version 1.0.0

jslfree080 · Feb 6, 2023 · f277c40 · f277c40
1 parent 645a150
commit f277c40
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Showing 123 changed files with 198 additions and 37 deletions.
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/build.gradle.kts b/build.gradle.kts
@@ -21,6 +21,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  */
+
 import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
 
 plugins {
@@ -30,7 +31,7 @@ plugins {
 }
 
 group = "com.jslfree080"
-version = "0.6.0"
+version = "1.0.0"
 
 repositories {
     mavenCentral()
@@ -87,4 +88,4 @@ tasks.withType<Jar> {
 }
 
 // ./gradlew build |or| ./gradlew clean build (Delete all the previous version of the dependencies)
-// java -jar build/libs/bamscope-X.X.X.jar 18:53253385 ~/Downloads/sample_CD005_tcf4.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/bamscope/RunBAMScopeKt.class b/build/classes/kotlin/main/com/jslfree080/bamscope/RunBAMScopeKt.class
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/classes/kotlin/main/com/jslfree080/process/BlockAdjustment.class b/build/classes/kotlin/main/com/jslfree080/process/BlockAdjustment.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/CheckWidthAgain.class b/build/classes/kotlin/main/com/jslfree080/process/CheckWidthAgain.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/CheckWidthFirst.class b/build/classes/kotlin/main/com/jslfree080/process/CheckWidthFirst.class
diff --git a/...ses/kotlin/main/com/jslfree080/process/ExtractReference$special$$inlined$sortedBy$1.class b/...ses/kotlin/main/com/jslfree080/process/ExtractReference$special$$inlined$sortedBy$1.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/ExtractReference.class b/build/classes/kotlin/main/com/jslfree080/process/ExtractReference.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/ParseRead.class b/build/classes/kotlin/main/com/jslfree080/process/ParseRead.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$1.class b/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$1.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$2.class b/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$2.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$3.class b/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$3.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$4.class b/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$4.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment.class b/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/ReadSamtools.class b/build/classes/kotlin/main/com/jslfree080/process/ReadSamtools.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/RunSamtools.class b/build/classes/kotlin/main/com/jslfree080/process/RunSamtools.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarDeletion.class b/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarDeletion.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarInsertion.class b/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarInsertion.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarMatch.class b/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarMatch.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarPadding.class b/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarPadding.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarSkippedRegion.class b/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarSkippedRegion.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarSoftClip.class b/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarSoftClip.class
diff --git a/build/classes/kotlin/main/com/jslfree080/process/cigars/ParameterMID.class b/build/classes/kotlin/main/com/jslfree080/process/cigars/ParameterMID.class
diff --git a/build/classes/kotlin/test/com/jslfree080/process/CheckWidthAgainTest.class b/build/classes/kotlin/test/com/jslfree080/process/CheckWidthAgainTest.class
diff --git a/build/classes/kotlin/test/com/jslfree080/process/CheckWidthFirstTest.class b/build/classes/kotlin/test/com/jslfree080/process/CheckWidthFirstTest.class
diff --git a/build/distributions/bamscope-0.6.0.tar → build/distributions/bamscope-1.0.0.tar b/build/distributions/bamscope-0.6.0.tar → build/distributions/bamscope-1.0.0.tar
diff --git a/build/distributions/bamscope-0.6.0.zip → build/distributions/bamscope-1.0.0.zip b/build/distributions/bamscope-0.6.0.zip → build/distributions/bamscope-1.0.0.zip
diff --git a/build/kotlin/bamscope060jar-classes.txt → build/kotlin/bamscope100jar-classes.txt b/build/kotlin/bamscope060jar-classes.txt → build/kotlin/bamscope100jar-classes.txt
@@ -1 +1 @@
-/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/bamscope/RunBAMScopeKt.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/cli/BAMScopeCommand.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/BlockAdjustment.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/CheckWidthAgain.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/CheckWidthFirst.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/ExtractReference$special$$inlined$sortedBy$1.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/ExtractReference.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/ParseRead.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$1.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$2.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/ReadSamtools.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/RunSamtools.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarDeletion.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarInsertion.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarMatch.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarPadding.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarSkippedRegion.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarSoftClip.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/ParameterMID.class
