Merge pull request #886 from chgibb/stable-staging

Promote 0.11.0-beta.1 to Stable
chgibb · Aug 6, 2019 · d525fcc · d525fcc
2 parents 57cd2dd + 1213c8b
commit d525fcc
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Showing 10 changed files with 58 additions and 15 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -12,6 +12,7 @@ addons:
     - fakeroot
     - gtk2.0
     - rpm
+    - libgconf-2-4
 before_install:
 - npm install -g greenkeeper-lockfile
 install:

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
     "name": "phat",
-    "version": "0.10.1",
+    "version": "0.11.0-beta.1",
     "description": "Pathogen Host Analysis Tool",
     "main": "main.js",
     "scripts": {

diff --git a/scripts/tsBundleRelease.bash b/scripts/tsBundleRelease.bash
@@ -33,7 +33,7 @@ fi
 mv $1.tmp $1
 
 if [ "$1" != "src/PileupRenderer.js" ]; then
-    ./node_modules/uglify-es/bin/uglifyjs --compress -- $1 > $1.tmp
+    ./node_modules/uglify-es/bin/uglifyjs --compress inline=false,reduce_vars=0,reduce_funcs=0 -- $1 > $1.tmp
     if [ $? != 0 ]; then
         rm $1.tmp
         exit $?

diff --git a/src/RenderCoverageTrackProcess.ts b/src/RenderCoverageTrackProcess.ts
@@ -9,6 +9,7 @@ let contiguuid : string;
 let circularFigure : cf.CircularFigure;
 let colour : string;
 let scaleFactor : number;
+let log10Scale : boolean;
 
 let flags : CompletionFlags = new CompletionFlags();
 process.on
@@ -22,13 +23,14 @@ process.on
             circularFigure = ev.data.circularFigure;
             colour = ev.data.colour;
             scaleFactor = ev.data.scaleFactor;
+            log10Scale = ev.data.log10Scale;
             process.send(<AtomicOperationForkEvent>{finishedSettingData : true});
             return;
         }
 
         if(ev.run == true)
         {
-            await cf.cacheCoverageTrackTemplate(circularFigure,contiguuid,align,colour,scaleFactor);
+            await cf.cacheCoverageTrackTemplate(circularFigure,contiguuid,align,colour,scaleFactor,log10Scale);
             let trackRecord : cf.RenderedCoverageTrackRecord = circularFigure.renderedCoverageTracks[circularFigure.renderedCoverageTracks.length - 1];
             let map : cf.CoverageTrackMap = await buildCoverageTrackMap(trackRecord,circularFigure);
             cf.cacheCoverageTrackPB(trackRecord,map);

diff --git a/src/req/atomicOperationsIPC.ts b/src/req/atomicOperationsIPC.ts
@@ -48,6 +48,7 @@ export interface AtomicOperationIPC
     figure? : CircularFigure;
 
     scaleFactor? : number;
+    log10Scale? : boolean;
 
     toDock? : string;
     dockTarget? : string;

diff --git a/src/req/main/main.ts b/src/req/main/main.ts
@@ -356,7 +356,8 @@ ipc.on(
 						contiguuid : arg.uuid,
 						alignData : alignData,
 						colour : arg.colour,
-						scaleFactor : arg.scaleFactor
+						scaleFactor : arg.scaleFactor,
+						log10Scale : arg.log10Scale
 					}
 				);
 			}

