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Project: BigDataScript (GitHub Link)
  • BigDataScript-master
    • src
      • org
        • bds
          • compile
            • TypeCheckedNodes.java
            • CompilerMessageBdsNode.java
            • BdsCompiler.java
            • CompileErrorStrategy.java
            • BdsNodeWalker.java
            • CompilerMessages.java
            • CompilerMessage.java
            • BdsCompilerExpression.java
            • CompilerErrorListener.java
          • vm
            • BdsVm.java
            • OpCode.java
            • VmDebugger.java
            • ExceptionHandler.java
            • CatchBlockInfo.java
            • VmState.java
            • CallFrame.java
            • BdsVmAsm.java
          • report
            • RTemplate.java
            • Report.java
          • task
            • Tail.java
            • TaskDependecies.java
            • Task.java
            • TaskVmOpcode.java
            • DepVmOpcode.java
            • TailFile.java
            • TailFileMulti.java
            • TaskDependency.java
            • TailStream.java
            • DependencyState.java
            • TaskState.java
            • SysVmOpcode.java
          • executioner
            • NotifyTaskState.java
            • CheckTasksRunningLocal.java
            • Executioner.java
            • Executioners.java
            • PidParser.java
            • CheckTasksRunningCluster.java
            • ExecutionerClusterPbs.java
            • ExecutionerCluster.java
            • ExecutionerMesos.java
            • ExecutionerClusterMoab.java
            • ExecutionerSsh.java
            • TaskLogger.java
            • ExecutionerClusterFake.java
            • ExecutionerClusterSlurm.java
            • CheckTasksRunning.java
            • ExecutionerClusterSge.java
            • ExecutionerClusterGeneric.java
            • ExecutionerLocal.java
            • MonitorTask.java
          • SummaryTemplate.html
          • test
            • TestSuiteAll.java
            • TestCasesRun3.java
            • TestCasesClusterSsh.java
            • TestCasesLang.java
            • TestCasesRemote.java
            • TestCasesExecutioners.java
            • TestCasesZzz.java
            • TestCasesRun2.java
            • TestCasesInterpolate.java
            • BdsTest.java
            • TestCasesVm.java
            • TestCasesReport.java
            • TestCasesGraph.java
            • TestCasesFunctionDeclaration.java
            • TestCasesTaskImproper.java
            • TestCasesTail.java
            • TestCasesCommandLineOptions.java
            • TestCasesTesting.java
            • TestCasesRun.java
            • TestCasesTaskDetached.java
            • TestCasesCheckpoint.java
            • TestCasesClusterGeneric.java
            • TestSuiteVm.java
            • TestCasesBase.java
          • Bds.java
          • util
            • TextTable.java
            • Tuple.java
            • AutoHashMap.java
            • Timer.java
            • GprString.java
            • Gpr.java
          • Zzz.java
          • osCmd
            • TeeOutputStream.java
            • StreamGobbler.java
            • Cmd.java
            • Ssh.java
            • LineFilter.java
            • CmdLocal.java
            • CmdSsh.java
            • CmdCluster.java
            • Progress.java
            • Exec.java
            • ExecResult.java
          • lang
            • ParentNode.java
            • GenericNode.java
            • Parameters.java
            • nativeClasses
              • ClassDeclarationNative.java
              • exception
                • ClassDeclarationException.java
                • ClassDeclarationExceptionConcurrentModification.java
                • MethodExceptionConstructor.java
            • nativeFunctions
              • FunctionNativePrintHelp.java
              • FunctionNativeAssertBool.java
              • FunctionNativeRandSeed.java
              • FunctionNativeAssertInt.java
              • FunctionNativeType.java
              • FunctionNativeMinReal.java
              • FunctionNativeRandInt.java
              • FunctionNativeAssertBoolNoMsg.java
              • FunctionNativeToIntFromBool.java
              • FunctionNativeMaxReal.java
