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jslfree080 · Feb 7, 2023 · c64a6a2 · c64a6a2
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diff --git a/.gradle/7.5.1/executionHistory/executionHistory.bin b/.gradle/7.5.1/executionHistory/executionHistory.bin
diff --git a/.gradle/7.5.1/executionHistory/executionHistory.lock b/.gradle/7.5.1/executionHistory/executionHistory.lock
diff --git a/.gradle/7.5.1/fileHashes/fileHashes.bin b/.gradle/7.5.1/fileHashes/fileHashes.bin
diff --git a/.gradle/7.5.1/fileHashes/fileHashes.lock b/.gradle/7.5.1/fileHashes/fileHashes.lock
diff --git a/.gradle/7.5.1/fileHashes/resourceHashesCache.bin b/.gradle/7.5.1/fileHashes/resourceHashesCache.bin
diff --git a/.gradle/buildOutputCleanup/buildOutputCleanup.lock b/.gradle/buildOutputCleanup/buildOutputCleanup.lock
diff --git a/.gradle/buildOutputCleanup/outputFiles.bin b/.gradle/buildOutputCleanup/outputFiles.bin
diff --git a/.gradle/file-system.probe b/.gradle/file-system.probe
diff --git a/README.md b/README.md
@@ -1,5 +1,56 @@
 # bamscope
-<img
-  src="example.png"
-  alt="Alt text"
-  style="display: inline-block; margin: 0 auto; max-width: 300px">
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/jslfree080/bamscope/blob/main/LICENSE)
+
+<img alt="demonstration" src="https://github.com/jslfree080/jslfree080/blob/main/example2.png" width=550>
+
+A command line tool (in Kotlin/JVM) for visualizing BAM alignments.
+
+## Prerequisites
+
+Bamscope requires **Java 11** or later versions to build and run.
+
+Also, [samtools](https://github.com/samtools/samtools) should be pre-installed to support accessing file formats such as BAM and FASTA.
+
+## Building
+
+* Clone the repo:
+```
+    git clone https://github.com/jslfree080/bamscope.git
+    cd bamscope/
+```
+
+* Build an executable Bamscope jar with all dependencies packaged:
+```
+    ./gradlew build
+```
+
+## Usage
+
+### Command line
+
+The resulting jar will be in `build/libs`.
+
+```
+Usage: java -jar build/libs/bamscope.jar <chrPos> <bamPath> [options]
+
+Parameters:
+      <chrPos>              Input chromosomal position.      ex) (chr)N:XXXXXXXX
+      <bamPath>             Path to an indexed bam file.       ex) path/to/x.bam
+     
+Options:
+  -f, --format=<format>     File format of an output image.         default) png
+  -h, --help                Show this help message and exit.
+  -o, --outPath=<outPath>   Path to an output image.                  default) .
+  -r, --refPath=<refPath>   Path to a reference fasta.       ex) path/to/x.fasta
+  -s, --sPath=<sPath>       Path to the samtools.    ex) /usr/local/bin/samtools
+  -w, --width=<width>       Width of start to interest position.     default) 50
+```
+
+* Example usage:
+```
+    java -jar build/libs/bamscope.jar 18:53254446 ~/Downloads/x.bam -r ~/Downloads/x.fasta -o ~/Desktop/
+```
+
+## License
+
+Code and documentation released under the [MIT license](https://github.com/jslfree080/bamscope/blob/master/LICENSE).
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -73,6 +73,7 @@ tasks.withType<Jar> {
     // Otherwise you'll get a "No main manifest attribute" error
     manifest {
         attributes["Main-Class"] = "com.jslfree080.bamscope.RunBAMScopeKt"
+        archiveFileName.set("bamscope.jar")
     }
 
     // To avoid the duplicate handling strategy error
@@ -88,4 +89,4 @@ tasks.withType<Jar> {
 }
 