diff --git a/src/req/operations/RenderCoverageTrack.ts b/src/req/operations/RenderCoverageTrack.ts
@@ -13,6 +13,7 @@ export class RenderCoverageTrackForContig extends atomic.AtomicOperation
     public circularFigure : cf.CircularFigure;
     public colour : string;
     public scaleFactor : number;
+    public log10Scale : boolean;
     public renderCoverageTrackProcess : cp.ChildProcess;
     constructor()
     {
@@ -23,27 +24,33 @@ export class RenderCoverageTrackForContig extends atomic.AtomicOperation
         contiguuid : string,
         alignData : AlignData,
         colour : string,
-        scaleFactor : number
+        scaleFactor : number,
+        log10Scale : boolean
     }) : void
     {
         this.circularFigure = data.circularFigure;
         this.contiguuid = data.contiguuid;
         this.alignData = data.alignData;
         this.colour = data.colour;
         this.scaleFactor = data.scaleFactor;
+        this.log10Scale = data.log10Scale;
     }
     public run() : void
     {
         this.logRecord = atomic.openLog(this.name,"Render Coverage Track");
         let self = this;
+
+        atomic.logString(this.logRecord,JSON.stringify(this,undefined,4));
+
         this.renderCoverageTrackProcess = atomic.makeFork("RenderCoverageTrack.js",<AtomicOperationForkEvent>{
             setData : true,
             data : {
                 alignData : self.alignData,
                 contiguuid : self.contiguuid,
                 circularFigure : self.circularFigure,
                 colour : self.colour,
-                scaleFactor : self.scaleFactor
+                scaleFactor : self.scaleFactor,
+                log10Scale : self.log10Scale
             }
         },function(ev : AtomicOperationForkEvent){
             if(ev.finishedSettingData == true)

diff --git a/src/req/operations/RunAlignment/samToolsDepth.ts b/src/req/operations/RunAlignment/samToolsDepth.ts
@@ -41,13 +41,19 @@ export function samToolsDepth(alignData: AlignData,logger : atomic.AtomicOperati
                     {
                         if(params.retCode == 0)
                         {
+                            atomic.logString(logger.logRecord,`Finished samtools`);
                             setTimeout(
                                 function(){
                                     samToolsCoverageFileStream.end();
+                                    atomic.logString(logger.logRecord,`Starting distillation`);
                                     let rl : readline.ReadLine = readline.createInterface(<readline.ReadLineOptions>{
                                         input : fs.createReadStream(getCoverage(alignData))
                                     });
+
+                                    atomic.logString(logger.logRecord,`Path is ${getCoverage(alignData)}`);
                                     rl.on("line",function(line){
+                                        atomic.logString(logger.logRecord,`Got a line`);
+
                                         //distill output from samtools depth into individual contig coverage files identified by uuid and without the contig name.
                                         let coverageTokens = line.split(/\s/g);
                                         for(let i = 0; i != alignData.fasta.contigs.length; ++i)
@@ -57,14 +63,22 @@ export function samToolsDepth(alignData: AlignData,logger : atomic.AtomicOperati
                                             {
                                                 if(coverageTokens[k] == contigTokens[0])
                                                 {
+
                                                     fs.appendFileSync(getCoverageForContig(alignData,alignData.fasta.contigs[i].uuid),`${coverageTokens[k+1]} ${coverageTokens[k+2]}\n`);
                                                 }
                                             }
                                         }
                                     });
+
                                     rl.on("close",function(){
+                                        atomic.logString(logger.logRecord,`Distillation closed`);
                                         resolve();
                                     });
+
+                                    rl.on("error",function(err){
+                                        atomic.logString(logger.logRecord,`Distillation threw error ${err}`);
+                                        reject(err);
+                                    });
                                 },500
                             );
                         }

diff --git a/src/req/renderer/circularFigure.ts b/src/req/renderer/circularFigure.ts
@@ -142,16 +142,19 @@ export class RenderedTrackRecord
  */
 export class RenderedCoverageTrackRecord extends RenderedTrackRecord
 {
-    scaleFactor : number;
+    public scaleFactor : number;
+    public log10Scaled : boolean;
     public constructor(
         uuidAlign : string,
         uuidContig : string,
         uuidFigure : string,
         colour : string,
-        scaleFactor : number)
+        scaleFactor : number,
+        log10Scaled : boolean)
     {
         super(uuidAlign,uuidContig,uuidFigure,colour);
         this.scaleFactor = scaleFactor;
+        this.log10Scaled = log10Scaled;
     }
 }
 
