| /dports/biology/bbmap/bbmap/current/var2/ |
| H A D | VcfLoader.java | 37 ArrayList<ProcessThread> alpt=loader.spawnThreads(false, false); in loadVarFile() local
44 ArrayList<ProcessThread> alpt=loader.spawnThreads(loadCoverage, extendedInfo); in loadVcfFile() local
59 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
75 private void waitForFinish(ArrayList<ProcessThread> alpt){ in waitForFinish()
286 final ArrayList<ProcessThread> alpt; field in VcfLoader.ProcessThread
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| H A D | FilterVCF.java | 199 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
215 private void waitForFinish(ArrayList<ProcessThread> alpt){ in waitForFinish()
398 ArrayList<ProcessThread> alpt=spawnThreads(bf, bsw); in processVcfVarsMT() local
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| H A D | MergeSamples.java | 186 ArrayList<MergeThread> alpt=spawnThreads(bswVcf); in mergeMT() local
377 ArrayList<MergeThread> alpt=new ArrayList<MergeThread>(threads); in spawnThreads() local
393 private void waitForFinish(ArrayList<MergeThread> alpt){ in waitForFinish()
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| H A D | VcfWriter.java | 116 ArrayList<ProcessThread> alpt=spawnThreads(bsw, inq, mode); in writeFile() local
147 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
163 private void waitForFinish(ArrayList<ProcessThread> alpt){ in waitForFinish()
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| H A D | CallVariants2.java | 717 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in prefilter() local
814 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
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| H A D | CallVariants.java | 448 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in prefilter_SF() local
490 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in prefilter_MF() local
804 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
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| H A D | VarMap.java | 350 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(WAYS); in processVariantsMT_inner() local
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| /dports/biology/bbmap/bbmap/current/stream/ |
| H A D | SamLineStreamer.java | 89 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
228 ArrayList<ProcessThread> alpt; field in SamLineStreamer.ProcessThread
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| H A D | SamReadStreamer.java | 89 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
233 ArrayList<ProcessThread> alpt; field in SamReadStreamer.ProcessThread
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| /dports/biology/bbmap/bbmap/current/assemble/ |
| H A D | Shaver.java | 100 ArrayList<AbstractExploreThread> alpt=new ArrayList<AbstractExploreThread>(threads); in shave() local
146 ArrayList<AbstractShaveThread> alpt=new ArrayList<AbstractShaveThread>(threads); in shave() local
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| H A D | AbstractRemoveThread.java | 50 ArrayList<AbstractRemoveThread> alpt=new ArrayList<AbstractRemoveThread>(threads); in process() local
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| /dports/biology/bbmap/bbmap/current/kmer/ |
| H A D | OwnershipThread.java | 33 ArrayList<OwnershipThread> alpt=new ArrayList<OwnershipThread>(threads); in process() local
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| /dports/biology/bbmap/bbmap/current/ukmer/ |
| H A D | OwnershipThread.java | 33 ArrayList<OwnershipThread> alpt=new ArrayList<OwnershipThread>(threads); in process() local
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| /dports/biology/bbmap/bbmap/current/prok/ |
| H A D | AnalyzeGenes.java | 296 ArrayList<FileThread> alpt=new ArrayList<FileThread>(threads); in spawnThreads() local
313 private GeneModel waitForThreads(ArrayList<FileThread> alpt){ in waitForThreads()
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| H A D | FetchProks.java | 36 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in main() local
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| H A D | MergeRibo.java | 373 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
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| /dports/biology/bbmap/bbmap/current/template/ |
| H A D | A_Sample_Generator.java | 286 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
304 private void waitForThreads(ArrayList<ProcessThread> alpt){ in waitForThreads()
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| /dports/biology/bbmap/bbmap/current/tax/ |
| H A D | AnalyzeAccession.java | 182 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in process_inner() local
195 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in process_perFile() local
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| /dports/biology/bbmap/bbmap/current/icecream/ |
| H A D | IceCreamMaker.java | 392 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
410 private void waitForThreads(ArrayList<ProcessThread> alpt){ in waitForThreads()
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| H A D | ReformatPacBio.java | 501 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
520 private void waitForThreads(ArrayList<ProcessThread> alpt){ in waitForThreads()
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | TetramerFrequencies.java | 131 ArrayList<PrintThread> alpt=spawnThreads(); in process() local
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| H A D | FindPrimers.java | 263 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
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| /dports/biology/bbmap/bbmap/current/sketch/ |
| H A D | BlacklistMaker2.java | 258 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
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| H A D | CompareSSU.java | 287 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
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| /dports/biology/bbmap/bbmap/current/consensus/ |
| H A D | FixScaffoldGaps.java | 352 ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads); in spawnThreads() local
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