 // ./gradlew build |or| ./gradlew clean build (Delete all the previous version of the dependencies)
-// java -jar build/libs/bamscope*.jar 18:53253385 ~/Downloads/*.bam -r ~/Downloads/human_g1k_v37_decoy.fasta -o ~/Desktop/
+// java -jar build/libs/bamscope.jar 18:53253385 ~/Downloads/*.bam -r ~/Downloads/human_g1k_v37_decoy.fasta -o ~/Desktop/
diff --git a/build/classes/kotlin/main/com/jslfree080/cli/BAMScopeCommand.class b/build/classes/kotlin/main/com/jslfree080/cli/BAMScopeCommand.class
diff --git a/build/distributions/bamscope-1.0.0.tar b/build/distributions/bamscope-1.0.0.tar
diff --git a/build/distributions/bamscope-1.0.0.zip b/build/distributions/bamscope-1.0.0.zip
diff --git a/build/kotlin/bamscope100jar-classes.txt → build/kotlin/bamscopejar-classes.txt b/build/kotlin/bamscope100jar-classes.txt → build/kotlin/bamscopejar-classes.txt
diff --git a/build/kotlin/compileKotlin/cacheable/last-build.bin b/build/kotlin/compileKotlin/cacheable/last-build.bin
diff --git a/build/kotlin/compileKotlin/local-state/build-history.bin b/build/kotlin/compileKotlin/local-state/build-history.bin
diff --git a/build/kotlin/compileTestKotlin/cacheable/last-build.bin b/build/kotlin/compileTestKotlin/cacheable/last-build.bin
diff --git a/build/kotlin/compileTestKotlin/local-state/build-history.bin b/build/kotlin/compileTestKotlin/local-state/build-history.bin
diff --git a/build/kotlin/kaptGenerateStubsKotlin/cacheable/last-build.bin b/build/kotlin/kaptGenerateStubsKotlin/cacheable/last-build.bin
diff --git a/build/kotlin/kaptGenerateStubsKotlin/local-state/build-history.bin b/build/kotlin/kaptGenerateStubsKotlin/local-state/build-history.bin
diff --git a/build/kotlin/kaptGenerateStubsTestKotlin/cacheable/last-build.bin b/build/kotlin/kaptGenerateStubsTestKotlin/cacheable/last-build.bin
diff --git a/build/kotlin/kaptGenerateStubsTestKotlin/local-state/build-history.bin b/build/kotlin/kaptGenerateStubsTestKotlin/local-state/build-history.bin
diff --git a/build/libs/bamscope-1.0.0.jar → build/libs/bamscope.jar b/build/libs/bamscope-1.0.0.jar → build/libs/bamscope.jar
diff --git a/build/reports/tests/test/classes/com.jslfree080.process.CheckWidthAgainTest.html b/build/reports/tests/test/classes/com.jslfree080.process.CheckWidthAgainTest.html
@@ -41,7 +41,7 @@ <h1>CheckWidthAgainTest</h1>
 </td>
 <td>
 <div class="infoBox" id="duration">
-<div class="counter">0.029s</div>
+<div class="counter">0.025s</div>
 <p>duration</p>
 </div>
 </td>
@@ -76,7 +76,7 @@ <h2>Tests</h2>
 </thead>
 <tr>
 <td class="success">testExpDecayResult()</td>
-<td class="success">0.029s</td>
+<td class="success">0.025s</td>
 <td class="success">passed</td>
 </tr>
 </table>
@@ -89,7 +89,7 @@ <h2>Tests</h2>
 <input id="line-wrapping-toggle" type="checkbox" autocomplete="off"/>
 </label>
 </div>Generated by 
-<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 6. 오후 7:13:54</p>
+<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 7. 오전 11:57:56</p>
 </div>
 </div>
 </body>

diff --git a/build/reports/tests/test/classes/com.jslfree080.process.CheckWidthFirstTest.html b/build/reports/tests/test/classes/com.jslfree080.process.CheckWidthFirstTest.html
@@ -41,7 +41,7 @@ <h1>CheckWidthFirstTest</h1>
 </td>
 <td>
 <div class="infoBox" id="duration">
-<div class="counter">0.002s</div>
+<div class="counter">0.001s</div>
 <p>duration</p>
 </div>
 </td>
@@ -76,7 +76,7 @@ <h2>Tests</h2>
 </thead>
 <tr>
 <td class="success">testFixedResult()</td>
-<td class="success">0.002s</td>
+<td class="success">0.001s</td>
 <td class="success">passed</td>
 </tr>
 </table>
@@ -89,7 +89,7 @@ <h2>Tests</h2>
 <input id="line-wrapping-toggle" type="checkbox" autocomplete="off"/>
 </label>
 </div>Generated by 
-<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 6. 오후 7:13:54</p>
+<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 7. 오전 11:57:56</p>
 </div>
 </div>
 </body>