              • FunctionNative_clone_real.java
              • FunctionNativeAssertString.java
              • FunctionNativeToIntFromReal.java
              • FunctionNativeTasksDone.java
              • FunctionNativeAssert.java
              • FunctionNativeSleepReal.java
              • NativeLibraryFunctions.java
              • FunctionNativeSleep.java
              • FunctionNativeMinInt.java
              • FunctionNativeLog.java
              • FunctionNativeConfigOri.java
              • FunctionNativeMaxInt.java
              • FunctionNative_clone_int.java
              • FunctionNativeTime.java
              • FunctionNativeRangeReal.java
              • FunctionNativeConfig.java
              • FunctionNativeTasksToRun.java
              • FunctionNativeRangeIntStep.java
              • math
                • FunctionNative_sin_real.java
                • FunctionNative_log_real.java
                • FunctionNative_sqrt_real.java
                • FunctionNative_scalb_real_int.java
                • FunctionNative_asin_real.java
                • FunctionNative_exp_real.java
                • FunctionNative_atan_real.java
                • FunctionNative_nextUp_real.java
                • FunctionNative_ulp_real.java
                • FunctionNative_nextAfter_real_real.java
                • FunctionNative_max_real_real.java
                • FunctionNative_log10_real.java
                • FunctionNative_rint_real.java
                • FunctionNative_ceil_real.java
                • FunctionNative_min_real_real.java
                • FunctionNative_abs_real.java
                • FunctionNative_expm1_real.java
                • FunctionNative_round_real.java
                • FunctionNative_cosh_real.java
                • FunctionNative_pow_real_real.java
                • FunctionNative_hypot_real_real.java
                • FunctionNative_log1p_real.java
                • FunctionNative_IEEEremainder_real_real.java
                • FunctionNative_tan_real.java
                • FunctionNative_acos_real.java
                • FunctionNative_signum_real.java
                • FunctionNative_toDegrees_real.java
                • FunctionNative_atan2_real_real.java
                • FunctionNative_cbrt_real.java
                • FunctionNative_sinh_real.java
                • FunctionNative_cos_real.java
                • FunctionNative_floor_real.java
                • FunctionNative_getExponent_real.java
                • FunctionNative_copySign_real_real.java
                • FunctionNative_tanh_real.java
                • FunctionNative_toRadians_real.java
                • FunctionNative_abs_int.java
              • FunctionNativeRangeInt.java
              • FunctionNative_clone_string.java
              • FunctionNative_clone_bool.java
              • FunctionNativeAssertIntNoMsg.java
              • FunctionNativeAssertStringNoMsg.java
              • FunctionNativeRand.java
              • FunctionNativePrintErr.java
              • FunctionNative.java
              • FunctionNativeTasksRunning.java
              • FunctionNativeRandIntRange.java
              • FunctionNativePrint.java
            • value
              • LiteralList.java
              • LiteralReal.java
              • ValueString.java
              • LiteralListEmpty.java
              • ValueInt.java
              • LiteralInt.java
              • ValueMap.java
              • LiteralMap.java
              • ValueComposite.java
              • LiteralString.java
              • ValueClass.java
              • ValueFunction.java
              • ValueUnique.java
              • LiteralNull.java
              • ValueBool.java
              • LiteralBool.java
              • ValueList.java
              • Value.java
              • Literal.java
              • ValuePrimitive.java
              • LiteralMapEmpty.java
              • InterpolateVars.java
              • ValueReal.java
              • LiteralListString.java
              • ValueArgs.java
            • type
              • TypeClassException.java
              • TypeFunction.java
              • TypeBool.java
              • TypeComposite.java
              • TypeNull.java
              • TypeAny.java
              • TypeVoid.java
              • TypeList.java
