barebones input bam operation

src/req/operations/InputBamFile.ts

@@ -0,0 +1,68 @@
+import * as cp from "child_process";
+
+import * as atomic from "./atomicOperations";
+import {AtomicOperationForkEvent} from "./../atomicOperationsIPC";
+import {getReadable} from "./../getAppPath";
+import {AlignData} from "./../alignData";
+export class InputBamFile extends atomic.AtomicOperation
+{
+    public bamPath : string;
+    public alignData : AlignData;
+    public inputBamFileProcess : cp.ChildProcess;
+    constructor()
+    {
+        super();
+    }
+    public setData(bamPath : string)
+    {
+        this.bamPath = bamPath;
+    }
+    public run() : void
+    {
+        this.closeLogOnFailure = false;
+        this.closeLogOnSuccess = false;
+        let self = this;
+        this.inputBamFileProcess = cp.fork(getReadable("InputBamFile.js"));
+        self.inputBamFileProcess.on(
+            "message",function(ev : AtomicOperationForkEvent){
+                if(ev.finishedSettingData == true)
+                {
+                    self.inputBamFileProcess.send(
+                        <AtomicOperationForkEvent>{
+                            run : true
+                        }
+                    );
+                }
+                if(ev.update == true)
+                {
+                    self.flags = ev.flags;
+                    if(ev.flags.success == true)
+                    {
+                        self.alignData = ev.data.alignData;
+                    }
+                    if(ev.flags.done)
+                    {
+                        self.logRecord = ev.logRecord;
+                        atomic.recordLogRecord(ev.logRecord);
+                    }
+                    self.progressMessage = ev.progressMessage;
+                    self.update();
+                }
+            }
+        );
+        setTimeout(
+            function(){
+                self.inputBamFileProcess.send(
+                    <AtomicOperationForkEvent>{
+                        setData : true,
+                        data : {
+                            bamPath : self.bamPath
+                        },
+                        name : self.name,
+                        description : "Input Bam File"
+                    }
+                );
+            }
+        );
+    }
+}