diff --git a/build/reports/tests/test/index.html b/build/reports/tests/test/index.html
@@ -38,7 +38,7 @@ <h1>Test Summary</h1>
 </td>
 <td>
 <div class="infoBox" id="duration">
-<div class="counter">0.031s</div>
+<div class="counter">0.026s</div>
 <p>duration</p>
 </div>
 </td>
@@ -85,7 +85,7 @@ <h2>Packages</h2>
 <td>2</td>
 <td>0</td>
 <td>0</td>
-<td>0.031s</td>
+<td>0.026s</td>
 <td class="success">100%</td>
 </tr>
 </tbody>
@@ -112,7 +112,7 @@ <h2>Classes</h2>
 <td>1</td>
 <td>0</td>
 <td>0</td>
-<td>0.029s</td>
+<td>0.025s</td>
 <td class="success">100%</td>
 </tr>
 <tr>
@@ -122,7 +122,7 @@ <h2>Classes</h2>
 <td>1</td>
 <td>0</td>
 <td>0</td>
-<td>0.002s</td>
+<td>0.001s</td>
 <td class="success">100%</td>
 </tr>
 </tbody>
@@ -136,7 +136,7 @@ <h2>Classes</h2>
 <input id="line-wrapping-toggle" type="checkbox" autocomplete="off"/>
 </label>
 </div>Generated by 
-<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 6. 오후 7:13:54</p>
+<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 7. 오전 11:57:56</p>
 </div>
 </div>
 </body>

diff --git a/build/reports/tests/test/packages/com.jslfree080.process.html b/build/reports/tests/test/packages/com.jslfree080.process.html
@@ -40,7 +40,7 @@ <h1>Package com.jslfree080.process</h1>
 </td>
 <td>
 <div class="infoBox" id="duration">
-<div class="counter">0.031s</div>
+<div class="counter">0.026s</div>
 <p>duration</p>
 </div>
 </td>
@@ -83,7 +83,7 @@ <h2>Classes</h2>
 <td>1</td>
 <td>0</td>
 <td>0</td>
-<td>0.029s</td>
+<td>0.025s</td>
 <td class="success">100%</td>
 </tr>
 <tr>
@@ -93,7 +93,7 @@ <h2>Classes</h2>
 <td>1</td>
 <td>0</td>
 <td>0</td>
-<td>0.002s</td>
+<td>0.001s</td>
 <td class="success">100%</td>
 </tr>
 </table>
@@ -106,7 +106,7 @@ <h2>Classes</h2>
 <input id="line-wrapping-toggle" type="checkbox" autocomplete="off"/>
 </label>
 </div>Generated by 
-<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 6. 오후 7:13:54</p>
+<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 7. 오전 11:57:56</p>
 </div>
 </div>
 </body>

diff --git a/build/scripts/bamscope b/build/scripts/bamscope
@@ -114,7 +114,7 @@ case "$( uname )" in                #(
   NONSTOP* )        nonstop=true ;;
 esac
 