              • TypeClassExceptionConcurrentModification.java
              • Types.java
              • TypeUniqueValue.java
              • TypeString.java
              • TypePrimitive.java
              • TypeInt.java
              • TypeReal.java
              • Type.java
              • TypeClass.java
              • PrimitiveType.java
              • TypeMap.java
            • BdsNode.java
            • BdsNodeFactory.java
            • nativeMethods
              • MethodNative.java
              • MethodDefaultConstructor.java
              • map
                • MethodNativeMapHashCode.java
                • MethodNativeMapKeys.java
                • MethodNativeMapValues.java
                • MethodNativeMapHasValue.java
                • MethodNativeMapClone.java
                • MethodNativeMapRemove.java
                • MethodNativeMapHasKey.java
                • MethodNativeMapSize.java
                • MethodNativeMap.java
                • MethodNativeMapGet.java
              • list
                • MethodNativeListPush.java
                • MethodNativeListAdd.java
                • MethodNativeListPop.java
                • MethodNativeListRm.java
                • MethodNativeListDelete.java
                • MethodNativeListAddList.java
                • MethodNativeListMapToString.java
                • MethodNativeListReverse.java
                • MethodNativeListIndexOf.java
                • MethodNativeListTail.java
                • MethodNativeListRmOnExit.java
                • MethodNativeListClone.java
                • MethodNativeListJoin.java
                • MethodNativeListHas.java
                • MethodNativeListCount.java
                • MethodNativeListForEach.java
                • MethodNativeListMapToInt.java
                • MethodNativeListRemove.java
                • MethodNativeListJoinStr.java
                • MethodNativeList.java
                • MethodNativeListSort.java
                • MethodNativeListRemoveIdx.java
                • MethodNativeListIsEmpty.java
                • MethodNativeListSize.java
                • MethodNativeListMapToReal.java
                • MethodNativeListFilter.java
                • MethodNativeListMap.java
                • MethodNativeListHead.java
                • MethodNativeListAddIndex.java
                • MethodNativeListHashCode.java
              • string
                • MethodNative_string_isEmpty.java
                • MethodNative_string_split_regex.java
                • MethodNative_string_swapExt.java
                • MethodNative_string_isFile.java
                • MethodNative_string_canWrite.java
                • MethodNative_string_dirPath_regex.java
                • MethodNative_string_startsWith_str.java
                • MethodNative_string_exitCode.java
                • MethodNative_string_removeExt.java
                • MethodNative_string_removeExt_ext.java
                • MethodNative_string_extName.java
                • MethodNative_string_isDir.java
                • MethodNative_string_readLines.java
                • MethodNative_string_stderr.java
                • MethodNative_string_substr_start_end.java
                • MethodNative_string_swapExt_extNew.java
                • MethodNative_string_size.java
                • MethodNative_string_canExec.java
                • MethodNative_string_baseName_ext.java
                • MethodNative_string_rm.java
                • MethodNative_string_delete.java
                • MethodNative_string_replace_regex_repl.java
                • MethodNative_string_dir.java
                • MethodNative_string_lastIndexOf_str.java
                • MethodNative_string_baseName.java
                • MethodNative_string_parseBool.java
                • MethodNative_string_pathCanonical.java
                • MethodNative_string_parseInt.java
                • MethodNative_string_exists.java
                • MethodNative_string_swapExt_ext.java
                • MethodNative_string_dir_regex.java
                • MethodNative_string_replace_str1_str2.java
                • MethodNative_string_path.java
                • MethodNative_string_length.java
                • MethodNative_string_rmOnExit.java