@@ -669,7 +672,8 @@ export async function buildCoverageTrackTemplate(
     contiguuid : string,
     align : AlignData,
     colour : string = "rgb(64,64,64)",
-    scaleFactor : number = 1
+    scaleFactor : number = 1,
+    log10Scale : boolean = false
 ) : Promise<string>
 {
     return new Promise<string>((resolve,reject) => {
@@ -691,6 +695,10 @@ export async function buildCoverageTrackTemplate(
         rl.on("line",function(line : string){
             let tokens = line.split(/\s/g);
             let depth = parseInt(tokens[1]);
+
+            if(log10Scale)
+                depth = Math.log10(depth);
+
             let found = false;
             for(let i = 0; i != depths.length; ++i)
             {
@@ -766,7 +774,8 @@ export async function cacheCoverageTrackTemplate(
     contiguuid : string,
     align : AlignData,
     colour : string = "rgb(64,64,64)",
-    scaleFactor : number = 1
+    scaleFactor : number = 1,
+    log10Scale : boolean = false
 ) : Promise<void>
 {
     return new Promise<void>(async (resolve,reject) => {
@@ -776,8 +785,8 @@ export async function cacheCoverageTrackTemplate(
         }
         catch(err){}
 
-        let coverageTracks = await buildCoverageTrackTemplate(figure,contiguuid,align,colour,scaleFactor);
-        let trackRecord = new RenderedCoverageTrackRecord(align.uuid,contiguuid,figure.uuid,colour,scaleFactor);
+        let coverageTracks = await buildCoverageTrackTemplate(figure,contiguuid,align,colour,scaleFactor,log10Scale);
+        let trackRecord = new RenderedCoverageTrackRecord(align.uuid,contiguuid,figure.uuid,colour,scaleFactor,log10Scale);
         fs.writeFileSync(getCachedCoverageTrackTemplatePath(trackRecord),coverageTracks);
         figure.renderedCoverageTracks.push(trackRecord);
         resolve();

diff --git a/src/req/renderer/circularGenomeBuilderRenderer/writeAvailableTracksModal.ts b/src/req/renderer/circularGenomeBuilderRenderer/writeAvailableTracksModal.ts
@@ -56,7 +56,7 @@ export function writeAvailableTracksModal() : void
                 if(genomeView.genome.renderedCoverageTracks[i].uuidContig == selectedAlign.fasta.contigs[j].uuid)
                 {
                     body += `
-                    <b>Scaled by ${genomeView.genome.renderedCoverageTracks[i].scaleFactor}</b><p id="${genomeView.genome.renderedCoverageTracks[i].uuid}Available" class="activeHover" style="color:${genomeView.genome.renderedCoverageTracks[i].colour}">${selectedAlign.fasta.contigs[j].name}</p>
+                    <b>${genomeView.genome.renderedCoverageTracks[i].log10Scaled ? "Log10 scaled, " : ""}Scaled by ${genomeView.genome.renderedCoverageTracks[i].scaleFactor}</b><p id="${genomeView.genome.renderedCoverageTracks[i].uuid}Available" class="activeHover" style="color:${genomeView.genome.renderedCoverageTracks[i].colour}">${selectedAlign.fasta.contigs[j].name}</p>
                     `;
                     foundTrack = true;
                 }
@@ -103,6 +103,10 @@ export function writeAvailableTracksModal() : void
         <input type="text" id="colourPicker" data-format="rgb" value="rgb(0, 0, 0)">
         <br />
         <br />
+        <div>
+            <input type="checkbox" name="log10scalecheckbox" id="log10scale">
+            <label for="log10scalecheckbox">Log10 Scale Before Applying Depth Scale</label>
+        </div>
         <p>Coverage Depth Scale</p>
         <input type="number" step="0.1" min="0" value="1" id="scaleFactor">
         <br />
@@ -210,7 +214,8 @@ export function writeAvailableTracksModal() : void
                         alignuuid : selectedAlign.uuid,
                         uuid : genomeView.genome.contigs[i].uuid,
                         colour : (<string>(<any>$(document.getElementById("colourPicker"))).minicolors("rgbString")),
-                        scaleFactor : parseFloat((<HTMLInputElement>document.getElementById("scaleFactor")).value)
+                        scaleFactor : parseFloat((<HTMLInputElement>document.getElementById("scaleFactor")).value),
+                        log10Scale : (<HTMLInputElement>document.getElementById("log10scale")).checked
                     }
                 );
             }
@@ -228,7 +233,10 @@ export function writeAvailableTracksModal() : void
                 );
             }
         }
-        catch(err){}
+        catch(err)
+        {
+            console.log(err);
+        }
     }
     for(let i = 0; i != genomeView.genome.renderedCoverageTracks.length; ++i)
     {