Cobalt renamed

count-bam-lines/README.md → cobalt/README.md

@@ -47,7 +47,7 @@ After installing [R](https://www.r-project.org/) or [RStudio](https://rstudio.co
 COBALT requires Java 1.8+ and can be run with the minimum set of arguments as follows:
 
 ```
-java -cp -Xmx8G cobalt.jar com.hartwig.hmftools.cobalt.CountBamLinesApplication \
+java -cp -Xmx8G cobalt.jar com.hartwig.hmftools.cobalt.CobaltApplication \
     -reference COLO829R -reference_bam /run_dir/COLO829R.bam \ 
     -tumor COLO829T -tumor_bam /run_dir/COLO829T.bam \ 
     -output_dir /run_dir/cobalt \ 

count-bam-lines/pom.xml → cobalt/pom.xml

@@ -8,7 +8,7 @@
         <version>local-SNAPSHOT</version>
     </parent>
 
-    <artifactId>count-bam-lines</artifactId>
+    <artifactId>cobalt</artifactId>
     <packaging>jar</packaging>
     <version>${cobalt.version}</version>
     <name>HMF Tools - COBALT</name>
@@ -54,7 +54,7 @@
                     <archive>
                         <manifest>
                             <addClasspath>true</addClasspath>
-                            <mainClass>com.hartwig.hmftools.cobalt.CountBamLinesApplication
+                            <mainClass>com.hartwig.hmftools.cobalt.CobaltApplication
                             </mainClass>
                         </manifest>
                     </archive>

count-bam-lines/src/main/java/com/hartwig/hmftools/cobalt/CountBamLinesApplication.java → cobalt/src/main/java/com/hartwig/hmftools/cobalt/CobaltApplication.java

@@ -40,17 +40,17 @@
 import htsjdk.tribble.bed.BEDFeature;
 import htsjdk.tribble.readers.LineIterator;
 
-public class CountBamLinesApplication implements AutoCloseable {
+public class CobaltApplication implements AutoCloseable {
 
-    private static final Logger LOGGER = LogManager.getLogger(CountBamLinesApplication.class);
+    private static final Logger LOGGER = LogManager.getLogger(CobaltApplication.class);
 
     private final CobaltConfig config;
     private final VersionInfo versionInfo;
     private final ExecutorService executorService;
 
     public static void main(final String... args) throws IOException, ExecutionException, InterruptedException {
         final Options options = CobaltConfig.createOptions();
-        try (final CountBamLinesApplication application = new CountBamLinesApplication(options, args)) {
+        try (final CobaltApplication application = new CobaltApplication(options, args)) {
             application.run();
         } catch (ParseException e) {
             LOGGER.warn(e);
@@ -60,7 +60,7 @@ public static void main(final String... args) throws IOException, ExecutionExcep
         }
     }
 
-    private CountBamLinesApplication(final Options options, final String... args) throws ParseException, IOException {
+    private CobaltApplication(final Options options, final String... args) throws ParseException, IOException {
         versionInfo = new VersionInfo("cobalt.version");
         LOGGER.info("COBALT version: {}", versionInfo.version());
 

count-bam-lines/src/main/java/com/hartwig/hmftools/cobalt/count/CountSupplier.java → cobalt/src/main/java/com/hartwig/hmftools/cobalt/count/CountSupplier.java

@@ -11,7 +11,7 @@
 import com.google.common.collect.ListMultimap;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Multimap;
-import com.hartwig.hmftools.cobalt.CountBamLinesApplication;
+import com.hartwig.hmftools.cobalt.CobaltApplication;
 import com.hartwig.hmftools.common.cobalt.CobaltCount;
 import com.hartwig.hmftools.common.cobalt.CobaltCountFactory;
 import com.hartwig.hmftools.common.cobalt.ReadCount;
@@ -29,7 +29,7 @@
 
 public class CountSupplier {
 
-    private static final Logger LOGGER = LogManager.getLogger(CountBamLinesApplication.class);
+    private static final Logger LOGGER = LogManager.getLogger(CobaltApplication.class);
 
     private final String tumor;
     private final String outputDirectory;

pom.xml

@@ -21,7 +21,7 @@
         <module>fastq-stats</module>
         <module>compar</module>
         <module>amber</module>
-        <module>count-bam-lines</module>
+        <module>cobalt</module>
         <module>purple</module>
         <module>sage</module>
         <module>bachelor</module>
@@ -60,7 +60,7 @@
         <id-generator.version>2.7</id-generator.version>
         <sage.version>2.8</sage.version>
         <amber.version>3.5</amber.version>
-        <cobalt.version>1.11</cobalt.version>
+        <cobalt.version>1.12</cobalt.version>
         <purple.version>3.0</purple.version>
         <bachelor.version>1.12</bachelor.version>
         <gripss.version>1.11</gripss.version>