updated max likelihood genotyper / placer module names

giffordlabcvr · Jan 8, 2020 · 14e5669 · 14e5669
1 parent 4c44986
commit 14e5669
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Showing 4 changed files with 9 additions and 9 deletions.
diff --git a/modules/phdrReportingController.js b/modules/phdrReportingController.js
@@ -1437,7 +1437,7 @@ function genotypeFasta(fastaMap, resultMap, placerResultContainer) {
 
 		// run the placer and generate a placer result document
 		var placerResultDocument;
-		glue.inMode("module/maxLikelihoodPlacer", function() {
+		glue.inMode("module/hcvMaxLikelihoodPlacer", function() {
 			placerResultDocument = glue.command({
 				"place": {
 					"fasta-document": {
@@ -1455,7 +1455,7 @@ function genotypeFasta(fastaMap, resultMap, placerResultContainer) {
 
 		// list the query summaries within the placer result document
 		var placementSummaries;
-		glue.inMode("module/maxLikelihoodPlacer", function() {
+		glue.inMode("module/hcvMaxLikelihoodPlacer", function() {
 			placementSummaries = glue.tableToObjects(glue.command({
 				"list": {
 					"query-from-document": {
@@ -1472,7 +1472,7 @@ function genotypeFasta(fastaMap, resultMap, placerResultContainer) {
 			var placements;
 
 			// list the placements for that query.
-			glue.inMode("module/maxLikelihoodPlacer", function() {
+			glue.inMode("module/hcvMaxLikelihoodPlacer", function() {
 				placements = glue.tableToObjects(glue.command({
 					"list": {
 						"placement-from-document": {
@@ -1491,7 +1491,7 @@ function genotypeFasta(fastaMap, resultMap, placerResultContainer) {
 
 
 		var genotypingResults;
-		glue.inMode("module/maxLikelihoodGenotyper", function() {
+		glue.inMode("module/hcvMaxLikelihoodGenotyper", function() {
 			genotypingResults = glue.command({
 				"genotype": {
 					"placer-result-document": {

diff --git a/modules/phdrSamReporter.xml b/modules/phdrSamReporter.xml
@@ -2,7 +2,7 @@
 <samReporter>
     <alignerModuleName>hcvCompoundAligner</alignerModuleName>
     <readLogInterval>30000</readLogInterval>
-    <maxLikelihoodPlacerModuleName>maxLikelihoodPlacer</maxLikelihoodPlacerModuleName>
+    <maxLikelihoodPlacerModuleName>hcvMaxLikelihoodPlacer</maxLikelihoodPlacerModuleName>
     <samReaderValidationStringency>SILENT</samReaderValidationStringency>
     <consensusAmbiguityMinReads>2</consensusAmbiguityMinReads>
     <consensusAmbiguityMinProportion>0.10</consensusAmbiguityMinProportion>

diff --git a/modules/phdrSvgPhyloVisualisation.js b/modules/phdrSvgPhyloVisualisation.js
@@ -60,7 +60,7 @@ function visualisePhyloAsSvg(document) {
 	var placerResult = document.inputDocument.placerResult;
 
 	// generate a tree for the placement, as a command document.
-	glue.inMode("module/maxLikelihoodPlacer", function() {
+	glue.inMode("module/hcvMaxLikelihoodPlacer", function() {
 		glueTree = glue.command({
 				"export": {
 					"placement-from-document": {
@@ -77,7 +77,7 @@ function visualisePhyloAsSvg(document) {
 
 	var neighbourObjs;
 
-	glue.inMode("module/maxLikelihoodPlacer", function() {
+	glue.inMode("module/hcvMaxLikelihoodPlacer", function() {
 		neighbourObjs = glue.tableToObjects(glue.command({
 				"list": {
 					"neighbour-from-document": {

diff --git a/testTreeVisualisation.js b/testTreeVisualisation.js
@@ -42,7 +42,7 @@ var minNeighboursToShow = 15;
 
 
 // generate a tree for the placement, as a command document.
-glue.inMode("module/maxLikelihoodPlacer", function() {
+glue.inMode("module/hcvMaxLikelihoodPlacer", function() {
 	glueTree = glue.command({
 			"export": {
 				"placement-from-document": {
@@ -59,7 +59,7 @@ glue.inMode("module/maxLikelihoodPlacer", function() {
 
 var neighbourObjs;
 
-glue.inMode("module/maxLikelihoodPlacer", function() {
+glue.inMode("module/hcvMaxLikelihoodPlacer", function() {
 	neighbourObjs = glue.tableToObjects(glue.command({
 			"list": {
 				"neighbour-from-document": {