Merge pull request #405 from chgibb/dev

398, 374, 372

.gitignore

@@ -4,7 +4,6 @@ phat-linux-x64
 phat-win32-x64
 *.*~
 npm-debug.log
-.vscode
 src/FastQC/bin/*
 src/pileup.js
 src/req/renderer/PathogenRenderer/pileup.js

.vscode/launch.json

@@ -0,0 +1,14 @@
+{
+    "version" : "0.2.0",
+    "configurations" : [
+        {
+            "name" : "Debug Main",
+            "type" : "node",
+            "request" : "launch",
+            "cwd" : "${workspaceRoot}/phat-linux-x64",
+            "runtimeExecutable" : "${workspaceRoot}/phat-linux-x64/phat",
+        "program" : "${workspaceRoot}/phat-linux-x64/resources/app/main.js",
+        "protocol" : "legacy"
+        }
+    ]
+}

package.json

@@ -1,6 +1,6 @@
 {
   "name": "phat",
-  "version": "0.0.21",
+  "version": "0.0.22",
   "description": "Pathogen Host Analysis Tool",
   "main": "main.js",
   "scripts": {

src/req/renderer/OutputRenderer/masterView.ts

@@ -19,7 +19,7 @@ export class View extends viewMgr.View
     public fastqInputs : Array<Fastq>;
     public fastaInputs : Array<Fasta>;
 
-    public displayInfo : "QCInfo" | "RefSeqInfo" | "AlignmentInfo" | "SNPPositions";
+    public displayInfo : "QCInfo" | "RefSeqInfo" | "AlignmentInfo" | "SNPPositions" | "MappedReadsPerContigInfo";
     public inspectingUUID : string;
     public constructor(div : string)
     {
@@ -92,8 +92,6 @@ export class View extends viewMgr.View
 
     public divClickEvents(event : JQueryEventObject) : void
     {
-        let self = this;
-        console.log(event.target.id);
-
+
     }
 }

src/req/renderer/OutputRenderer/reportView.ts

@@ -15,6 +15,7 @@ import {VCF2JSONRow} from "./../../varScanMPileup2SNPVCF2JSON";
 import {renderQCReportTable} from "./reportView/renderQCReportTable";
 import {renderAlignmentReportTable} from "./reportView/renderAlignmentReportTable";
 import {renderSNPPositionsTable} from "./reportView/renderSNPPositionsTable";
+import {renderMappedReadsPerContigTable} from "./reportView/renderMappedReadsPerContigTable";
 
 export function addView(arr : Array<viewMgr.View>,div : string)
 {
@@ -37,8 +38,6 @@ export class View extends viewMgr.View
         let masterView = <masterView.View>viewMgr.getViewByName("masterView");
         let rightPanel = <rightPanel.View>viewMgr.getViewByName("rightPanel",masterView.views);
 
-
-
         //if we're looking at SNP position, refresh table information if the alignment being inspected has changed
         if(masterView.displayInfo == "SNPPositions")
         {
@@ -56,6 +55,7 @@ export class View extends viewMgr.View
             ${renderQCReportTable()}
             ${renderAlignmentReportTable()}
             ${renderSNPPositionsTable(this.vcfRows)}
+            ${renderMappedReadsPerContigTable()}
 
         `;
     }
@@ -95,6 +95,18 @@ export class View extends viewMgr.View
                     }
                 );
             }
+            if(event.target.id == masterView.alignData[i].uuid+"AlignmentRate")
+            {
+                if(!masterView.alignData[i].summary.overallAlignmentRate)
+                {
+                    alert(`Can't view an alignment with 0% alignment rate`);
+                    return;
+                }
+                masterView.inspectingUUID = masterView.alignData[i].uuid;
+                masterView.displayInfo = "MappedReadsPerContigInfo";
+                viewMgr.render();
+                return;
+            }
             if(masterView.alignData[i].uuid == masterView.inspectingUUID)
             {
                 for(let k = 0; k != this.vcfRows.length; ++k)

src/req/renderer/OutputRenderer/reportView/renderAlignmentReportTable.ts

@@ -83,7 +83,7 @@ export function renderAlignmentReportTable() : string
                         res += `<td>${masterView.alignData[i].summary.mates}</td>`;
 
                     if(rightPanel.alignmentInfoSelection.overallAlignmentRate)
-                        res += `<td>${masterView.alignData[i].summary.overallAlignmentRate}</td>`;
+                        res += `<td class="activeHover" id="${masterView.alignData[i].uuid}AlignmentRate">${masterView.alignData[i].summary.overallAlignmentRate}</td>`;
 
                     if(rightPanel.alignmentInfoSelection.minimumCoverage)
                         res += `<td>${masterView.alignData[i].varScanSNPSummary.minCoverage}</td>`;