                • NativeLibraryString.java
                • MethodNative_string_endsWith_str.java
                • MethodNative_string_dirName.java
                • MethodNative_string_indexOf_str.java
                • MethodNative_string_lines.java
                • MethodNative_string_pathName.java
                • MethodNative_string_toLower.java
                • MethodNative_string_trim.java
                • MethodNative_string_parseReal.java
                • MethodNative_string_stdout.java
                • MethodNative_string_download.java
                • MethodNative_string_isDoneOk.java
                • MethodNative_string_dirPath.java
                • MethodNative_string_mkdir.java
                • MethodNative_string_chdir.java
                • MethodNative_string_read.java
                • MethodNative_string_upload.java
                • MethodNative_string_canRead.java
                • MethodNative_string_substr_start.java
                • MethodNative_string_download_localname.java
                • MethodNative_string_toUpper.java
                • MethodNative_string_swapExt_extOld_extNew.java
                • MethodNative_string_upload_localname.java
                • MethodNative_string_isDone.java
                • MethodNative_string_write_str.java
                • MethodNativeString.java
            • ProgramUnit.java
            • expression
              • ExpressionCond.java
              • ExpressionUnaryPlus.java
              • ExpressionBinary.java
              • ExpressionLogic.java
              • ExpressionWithScope.java
              • ExpressionBitAnd.java
              • PrePostOperation.java
              • ExpressionBitOr.java
              • ExpressionParallel.java
              • ExpressionPlus.java
              • ExpressionAssignmentPlus.java
              • ExpressionEq.java
              • ExpressionDelegateBinary.java
              • ReferenceMap.java
              • ExpressionAssignmentList.java
              • ExpressionNe.java
              • ExpressionSys.java
              • ExpressionLe.java
              • ReferenceField.java
              • ExpressionAssignmentDiv.java
              • ExpressionComp.java
              • ExpressionBitXor.java
              • ExpressionDivide.java
              • ExpressionUnaryMinus.java
              • ExpressionAssignmentBitOr.java
              • ExpressionTimes.java
              • ExpressionDepOperator.java
              • ExpressionGoal.java
              • ExpressionMinus.java
              • ExpressionVariableInitImplicit.java
              • ExpressionGe.java
              • ReferenceThis.java
              • ExpressionList.java
              • ExpressionPlusMinus.java
              • ExpressionAssignment.java
              • ExpressionAssignmentMinus.java
              • ExpressionTaskOptions.java
              • ExpressionCast.java
              • Reference.java
              • ExpressionMath.java
              • ExpressionGt.java
              • ExpressionModulo.java
              • ExpressionAssignmentBitAnd.java
              • ExpressionLt.java
              • Post.java
              • ExpressionUnaryPlusMinus.java
              • ExpressionLogicAnd.java
              • ExpressionAssignmentBinary.java
              • ExpressionCompare.java
              • ExpressionAssignmentMult.java
              • ExpressionLogicOp.java
              • ExpressionNew.java
              • ExpressionWrapper.java
              • ExpressionUnary.java
              • ReferenceList.java
              • ExpressionBitNegation.java
              • ExpressionBitOp.java
              • ExpressionDep.java
              • ExpressionBit.java
              • Pre.java
              • ExpressionTask.java
              • ExpressionTimesDivMod.java
              • ExpressionLogicNot.java
              • Expression.java
              • ExpressionTaskLiteral.java
              • ReferenceVar.java
              • ExpressionLogicOr.java
            • statement
              • Catch.java
              • Println.java
              • Continue.java
              • VarDeclaration.java
              • While.java
              • Return.java
              • Switch.java
              • Break.java
              • Help.java
