diff --git a/README.md b/README.md index 8ab793c..d1b1507 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ These parameters are optional and may be omitted using the default values: | parameter | description | default value | |-------| ----------- |-----| -| *enableClustering* | Group together calls with same chromosome values and similar breakpoint values | `true` | +| *enableGrouping* | Group together calls with same chromosome values and similar breakpoint values | `true` | | *breakpointTolerance* | If grouping is enabled, this is the maximum distance where two breakpoints are considered similar. | `3` | | *csvDelimiter* | Character that delimits csv columns. | `";"` | | *collectionDelimiter* | A single cell in a csv table may have multiple values. These values are seperated by this character. |`","` | diff --git a/src/main/java/de/imi/marw/viper/api/ViperServerConfig.java b/src/main/java/de/imi/marw/viper/api/ViperServerConfig.java index 5474944..f323f0c 100644 --- a/src/main/java/de/imi/marw/viper/api/ViperServerConfig.java +++ b/src/main/java/de/imi/marw/viper/api/ViperServerConfig.java @@ -29,7 +29,7 @@ public class ViperServerConfig { private int igvPort = 9090; private char csvDelimiter = ';'; private String collectionDelimiter = ","; - private boolean enableClustering = true; + private boolean enableGrouping = true; private int breakpointTolerance = 3; private String workDir = "/tmp/viper"; private String fastaRef = "hg19"; @@ -201,16 +201,16 @@ public void setIgvMaxMemory(int igvMaxMemory) { } public boolean isClusteringEnabled() { - return enableClustering; + return enableGrouping; } - public void setEnableClustering(boolean enableClustering) { - this.enableClustering = enableClustering; + public void setEnableGrouping(boolean enableGrouping) { + this.enableGrouping = enableGrouping; } @Override public String toString() { - return "ViperServerConfig{" + "analysisFile=" + analysisFile + ", viperPort=" + viperPort + ", igvPort=" + igvPort + ", csvDelimiter=" + csvDelimiter + ", collectionDelimiter=" + collectionDelimiter + ", enableClustering=" + enableClustering + ", breakpointTolerance=" + breakpointTolerance + ", workDir=" + workDir + ", fastaRef=" + fastaRef + ", igvJar=" + igvJar + ", bamDir=" + bamDir + ", keepVcfSimple=" + keepVcfSimple + ", excludeRefVcfCalls=" + excludeRefVcfCalls + ", numPrecomputedSnapshots=" + numPrecomputedSnapshots + ", xslxExportWindowSize=" + xslxExportWindowSize + ", viewRange=" + viewRange + ", xvfbDisplay=" + xvfbDisplay + ", xvfbWidth=" + xvfbWidth + ", xvfbHeight=" + xvfbHeight + ", igvMaxMemory=" + igvMaxMemory + '}'; + return "ViperServerConfig{" + "analysisFile=" + analysisFile + ", viperPort=" + viperPort + ", igvPort=" + igvPort + ", csvDelimiter=" + csvDelimiter + ", collectionDelimiter=" + collectionDelimiter + ", enableClustering=" + enableGrouping + ", breakpointTolerance=" + breakpointTolerance + ", workDir=" + workDir + ", fastaRef=" + fastaRef + ", igvJar=" + igvJar + ", bamDir=" + bamDir + ", keepVcfSimple=" + keepVcfSimple + ", excludeRefVcfCalls=" + excludeRefVcfCalls + ", numPrecomputedSnapshots=" + numPrecomputedSnapshots + ", xslxExportWindowSize=" + xslxExportWindowSize + ", viewRange=" + viewRange + ", xvfbDisplay=" + xvfbDisplay + ", xvfbWidth=" + xvfbWidth + ", xvfbHeight=" + xvfbHeight + ", igvMaxMemory=" + igvMaxMemory + '}'; } }