-CLASSPATH=$APP_HOME/lib/bamscope-1.0.0.jar:$APP_HOME/lib/lets-plot-batik-3.0.0.jar:$APP_HOME/lib/lets-plot-jfx-3.0.0.jar:$APP_HOME/lib/plot-api-jvm-4.2.0.jar:$APP_HOME/lib/lets-plot-common-3.0.0.jar:$APP_HOME/lib/kotlinx-html-jvm-0.7.3.jar:$APP_HOME/lib/plot-config-portable-jvm-3.0.0.jar:$APP_HOME/lib/plot-builder-portable-jvm-3.0.0.jar:$APP_HOME/lib/plot-base-portable-jvm-3.0.0.jar:$APP_HOME/lib/plot-common-portable-jvm-3.0.0.jar:$APP_HOME/lib/vis-svg-portable-jvm-3.0.0.jar:$APP_HOME/lib/base-portable-jvm-3.0.0.jar:$APP_HOME/lib/kotlin-stdlib-jdk8-1.8.0.jar:$APP_HOME/lib/picocli-4.7.0.jar:$APP_HOME/lib/lets-plot-image-export-3.0.0.jar:$APP_HOME/lib/slf4j-simple-2.0.6.jar:$APP_HOME/lib/kotlin-stdlib-jdk7-1.8.0.jar:$APP_HOME/lib/kotlin-logging-jvm-2.0.5.jar:$APP_HOME/lib/kotlin-stdlib-1.8.0.jar:$APP_HOME/lib/batik-codec-1.16.jar:$APP_HOME/lib/kotlin-stdlib-common-1.8.0.jar:$APP_HOME/lib/batik-transcoder-1.16.jar:$APP_HOME/lib/imageio-tiff-3.8.1.jar:$APP_HOME/lib/slf4j-api-2.0.6.jar:$APP_HOME/lib/annotations-13.0.jar:$APP_HOME/lib/batik-bridge-1.16.jar:$APP_HOME/lib/batik-script-1.16.jar:$APP_HOME/lib/batik-anim-1.16.jar:$APP_HOME/lib/batik-gvt-1.16.jar:$APP_HOME/lib/batik-svggen-1.16.jar:$APP_HOME/lib/batik-svg-dom-1.16.jar:$APP_HOME/lib/batik-parser-1.16.jar:$APP_HOME/lib/batik-awt-util-1.16.jar:$APP_HOME/lib/batik-dom-1.16.jar:$APP_HOME/lib/batik-xml-1.16.jar:$APP_HOME/lib/batik-css-1.16.jar:$APP_HOME/lib/batik-util-1.16.jar:$APP_HOME/lib/batik-constants-1.16.jar:$APP_HOME/lib/batik-i18n-1.16.jar:$APP_HOME/lib/batik-ext-1.16.jar:$APP_HOME/lib/batik-shared-resources-1.16.jar:$APP_HOME/lib/xml-apis-ext-1.3.04.jar:$APP_HOME/lib/imageio-metadata-3.8.1.jar:$APP_HOME/lib/imageio-core-3.8.1.jar:$APP_HOME/lib/common-image-3.8.1.jar:$APP_HOME/lib/common-io-3.8.1.jar:$APP_HOME/lib/common-lang-3.8.1.jar:$APP_HOME/lib/xmlgraphics-commons-2.7.jar:$APP_HOME/lib/xml-apis-1.4.01.jar:$APP_HOME/lib/commons-io-1.3.1.jar:$APP_HOME/lib/commons-logging-1.0.4.jar
+CLASSPATH=$APP_HOME/lib/bamscope.jar:$APP_HOME/lib/lets-plot-batik-3.0.0.jar:$APP_HOME/lib/lets-plot-jfx-3.0.0.jar:$APP_HOME/lib/plot-api-jvm-4.2.0.jar:$APP_HOME/lib/lets-plot-common-3.0.0.jar:$APP_HOME/lib/kotlinx-html-jvm-0.7.3.jar:$APP_HOME/lib/plot-config-portable-jvm-3.0.0.jar:$APP_HOME/lib/plot-builder-portable-jvm-3.0.0.jar:$APP_HOME/lib/plot-base-portable-jvm-3.0.0.jar:$APP_HOME/lib/plot-common-portable-jvm-3.0.0.jar:$APP_HOME/lib/vis-svg-portable-jvm-3.0.0.jar:$APP_HOME/lib/base-portable-jvm-3.0.0.jar:$APP_HOME/lib/kotlin-stdlib-jdk8-1.8.0.jar:$APP_HOME/lib/picocli-4.7.0.jar:$APP_HOME/lib/lets-plot-image-export-3.0.0.jar:$APP_HOME/lib/slf4j-simple-2.0.6.jar:$APP_HOME/lib/kotlin-stdlib-jdk7-1.8.0.jar:$APP_HOME/lib/kotlin-logging-jvm-2.0.5.jar:$APP_HOME/lib/kotlin-stdlib-1.8.0.jar:$APP_HOME/lib/batik-codec-1.16.jar:$APP_HOME/lib/kotlin-stdlib-common-1.8.0.jar:$APP_HOME/lib/batik-transcoder-1.16.jar:$APP_HOME/lib/imageio-tiff-3.8.1.jar:$APP_HOME/lib/slf4j-api-2.0.6.jar:$APP_HOME/lib/annotations-13.0.jar:$APP_HOME/lib/batik-bridge-1.16.jar:$APP_HOME/lib/batik-script-1.16.jar:$APP_HOME/lib/batik-anim-1.16.jar:$APP_HOME/lib/batik-gvt-1.16.jar:$APP_HOME/lib/batik-svggen-1.16.jar:$APP_HOME/lib/batik-svg-dom-1.16.jar:$APP_HOME/lib/batik-parser-1.16.jar:$APP_HOME/lib/batik-awt-util-1.16.jar:$APP_HOME/lib/batik-dom-1.16.jar:$APP_HOME/lib/batik-xml-1.16.jar:$APP_HOME/lib/batik-css-1.16.jar:$APP_HOME/lib/batik-util-1.16.jar:$APP_HOME/lib/batik-constants-1.16.jar:$APP_HOME/lib/batik-i18n-1.16.jar:$APP_HOME/lib/batik-ext-1.16.jar:$APP_HOME/lib/batik-shared-resources-1.16.jar:$APP_HOME/lib/xml-apis-ext-1.3.04.jar:$APP_HOME/lib/imageio-metadata-3.8.1.jar:$APP_HOME/lib/imageio-core-3.8.1.jar:$APP_HOME/lib/common-image-3.8.1.jar:$APP_HOME/lib/common-io-3.8.1.jar:$APP_HOME/lib/common-lang-3.8.1.jar:$APP_HOME/lib/xmlgraphics-commons-2.7.jar:$APP_HOME/lib/xml-apis-1.4.01.jar:$APP_HOME/lib/commons-io-1.3.1.jar:$APP_HOME/lib/commons-logging-1.0.4.jar
 