              • MethodCall.java
              • ForLoopList.java
              • Debug.java
              • Statement.java
              • StatementWithScope.java
              • Finally.java
              • FunctionDeclaration.java
              • Error.java
              • MethodDeclaration.java
              • Args.java
              • Block.java
              • Case.java
              • ForCondition.java
              • ForLoop.java
              • If.java
              • ForEnd.java
              • StatementFunctionDeclaration.java
              • Exit.java
              • Default.java
              • VariableInitImplicit.java
              • StatementExpr.java
              • VariableInit.java
              • Throw.java
              • Kill.java
              • Breakpoint.java
              • Checkpoint.java
              • FunctionCall.java
              • Wait.java
              • ClassDeclaration.java
              • FieldDeclaration.java
              • StatementInclude.java
              • ForInit.java
              • TryCatchFinally.java
              • Warning.java
              • BlockWithFile.java
              • Print.java
              • Try.java
          • Config.java
          • Pcingola.java
          • data
            • DataS3.java
            • DataFtp.java
            • Data.java
            • FtpConnectionFactory.java
            • DataHttp.java
            • S3Sample.java
            • DataSftp.java
            • DataRemote.java
            • DataFile.java
          • BdsParseArgs.java
          • symbol
            • SymbolTable.java
            • GlobalSymbolTable.java
          • DagTaskTemplate.js
          • run
            • RunState.java
            • DebugMode.java
            • Coverage.java
            • BdsThreads.java
            • Freeze.java
            • BdsRun.java
            • HelpCreator.java
            • BdsThread.java
          • cluster
            • healthCondition
              • HealthConditionLoggedInUsers.java
              • HealthConditionLoadAvg.java
              • HealthConditionMem.java
              • HealthCondition.java
              • HealthConditionLoadAvgByCpu.java
            • commandParser
              • CommandParserUptime.java
              • CommandParserMemInfo.java
              • CommandParserSystemProfiler.java
              • CommandParserCpuInfo.java
              • CommandParserUname.java
              • CommandParserWho.java
              • CommandParserTop.java
              • CommandParser.java
              • CommandParserDf.java
            • ClusterSsh.java
            • Cluster.java
            • host
              • HostInifinte.java
              • HostHealth.java
              • HostLocal.java
              • HostSsh.java
              • HostHealthUpdater.java
              • Host.java
              • HostResourcesInf.java
              • HostResources.java
          • scope
            • GlobalScope.java
            • Scope.java
          • mesos
            • BdsMesosFramework.java
            • BdsMesosExecutor.java
            • BdsMesosScheduler.java
          • antlr
            • BigDataScriptParser.java
            • BigDataScriptBaseListener.java
            • BigDataScriptListener.java
            • BigDataScriptLexer.java
          • SummaryTemplate.yaml
    • build.xml
    • null
      • bds
        • http
          • www
            • google
              • com
                • index.html
    • README_Eclipse_Os_X.txt
    • vm
      • README
    • include
      • bio
        • seq
          • callableCollapseSplit.py
          • fastq.bds
          • map.bds
          • mapReads.bds
          • gatk.bds
          • annotate.bds
          • snpeff.bds
          • java.bds
      • java.bds
    • go
      • signal_test
        • h.go
      • bds
        • src
          • tee
            • tee.go
          • fileutil
            • fileutil.go
          • tmpfile
            • tmpfile.go
          • exec
            • exec.go
        • .DS_Store
        • bds.go
        • make.sh
      • .DS_Store
      • old
        • bds.go
    • nativeFunctions
      • native.txt
      • math.double.txt
      • native.pl
      • math.txt
      • native.sh
    • mesos.txt
    • atom_bds.tgz
    • test
      • run_167.bds
      • run_139.bds