src/req/renderer/OutputRenderer/reportView/renderMappedReadsPerContigTable.ts

@@ -0,0 +1,52 @@
+import * as viewMgr from "./../../viewMgr";
+import * as masterView from "./../masterView";
+import * as rightPanel from "./../rightPanel";
+
+export function renderMappedReadsPerContigTable() : string
+{
+    let masterView = <masterView.View>viewMgr.getViewByName("masterView");
+    let rightPanel = <rightPanel.View>viewMgr.getViewByName("rightPanel",masterView.views);
+    if(masterView.displayInfo != "MappedReadsPerContigInfo")
+        return "";
+    return `
+        <table style="width:100%">
+            ${(()=>{
+                let res = "";
+                res += `
+                    <tr>
+                        ${rightPanel.mapppedReadsPerContigInfoSelection.refSeqName != false ? "<th>Contig Name</th>" : ""}
+                        ${rightPanel.mapppedReadsPerContigInfoSelection.seqLength != false ? "<th>Length</th>" : ""}
+                        ${rightPanel.mapppedReadsPerContigInfoSelection.mappedReads != false ? "<th>Mapped Reads</th>" : ""}
+                        ${rightPanel.mapppedReadsPerContigInfoSelection.unMappedReads != false ? "<th>Unmapped Reads</th>" : ""}
+                    </tr>
+                `;
+                return res;
+            })()}
+            ${(()=>{
+                let res = "";
+                for(let i = 0; i != masterView.alignData.length; ++i)
+                {
+                    
+                    if(masterView.alignData[i].uuid == masterView.inspectingUUID)
+                    {
+                        for(let k = 0; k != masterView.alignData[i].idxStatsReport.length; ++k)
+                        {
+                                res += "<tr>";
+                                if(rightPanel.mapppedReadsPerContigInfoSelection.refSeqName)
+                                    res += `<td>${masterView.alignData[i].idxStatsReport[k].refSeqName}</td>`;
+                                if(rightPanel.mapppedReadsPerContigInfoSelection.seqLength)
+                                    res += `<td>${masterView.alignData[i].idxStatsReport[k].seqLength}</td>`;
+                                if(rightPanel.mapppedReadsPerContigInfoSelection.mappedReads)
+                                    res += `<td>${masterView.alignData[i].idxStatsReport[k].mappedReads}</td>`;
+                                if(rightPanel.mapppedReadsPerContigInfoSelection.unMappedReads)
+                                    res += `<td>${masterView.alignData[i].idxStatsReport[k].unMappedReads}</td>`;
+                                res += "</tr>";
+                        }
+                        break;
+                    }
+                }
+                return res;
+            })()}
+        </table>
+    `;
+}

src/req/renderer/OutputRenderer/reportView/renderQCReportTable.ts

@@ -23,7 +23,7 @@ export function renderQCReportTable() : string
                         ${rightPanel.fastQInfoSelection.PBSQ != false ? "<th>Per Base Sequence Quality</th>" : ""}
                         ${rightPanel.fastQInfoSelection.PSQS != false ? "<th>Per Sequence Quality Score</th>" : ""}
                         ${rightPanel.fastQInfoSelection.PSGCC != false ? "<th>Per Sequence GC Content</th>" : ""}
-                        ${rightPanel.fastQInfoSelection.SDL != false ? "<th>Sequence Duplication Levelsias</th>" : ""}
+                        ${rightPanel.fastQInfoSelection.SDL != false ? "<th>Sequence Duplication Levels</th>" : ""}
                         ${rightPanel.fastQInfoSelection.ORS != false ? "<th>Over Represented Sequences</th>" : ""}
                     </tr>
             `;

src/req/renderer/OutputRenderer/rightPanel.ts

@@ -16,16 +16,16 @@ export class FastQInfoSelection
     [index : string] : boolean;
     public constructor()
     {
-        this.alias = false;
+        this.alias = true;
         this.fullName = false;
         this.sizeInBytes = false;
-        this.formattedSize = false;
+        this.formattedSize = true;
         this.numberOfSequences = false;
-        this.PBSQ = false;
-        this.PSQS = false;
-        this.PSGCC = false;
-        this.SDL = false;
-        this.ORS = false;
+        this.PBSQ = true;
+        this.PSQS = true;
+        this.PSGCC = true;
+        this.SDL = true;
+        this.ORS = true;
     }
 