 
 # Determine the Java command to use to start the JVM.

diff --git a/build/scripts/bamscope.bat b/build/scripts/bamscope.bat
@@ -67,7 +67,7 @@ goto fail
 :execute
 @rem Setup the command line
 
-set CLASSPATH=%APP_HOME%\lib\bamscope-1.0.0.jar;%APP_HOME%\lib\lets-plot-batik-3.0.0.jar;%APP_HOME%\lib\lets-plot-jfx-3.0.0.jar;%APP_HOME%\lib\plot-api-jvm-4.2.0.jar;%APP_HOME%\lib\lets-plot-common-3.0.0.jar;%APP_HOME%\lib\kotlinx-html-jvm-0.7.3.jar;%APP_HOME%\lib\plot-config-portable-jvm-3.0.0.jar;%APP_HOME%\lib\plot-builder-portable-jvm-3.0.0.jar;%APP_HOME%\lib\plot-base-portable-jvm-3.0.0.jar;%APP_HOME%\lib\plot-common-portable-jvm-3.0.0.jar;%APP_HOME%\lib\vis-svg-portable-jvm-3.0.0.jar;%APP_HOME%\lib\base-portable-jvm-3.0.0.jar;%APP_HOME%\lib\kotlin-stdlib-jdk8-1.8.0.jar;%APP_HOME%\lib\picocli-4.7.0.jar;%APP_HOME%\lib\lets-plot-image-export-3.0.0.jar;%APP_HOME%\lib\slf4j-simple-2.0.6.jar;%APP_HOME%\lib\kotlin-stdlib-jdk7-1.8.0.jar;%APP_HOME%\lib\kotlin-logging-jvm-2.0.5.jar;%APP_HOME%\lib\kotlin-stdlib-1.8.0.jar;%APP_HOME%\lib\batik-codec-1.16.jar;%APP_HOME%\lib\kotlin-stdlib-common-1.8.0.jar;%APP_HOME%\lib\batik-transcoder-1.16.jar;%APP_HOME%\lib\imageio-tiff-3.8.1.jar;%APP_HOME%\lib\slf4j-api-2.0.6.jar;%APP_HOME%\lib\annotations-13.0.jar;%APP_HOME%\lib\batik-bridge-1.16.jar;%APP_HOME%\lib\batik-script-1.16.jar;%APP_HOME%\lib\batik-anim-1.16.jar;%APP_HOME%\lib\batik-gvt-1.16.jar;%APP_HOME%\lib\batik-svggen-1.16.jar;%APP_HOME%\lib\batik-svg-dom-1.16.jar;%APP_HOME%\lib\batik-parser-1.16.jar;%APP_HOME%\lib\batik-awt-util-1.16.jar;%APP_HOME%\lib\batik-dom-1.16.jar;%APP_HOME%\lib\batik-xml-1.16.jar;%APP_HOME%\lib\batik-css-1.16.jar;%APP_HOME%\lib\batik-util-1.16.jar;%APP_HOME%\lib\batik-constants-1.16.jar;%APP_HOME%\lib\batik-i18n-1.16.jar;%APP_HOME%\lib\batik-ext-1.16.jar;%APP_HOME%\lib\batik-shared-resources-1.16.jar;%APP_HOME%\lib\xml-apis-ext-1.3.04.jar;%APP_HOME%\lib\imageio-metadata-3.8.1.jar;%APP_HOME%\lib\imageio-core-3.8.1.jar;%APP_HOME%\lib\common-image-3.8.1.jar;%APP_HOME%\lib\common-io-3.8.1.jar;%APP_HOME%\lib\common-lang-3.8.1.jar;%APP_HOME%\lib\xmlgraphics-commons-2.7.jar;%APP_HOME%\lib\xml-apis-1.4.01.jar;%APP_HOME%\lib\commons-io-1.3.1.jar;%APP_HOME%\lib\commons-logging-1.0.4.jar