      • run_200.bds
      • report_01.bds
      • test53.bds
      • run_102.bds
      • run_36.bds
      • graph_12.bds
      • checkpoint_17.bds
      • graph_10.out.txt
      • remote_20.bds
      • run_221.bds
      • run_33.bds
      • run_109.bds
      • test19.bds
      • run_34.bds
      • chdir_test
        • chdir_test_file.txt
        • chdir_test_file_02.txt
      • run_09.bds
      • z1.bds
      • run_92.bds
      • test54.bds
      • run_81.bds
      • checkpoint_22.bds
      • test63.bds
      • test_case_run_11.bds
      • run_210.bds
      • run_234.bds
      • run_143.bds
      • run_135_clone.bds
      • run_13.bds
      • test01.bds
      • run_03.bds
      • test_parsePidQstatColumn_qstat.txt
      • run_136.bds
      • tail_02.txt
      • test_case_run_15.bds
      • run_85.bds
      • clusterGeneric_localhost
        • postMortemInfo.pl
        • kill.pl
        • run.pl
        • README.txt
        • stat.pl
      • graph_05.txt
      • checkpoint_04.bds
      • run_01.bds
      • checkpoint_19.bds
      • run_205.bds
      • run_38.bds
      • test28.bds
      • run_23.bds
      • clusterSsh_localhost_01.config
      • run_44.bds
      • test42.bds
      • run_122.bds
      • test30.bds
      • run_141.bds
      • graph_07.xml
      • graph_10.mid1.txt
      • test06.bds
      • run_250.bds
      • checkpoint_01.bds
      • run_43.bds
      • run_158.bds
      • checkpoint_07.bds
      • run_137.bds
      • run_47.bds
      • run_32.bds
      • run_50.bds
      • run_115.bds
      • run_125.bds
      • remote_26.bds
      • run_162.bds
      • run_39.bds
      • run_138.bds
      • run_207.bds
      • test08.bds
      • run_246.bds
      • remote_17.bds
      • out2_1.txt
      • checkpoint_05.bds
      • remote_24.bds
      • run_22.bds
      • remote_29.bds
      • run_task_improper_06.bds
      • checkpoint_20.bds
      • run_125c.bds
      • run_74.bds
      • run_87.bds
      • run_239.bds
      • run_task_detached_02.bds
      • test33.bds
      • test55.bds
      • run_202.bds
      • test03.bds
      • checkpoint_10.bds
      • checkpoint_09.xml
      • run_117.bds
      • test26.bds
      • graph_01.bds
      • test62.bds
      • myfile.config
      • graph_10.in2.txt
      • graph_07.csv
      • run_51.bds
      • checkpoint_18.bds
      • run_30.bds
      • graph_14.bds
      • run_15.bds
      • run_161.bds
      • run_53.bds
      • run_238.bds
      • run_27.bds
      • checkpoint_08.bds
      • test24.bds
      • run_248.bds
      • test29.bds
      • graph_03.bds
      • test41.bds
      • test_case_run_05.bds
      • z.9.txt
      • run_218.bds
      • run_24.bds
      • tail_06.txt
      • run_11.bds
      • checkpoint_02.bds
      • test_case_run_03.bds
      • test_case_run_12.bds
      • test159_prelude_task.config
      • test56.bds
      • run_114.bds
      • remote_11.bds
      • run_156.bds
      • run_151.bds
      • test17.bds
      • run_69.bds
      • run_65.bds
      • run_112.bds
      • tmp
        • testinclude.bds
      • gusevfe.sh
      • run_26.bds
      • test_case_run_16.bds
      • run_144.bds
      • run_209.bds
      • run_140.bds
      • run_78.bds
      • run_21.bds
      • run_76.bds
      • run_155.bds
      • checkpoint_03.bds
      • run_46.bds
      • run_60.bds
      • run_77.bds
      • graph_13.bds
      • run_147.bds
      • run_146.bds
      • checkpoint_11.bds
      • run_216.bds
      • run_243.bds
      • run_103.bds
      • run_104.bds
      • remote_08.bds
      • run_113.bds
      • remote_16.bds
      • test_case_run_14.bds
      • remote_03.bds
      • run_55.bds
      • run_249.bds
      • run_66.bds
      • run_70.bds
      • run_80.bds
      • run_149.bds
      • test16.bds
      • run_96.bds
      • clusterSsh_01.bds
      • test15.bds
      • run_task_detached_01.bds
      • run_29.bds
      • run_83.bds
      • remote_19.bds
      • run_231.bds
      • run_90.bds
      • test07.bds
      • run_129.bds
      • test46.bds
      • run_153.bds
      • test57.bds
      • run_242.bds
      • chdir_test_file_01.txt
      • chdir_test_file.txt
      • graph_10.bds
      • run_142.bds
      • run_71.bds
      • gusevfe.bds
      • test_case_run_10.bds
      • run_107.bds
      • run_154.bds
      • run_150.bds