 }
@@ -53,19 +53,19 @@ export class AlignmentInfoSelection
     [index : string] : boolean;
     public constructor()
     {
-        this.alias = false;
+        this.alias = true;
         this.fullName = false;
         this.sizeInBytes = false;
-        this.formattedSize = false;
-        this.reads = false;
-        this.mates = false;
-        this.overallAlignmentRate = false;
+        this.formattedSize = true;
+        this.reads = true;
+        this.mates = true;
+        this.overallAlignmentRate = true;
         this.minimumCoverage = false;
         this.minimumVariableFrequency = false;
         this.minimumAverageQuality = false;
         this.pValueThreshold = false;
-        this.SNPsPredicted = false;
-        this.indelsPredicted = false;
+        this.SNPsPredicted = true;
+        this.indelsPredicted = true;
         this.dateRan = false;
         this.SNPPositions = false;
     }
@@ -87,10 +87,10 @@ export class SNPPositionsInfoSelection
     [index : string] : boolean;
     public constructor()
     {
-        this.chrom = false;
-        this.position = false;
-        this.ref = false;
-        this.var = false;
+        this.chrom = true;
+        this.position = true;
+        this.ref = true;
+        this.var = true;
         this.consCovReads1Reads2FreqPValue = false;
         this.strandFilterR1R1R2R2pVal = false;
         this.samplesRef = false;
@@ -101,19 +101,37 @@ export class SNPPositionsInfoSelection
     }
 }
 
+export class MappedReadsPerContigInfoSelection
+{
+    public refSeqName : boolean;
+    public seqLength : boolean;
+    public mappedReads : boolean;
+    public unMappedReads : boolean;
+    [index : string] : boolean;
+    public constructor()
+    {
+        this.refSeqName = true;
+        this.seqLength = true;
+        this.mappedReads = true;
+        this.unMappedReads = true;
+    }
+}
+
 export class View extends viewMgr.View
 {
     public fastQInfoSelection : FastQInfoSelection;
     public refSeqInfoSelection : FastaInfoSelection;
     public alignmentInfoSelection : AlignmentInfoSelection;
     public snpPositionsInfoSelection : SNPPositionsInfoSelection;
+    public mapppedReadsPerContigInfoSelection : MappedReadsPerContigInfoSelection;
     public constructor(name : string,div : string)
     {
         super(name,div);
         this.fastQInfoSelection = new FastQInfoSelection();
         this.refSeqInfoSelection = new FastaInfoSelection();
         this.alignmentInfoSelection = new AlignmentInfoSelection();
         this.snpPositionsInfoSelection = new SNPPositionsInfoSelection();
+        this.mapppedReadsPerContigInfoSelection = new MappedReadsPerContigInfoSelection();
     }
 
     public onMount() : void{}
@@ -268,6 +286,36 @@ export class View extends viewMgr.View
                         <br />
                     `;
                 }
+                if(masterView.displayInfo == "MappedReadsPerContigInfo")
+                {
+                    res += `
+                        <input type="checkbox" id="refSeqName">Contig Name</input>
+                        <br />
+
+                        <input type="checkbox" id="seqLength">Length</input>
+                        <br />
+
+                        <input type="checkbox" id="mappedReads">Mapped Reads</input>
+                        <br />
+
+                        <input type="checkbox" id="unMappedReads">Unmapped Reads</input>
+                        <br />
+                    `;
+                    let found = false;
+                    for(let i = 0; i != masterView.alignData.length; ++i)
+                    {
+                        if(masterView.inspectingUUID == masterView.alignData[i].uuid)
+                        {
+                            res += `
+                                <h5>Mapped reads per contig for ${masterView.alignData[i].alias}</h5>
+                            `;
+                            found = true;
+                            break;
+                        }
+                    }
+                    if(!found)
+                        throw new Error("No alignment to inspect");
+                }
 
                 return res;
             })()}
@@ -277,7 +325,6 @@ export class View extends viewMgr.View
     public postRender() : void
     {
         let masterView = <masterView.View>viewMgr.getViewByName("masterView");
-        console.log("post render");
         try
         {
             if(masterView.displayInfo == "QCInfo")
@@ -333,7 +380,20 @@ export class View extends viewMgr.View
                         try
                         {
                             (<HTMLInputElement>document.getElementById(i)).checked = this.snpPositionsInfoSelection[i];
-                            console.log("restored "+i+" to "+this.snpPositionsInfoSelection[i]);
+                        }
+                        catch(err){}
+                    }
+                }
+            }
+            if(masterView.displayInfo == "MappedReadsPerContigInfo")
+            {
+                for(let i in this.mapppedReadsPerContigInfoSelection)
+                {
+                    if(this.mapppedReadsPerContigInfoSelection.hasOwnProperty(i))
+                    {
+                        try
+                        {
+                            (<HTMLInputElement>document.getElementById(i)).checked = this.mapppedReadsPerContigInfoSelection[i];
                         }
                         catch(err){}
                     }
@@ -382,6 +442,12 @@ export class View extends viewMgr.View
                 viewMgr.render();
                 return;
             }
+            else if(masterView.displayInfo == "MappedReadsPerContigInfo")
+            {
+                this.mapppedReadsPerContigInfoSelection[event.target.id] = checked;
+                viewMgr.render();
+                return;
+            }
         }
     }
 }