+set CLASSPATH=%APP_HOME%\lib\bamscope.jar;%APP_HOME%\lib\lets-plot-batik-3.0.0.jar;%APP_HOME%\lib\lets-plot-jfx-3.0.0.jar;%APP_HOME%\lib\plot-api-jvm-4.2.0.jar;%APP_HOME%\lib\lets-plot-common-3.0.0.jar;%APP_HOME%\lib\kotlinx-html-jvm-0.7.3.jar;%APP_HOME%\lib\plot-config-portable-jvm-3.0.0.jar;%APP_HOME%\lib\plot-builder-portable-jvm-3.0.0.jar;%APP_HOME%\lib\plot-base-portable-jvm-3.0.0.jar;%APP_HOME%\lib\plot-common-portable-jvm-3.0.0.jar;%APP_HOME%\lib\vis-svg-portable-jvm-3.0.0.jar;%APP_HOME%\lib\base-portable-jvm-3.0.0.jar;%APP_HOME%\lib\kotlin-stdlib-jdk8-1.8.0.jar;%APP_HOME%\lib\picocli-4.7.0.jar;%APP_HOME%\lib\lets-plot-image-export-3.0.0.jar;%APP_HOME%\lib\slf4j-simple-2.0.6.jar;%APP_HOME%\lib\kotlin-stdlib-jdk7-1.8.0.jar;%APP_HOME%\lib\kotlin-logging-jvm-2.0.5.jar;%APP_HOME%\lib\kotlin-stdlib-1.8.0.jar;%APP_HOME%\lib\batik-codec-1.16.jar;%APP_HOME%\lib\kotlin-stdlib-common-1.8.0.jar;%APP_HOME%\lib\batik-transcoder-1.16.jar;%APP_HOME%\lib\imageio-tiff-3.8.1.jar;%APP_HOME%\lib\slf4j-api-2.0.6.jar;%APP_HOME%\lib\annotations-13.0.jar;%APP_HOME%\lib\batik-bridge-1.16.jar;%APP_HOME%\lib\batik-script-1.16.jar;%APP_HOME%\lib\batik-anim-1.16.jar;%APP_HOME%\lib\batik-gvt-1.16.jar;%APP_HOME%\lib\batik-svggen-1.16.jar;%APP_HOME%\lib\batik-svg-dom-1.16.jar;%APP_HOME%\lib\batik-parser-1.16.jar;%APP_HOME%\lib\batik-awt-util-1.16.jar;%APP_HOME%\lib\batik-dom-1.16.jar;%APP_HOME%\lib\batik-xml-1.16.jar;%APP_HOME%\lib\batik-css-1.16.jar;%APP_HOME%\lib\batik-util-1.16.jar;%APP_HOME%\lib\batik-constants-1.16.jar;%APP_HOME%\lib\batik-i18n-1.16.jar;%APP_HOME%\lib\batik-ext-1.16.jar;%APP_HOME%\lib\batik-shared-resources-1.16.jar;%APP_HOME%\lib\xml-apis-ext-1.3.04.jar;%APP_HOME%\lib\imageio-metadata-3.8.1.jar;%APP_HOME%\lib\imageio-core-3.8.1.jar;%APP_HOME%\lib\common-image-3.8.1.jar;%APP_HOME%\lib\common-io-3.8.1.jar;%APP_HOME%\lib\common-lang-3.8.1.jar;%APP_HOME%\lib\xmlgraphics-commons-2.7.jar;%APP_HOME%\lib\xml-apis-1.4.01.jar;%APP_HOME%\lib\commons-io-1.3.1.jar;%APP_HOME%\lib\commons-logging-1.0.4.jar
 