      • run_104.in
      • test66.bds
      • run_241.bds
      • test10.bds
      • checkpoint_08.xml
      • run_133.bds
      • run_101.bds
      • run_224.bds
      • run_84.bds
      • z.10.txt
      • vm00.asm
      • remote_25.bds
      • graph_06.bds
      • test67.bds
      • run_203.bds
      • test_case_run_06.bds
      • in2.txt
      • myfile_new.config
      • run_37.bds
      • graph_07.txt
      • test_case_run_07.bds
      • graph_04.bds
      • checkpoint_09.bds
      • vm02.asm
      • bds_exec_test
        • z.err
        • test.xml
        • test.txt
        • z.bds
        • z.exitCode
        • bds_exec.sh
        • z.sh
      • run_131.bds
      • run_135.bds
      • run_40.bds
      • run_20.bds
      • test32.bds
      • test49.bds
      • test64.bds
      • test34.bds
      • run_108.bds
      • vm01.asm
      • test25.bds
      • run_31.bds
      • test.txt
      • BIOINF_2014_reviewer_1
        • test.xml
        • test.sh
        • test.bds.20140723_011839_351.report.html
        • test.bds.20140723_011841_561.report.html
        • test.txt
        • test.bds
        • test.1.err
        • test.csv
        • test.2.err
      • test37.bds
      • graph_15.bds
      • test_case_run_13.bds
      • run_06.bds
      • run_task_improper_02.bds
      • graph_09.bds
      • run_59.bds
      • test.bds
      • run_152.bds
      • remote_18.bds
      • test60a.bds
      • test09.bds
      • test_case_run_04.bds
      • run_12.bds
      • run_163.bds
      • run_35.bds
      • cal.bds
      • run_56.bds
      • remote_23.bds
      • run_148.bds
      • run_73.bds
      • checkpoint_23.bds
      • run_206.bds
      • remote_30.bds
      • run_121.bds
      • failOnce.pl
      • tail_03.txt
      • z.bds
      • test58.bds
      • run_57.bds
      • run_91.bds
      • checkpoint_09.txt
      • remote_31.bds
      • checkpoint_25.bds
      • run_116.bds
      • run_244.bds
      • run_75.bds
      • checkpoint_26.bds
      • run_125b.bds
      • out1_2.txt
      • run_245.bds
      • test27.bds
      • run_task_detached_04.bds
      • remote_14.bds
      • test_case_run_02.bds
      • run_123_literals_sys.bds
      • run_04.bds
      • test21.bds
      • checkpoint_08.csv
      • cmdLineOptions_01.bds
      • test66b.bds
      • test13.bds
      • test05.bds
      • run_89.bds
      • run_222.bds
      • run_123_literals_task.bds
      • run_02.bds
      • checkpoint_08.txt
      • graph_08.mid2.txt
      • run_130.bds
      • run_105.in
      • run_08.bds
      • out1.txt
      • test_case_run_01.bds
      • run_97.bds
      • test22.bds
      • run_100.bds
      • run_120.bds
      • remote_15.bds
      • run_233.bds
      • test44.bds
      • run_215.bds
      • run_82.bds
      • in1.txt
      • run_54.bds
      • run_48.bds
      • graph_05.xml
      • remote_07.bds
      • tail_04.txt
      • run_16.bds
      • run_235.bds
      • checkpoint_12_include.bds
      • run_204.bds
      • test50.bds
      • run_88.bds
      • run_213.bds
      • run_95.bds
      • run_217.bds
      • run_132.bds
      • checkpoint_15.bds
      • test40.bds
      • test45.bds
      • run_240.bds
      • run_task_improper_04.bds
      • run_68.bds
      • run_128.bds
      • remote_10.bds
      • run_232.bds
      • run_226.bds
      • run_task_improper_03.bds
      • graph_06.xml
      • checkpoint_24.bds
      • test_parsePidQstatRegex_qstat.config
      • run_99.bds
      • run_98.bds
      • run_126.bds
      • run_07.bds
      • test04.bds
      • run_05.bds
      • run_225.bds
      • run_52.bds
      • run_124.bds
      • run_106.bds
      • run_165.bds
      • inc
        • test-inc.bds
        • test-inc2.bds
      • run_94.bds
      • dirTest
        • file_2.txt
        • file_3.txt
        • file_1.txt
      • checkpoint_28.bds
      • remote_32.bds
      • run_145.bds
      • run_110.bds
      • run_212.bds
      • run_247.bds
      • run_252.bds
      • run_64.bds
      • run_127.bds
      • test00.bds
      • run_228.bds
      • .remote_29.bds.swp
      • test14.bds
      • run_220.bds
      • run_63.bds
      • remote_13.bds
      • in.txt
      • graph_06.txt
      • run_229.bds
      • graph_08.out.txt
      • test_parsePidQstatRegex_qstat.txt
      • run_67.bds
      • run_157.bds
