bbmap/
  23. http://ufpr.dl.sourceforge.net/project/bbmap/
  24. http://versaweb.dl.sourceforge.net/project/bbmap/
  25. https://cfhcable.dl.sourceforge.net/project/bbmap/
  26. https://cytranet.dl.sourceforge.net/project/bbmap/
  27. https://deac-ams.dl.sourceforge.net/project/bbmap/
  28. https://deac-fra.dl.sourceforge.net/project/bbmap/
  29. https://deac-riga.dl.sourceforge.net/project/bbmap/
  30. https://downloads.sourceforge.net/project/bbmap/
  31. https://excellmedia.dl.sourceforge.net/project/bbmap/
  32. https://freefr.dl.sourceforge.net/project/bbmap/
  33. https://gigenet.dl.sourceforge.net/project/bbmap/
  34. https://ixpeering.dl.sourceforge.net/project/bbmap/
  35. https://jaist.dl.sourceforge.net/project/bbmap/
  36. https://kumisystems.dl.sourceforge.net/project/bbmap/
  37. https://liquidtelecom.dl.sourceforge.net/project/bbmap/
  38. https://nchc.dl.sourceforge.net/project/bbmap/
  39. https://netactuate.dl.sourceforge.net/project/bbmap/
  40. https://netcologne.dl.sourceforge.net/project/bbmap/
  41. https://onboardcloud.dl.sourceforge.net/project/bbmap/
  42. https://phoenixnap.dl.sourceforge.net/project/bbmap/
  43. https://razaoinfo.dl.sourceforge.net/project/bbmap/
  44. https://sinalbr.dl.sourceforge.net/project/bbmap/
  45. https://sitsa.dl.sourceforge.net/project/bbmap/
  46. https://tenet.dl.sourceforge.net/project/bbmap/
  47. https://ufpr.dl.sourceforge.net/project/bbmap/
  48. https://versaweb.dl.sourceforge.net/project/bbmap/
Collapse this list.

Number of commits found: 9

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
39.34
21 Aug 2025 20:31:40
commit hash: 5d8f84ce55c7a5606228380c07d125d75c7371e5commit hash: 5d8f84ce55c7a5606228380c07d125d75c7371e5commit hash: 5d8f84ce55c7a5606228380c07d125d75c7371e5commit hash: 5d8f84ce55c7a5606228380c07d125d75c7371e5 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bbmap: Update to 39.34

A few improvements and fixes
Changes:
    https://bitbucket.org/berkeleylab/jgi-bbtools/commits/branch/master

Reported by:    portscout
39.33
29 Jul 2025 08:02:38
commit hash: 9c42a68c3ffcfff62f415baf9d4e1caa2af3f44ecommit hash: 9c42a68c3ffcfff62f415baf9d4e1caa2af3f44ecommit hash: 9c42a68c3ffcfff62f415baf9d4e1caa2af3f44ecommit hash: 9c42a68c3ffcfff62f415baf9d4e1caa2af3f44e files touched by this commit
Älven (alven) search for other commits by this committer
biology/bbmap: update 39.15 => 39.33

* Sort RUN_DEPENDS

PR:		288480
Approved by:	yuri@ (Mentor)
39.15
16 Jan 2025 12:35:49
commit hash: 25e2eac767b4fbfe69d5307fc027c5cfb8f44b77commit hash: 25e2eac767b4fbfe69d5307fc027c5cfb8f44b77commit hash: 25e2eac767b4fbfe69d5307fc027c5cfb8f44b77commit hash: 25e2eac767b4fbfe69d5307fc027c5cfb8f44b77 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bbmap: Update to 39.15

Add bitbucket link to WWW for some level of change tracking
Release highlights:
    https://bitbucket.org/berkeleylab/jgi-bbtools/commits/branch/master

Reported by:    portscout
39.14
13 Jan 2025 21:50:59
commit hash: 1f224e0bb61a439d5b82958b5bbdfa2041c55c3dcommit hash: 1f224e0bb61a439d5b82958b5bbdfa2041c55c3dcommit hash: 1f224e0bb61a439d5b82958b5bbdfa2041c55c3dcommit hash: 1f224e0bb61a439d5b82958b5bbdfa2041c55c3d files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bbmap: Update to 39.14

Changes: Cannot find any release notes

PR:             283240
Reported by:    alster@vinterdalen.se
38.92
31 Dec 2024 08:57:55
commit hash: 0835676e361bca74b28b09fe0425ed5ee958f26bcommit hash: 0835676e361bca74b28b09fe0425ed5ee958f26bcommit hash: 0835676e361bca74b28b09fe0425ed5ee958f26bcommit hash: 0835676e361bca74b28b09fe0425ed5ee958f26b files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
Mk/**java.mk: Convert bsd.java.mk to USES

The following features have been added or changed:
- Instead of USE_JAVA use USES=java. This defaults to
  USES=java:build,run if NO_BUILD is undefined. Else it defaults to
  USES=java:run
- Instead of USE_ANT=yes use USES=java:ant which also implies
  USES=java:build
- Instead of JAVA_BUILD=yes use USES=java:build. Does not imply run or
  extract
- Instead of JAVA_EXTRACT=yes use USES=java:extract does not imply
  build or run
- Instead of JAVA_RUN=yes use USES=java:run does not imply extract or
  build
- Instead of USE_JAVA=<version> use USES=java and JAVA_VERSION=<version>

Approved by: mat (portmgr), glewis
Differential Revision:  https://reviews.freebsd.org/D48201
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
38.92
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
38.92
22 Aug 2021 13:59:58
commit hash: c5efaea23b875a30e9a7652734d2c992d44f9fbccommit hash: c5efaea23b875a30e9a7652734d2c992d44f9fbccommit hash: c5efaea23b875a30e9a7652734d2c992d44f9fbccommit hash: c5efaea23b875a30e9a7652734d2c992d44f9fbc files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bbmap: Update to 38.92

Numerous small fixes and enhancements

Reported by:    portscout
38.90
18 Apr 2021 16:21:29
commit hash: 15458dfbacb842d71a41dcfdb6be83301ef0b7b6commit hash: 15458dfbacb842d71a41dcfdb6be83301ef0b7b6commit hash: 15458dfbacb842d71a41dcfdb6be83301ef0b7b6commit hash: 15458dfbacb842d71a41dcfdb6be83301ef0b7b6 files touched by this commit
Jason W. Bacon (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: 9