 
 @rem Execute bamscope

diff --git a/build/test-results/test/TEST-com.jslfree080.process.CheckWidthAgainTest.xml b/build/test-results/test/TEST-com.jslfree080.process.CheckWidthAgainTest.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="com.jslfree080.process.CheckWidthAgainTest" tests="1" skipped="0" failures="0" errors="0" timestamp="2023-02-06T10:13:54" hostname="jungsoo080ui-MacBookPro.local" time="0.029">
+<testsuite name="com.jslfree080.process.CheckWidthAgainTest" tests="1" skipped="0" failures="0" errors="0" timestamp="2023-02-07T02:57:56" hostname="jungsoo080ui-MacBookPro.local" time="0.025">
   <properties/>
-  <testcase name="testExpDecayResult()" classname="com.jslfree080.process.CheckWidthAgainTest" time="0.029"/>
+  <testcase name="testExpDecayResult()" classname="com.jslfree080.process.CheckWidthAgainTest" time="0.025"/>
   <system-out><![CDATA[]]></system-out>
   <system-err><![CDATA[]]></system-err>
 </testsuite>
diff --git a/build/test-results/test/TEST-com.jslfree080.process.CheckWidthFirstTest.xml b/build/test-results/test/TEST-com.jslfree080.process.CheckWidthFirstTest.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="com.jslfree080.process.CheckWidthFirstTest" tests="1" skipped="0" failures="0" errors="0" timestamp="2023-02-06T10:13:54" hostname="jungsoo080ui-MacBookPro.local" time="0.002">
+<testsuite name="com.jslfree080.process.CheckWidthFirstTest" tests="1" skipped="0" failures="0" errors="0" timestamp="2023-02-07T02:57:56" hostname="jungsoo080ui-MacBookPro.local" time="0.001">
   <properties/>
-  <testcase name="testFixedResult()" classname="com.jslfree080.process.CheckWidthFirstTest" time="0.002"/>
+  <testcase name="testFixedResult()" classname="com.jslfree080.process.CheckWidthFirstTest" time="0.001"/>
   <system-out><![CDATA[]]></system-out>
   <system-err><![CDATA[]]></system-err>
 </testsuite>
diff --git a/build/test-results/test/binary/results.bin b/build/test-results/test/binary/results.bin
diff --git a/build/tmp/kapt3/incApCache/test/classpath-structure.bin b/build/tmp/kapt3/incApCache/test/classpath-structure.bin
diff --git a/build/tmp/kapt3/incrementalData/main/com/jslfree080/cli/BAMScopeCommand.class b/build/tmp/kapt3/incrementalData/main/com/jslfree080/cli/BAMScopeCommand.class
diff --git a/build/tmp/kapt3/stubs/main/com/jslfree080/cli/BAMScopeCommand.java b/build/tmp/kapt3/stubs/main/com/jslfree080/cli/BAMScopeCommand.java
@@ -7,7 +7,7 @@
 public final class BAMScopeCommand implements java.lang.Runnable {
     @picocli.CommandLine.Parameters(index = "0", description = {"Input chromosomal position.      ex) (chr)N:XXXXXXXX"})
     private java.lang.String chrPos;
-    @picocli.CommandLine.Parameters(index = "1", description = {"Path to an input bam file.         ex) path/to/x.bam"})
+    @picocli.CommandLine.Parameters(index = "1", description = {"Path to an indexed bam file.       ex) path/to/x.bam"})
     private java.lang.String bamPath;
     @picocli.CommandLine.Option(names = {"-f", "--format"}, description = {"File format of an output image.         default) png"})
     private java.lang.String format = "png";

diff --git a/example.png b/example.png
diff --git a/src/main/kotlin/com/jslfree080/cli/CommandLine.kt b/src/main/kotlin/com/jslfree080/cli/CommandLine.kt
@@ -34,7 +34,7 @@ class BAMScopeCommand : Runnable {
     @CommandLine.Parameters(index = "0", description = ["Input chromosomal position.      ex) (chr)N:XXXXXXXX"])
     private lateinit var chrPos: String
 
-    @CommandLine.Parameters(index = "1", description = ["Path to an input bam file.         ex) path/to/x.bam"])
+    @CommandLine.Parameters(index = "1", description = ["Path to an indexed bam file.       ex) path/to/x.bam"])
     private lateinit var bamPath: String
 
     @CommandLine.Option(names = ["-f", "--format"], description = ["File format of an output image.         default) png"])