      • graph_02.bds
      • run_134.bds
      • run_201.bds
      • test61.bds
      • run_task_improper_07.bds
      • checkpoint_08.2.csv
      • test20.bds
      • graph_05.csv
      • remote_27.bds
      • run_17.bds
      • test_case_run_09.bds
      • graph_08.mid1.txt
      • clusterGeneric_01.bds
      • test60.bds
      • test51.bds
      • test36.bds
      • vm03.asm
      • run_79.bds
      • run_14.bds
      • run_237.bds
      • run_task_improper_05.bds
      • run_123.bds
      • test02.bds
      • remote_22.bds
      • graph_11.bds
      • checkpoint_12.bds
      • test12.bds
      • graph_08.bds
      • test65.bds
      • checkpoint_16.bds
      • test60d.bds
      • run_105.bds
      • test47.bds
      • run_164.bds
      • remote_33.bds
      • run_28.bds
      • remote_06.bds
      • remote_04.bds
      • graph_08.in.txt
      • remote_09.bds
      • run_25.bds
      • out2.txt
      • run_166.bds
      • test59.bds
      • run_task_improper_01.bds
      • remote_21.bds
      • run_208.bds
      • checkpoint_21.bds
      • run_219.bds
      • run_42.bds
      • test52.bds
      • tail_01.txt
      • graph_10.mid22.txt
      • checkpoint_13.bds
      • graph_05.bds
      • test23.bds
      • run_211.bds
      • test31.bds
      • run_58.bds
      • run_18.bds
      • checkpoint_27.bds
      • run_19.bds
      • graph_09.in.txt
      • remote_12.bds
      • test43.bds
      • run_214.bds
      • run_227.bds
      • zz.bds
      • test35.bds
      • clusterGeneric_localhost_01.config
      • graph_10.in1.txt
      • remote_05.bds
      • test11.bds
      • test38.bds
      • cmdLineOptions_02.bds
      • run_45.bds
      • run_task_detached_03.bds
      • run_223.bds
      • test_case_run_08.bds
      • run_236.bds
      • test_case_run_17.bds
      • checkpoint_14.bds
      • run_93.bds
      • test48.bds
      • remote_28.bds
      • run_10.bds
      • test39.bds
      • run_159.bds
      • checkpoint_06.bds
      • run_230.bds
      • run_72.bds
      • run_251.bds
      • run_118.bds
      • test18.bds
      • run_119.bds
      • run_111.bds
      • test67b.bds
    • lib
    • task.md
    • README.txt
    • .settings
      • org.eclipse.jdt.ui.prefs
      • org.eclipse.ltk.core.refactoring.prefs
      • org.eclipse.jdt.core.prefs
      • org.eclipse.core.resources.prefs
    • .DS_Store
    • config
      • clusterGeneric_localhost
        • postMortemInfo.pl
        • kill.pl
        • run.pl
        • README.txt
        • stat.pl
      • bds.config
      • clusterGeneric_LSF
        • postMortemInfo.pl
        • kill.pl
        • run.pl
        • README.txt
        • stat.pl
      • clusterGeneric
        • postMortemInfo.pl
        • kill.pl
        • run.pl
        • README.txt
        • stat.pl
      • clusterGeneric_SLURM
        • stat.sh
        • kill.sh
        • run.pl
        • postMortemInfo.sh
    • fakeCluster
      • reset
      • qstat
      • msub
      • qsub
      • canceljob
      • fakeCluster.sh
      • qdel
    • fork.md
    • distro
    • starcluster
      • install.sh
      • starcluster.txt
    • pcingola_formatter.xml
    • pcingola_cleanup.xml
    • scripts
      • scp_home.sh
      • bds_mesos_executor.sh
      • clean.sh
      • qstat
      • run_z.sh
      • distro.sh
      • scp.sh
      • install.sh
      • watch.sh
      • make_go.sh
      • timeout.sh
      • scp_ehs.sh
      • make.sh
    • bds_pipelines
      • chipSeq.bds
      • mdip.bds
      • bds_timeline.html
      • align.bds
      • qc.bds
      • baseCalling.bds
    • taskOpt.md
    • git
      • update_force
      • commit
      • update
      • release
    • etc
      • eclipse_formatter.xml
      • eclipse_cleanup.xml
    • grammars
      • BigDataScriptParser.java
      • BigDataScriptLexer.tokens
      • BigDataScript.interp
      • BigDataScript.g4
      • test.sh
      • BigDataScriptLexer.interp
      • BigDataScriptBaseListener.java
      • BigDataScriptLexerRules.g4
      • BigDataScriptListener.java
      • BigDataScript.20180315.g4
      • BigDataScriptLexer.java
      • BigDataScript.tokens
      • build.sh
    • nativeMethods
      • native.txt
      • native.pl
      • native.sh
    • .gitignore
    • LICENSE.txt
    • .project
    • .classpath
    • doc
      • Cluster_bugs.txt