+/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/bamscope/RunBAMScopeKt.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/cli/BAMScopeCommand.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/BlockAdjustment.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/CheckWidthAgain.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/CheckWidthFirst.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/ExtractReference$special$$inlined$sortedBy$1.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/ExtractReference.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/ParseRead.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$1.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$2.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$3.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment$letsPlot$p$4.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/PlotAlignment.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/ReadSamtools.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/RunSamtools.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarDeletion.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarInsertion.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarMatch.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarPadding.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarSkippedRegion.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/CigarSoftClip.class:/Users/jslit/IdeaProjects/bamscope/build/classes/kotlin/main/com/jslfree080/process/cigars/ParameterMID.class
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/inputs/source-to-output.tab b/build/kotlin/compileKotlin/cacheable/caches-jvm/inputs/source-to-output.tab
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/inputs/source-to-output.tab.values.at b/build/kotlin/compileKotlin/cacheable/caches-jvm/inputs/source-to-output.tab.values.at
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab b/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab
diff --git a/...otlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab.keystream b/...otlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab.keystream
diff --git a/...n/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab.keystream.len b/...n/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab.keystream.len
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab.len b/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab.len
diff --git a/...otlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab.values.at b/...otlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab.values.at
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab_i b/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/internal-name-to-source.tab_i
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/proto.tab b/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/proto.tab
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/proto.tab.values.at b/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/proto.tab.values.at
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/source-to-classes.tab b/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/source-to-classes.tab
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/source-to-classes.tab.values.at b/build/kotlin/compileKotlin/cacheable/caches-jvm/jvm/kotlin/source-to-classes.tab.values.at
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab b/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab.keystream b/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab.keystream
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab.keystream.len b/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab.keystream.len
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab.len b/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab.len
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab.values.at b/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab.values.at
diff --git a/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab_i b/build/kotlin/compileKotlin/cacheable/caches-jvm/lookups/lookups.tab_i
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/caches-jvm/jvm/kotlin/proto.tab b/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/jvm/kotlin/proto.tab
diff --git a/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/jvm/kotlin/proto.tab.values.at b/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/jvm/kotlin/proto.tab.values.at
diff --git a/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab b/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab
diff --git a/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab.keystream b/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab.keystream
diff --git a/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab.keystream.len b/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab.keystream.len
diff --git a/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab.len b/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab.len
diff --git a/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab.values.at b/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab.values.at
diff --git a/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab_i b/build/kotlin/kaptGenerateStubsKotlin/cacheable/caches-jvm/lookups/lookups.tab_i
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-0.6.0.jar → build/libs/bamscope-1.0.0.jar b/build/libs/bamscope-0.6.0.jar → build/libs/bamscope-1.0.0.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">0.025s</div>
+<div class="counter">0.029s</div>
 <p>duration</p>
 </div>
 </td>
@@ -76,7 +76,7 @@ <h2>Tests</h2>
 </thead>
 <tr>
 <td class="success">testExpDecayResult()</td>
-<td class="success">0.025s</td>
+<td class="success">0.029s</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. 5. 오후 2:38:40</p>
+<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 6. 오후 7:13:54</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">0.001s</div>
+<div class="counter">0.002s</div>
 <p>duration</p>
 </div>
 </td>
@@ -76,7 +76,7 @@ <h2>Tests</h2>
 </thead>
 <tr>
 <td class="success">testFixedResult()</td>
-<td class="success">0.001s</td>
+<td class="success">0.002s</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. 5. 오후 2:38:40</p>
+<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 6. 오후 7:13:54</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">0.026s</div>
+<div class="counter">0.031s</div>
 <p>duration</p>
 </div>
 </td>
@@ -85,7 +85,7 @@ <h2>Packages</h2>
 <td>2</td>
 <td>0</td>
 <td>0</td>
-<td>0.026s</td>
+<td>0.031s</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>0.025s</td>
+<td>0.029s</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>0.001s</td>
+<td>0.002s</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. 5. 오후 2:38:40</p>
+<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 6. 오후 7:13:54</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">0.026s</div>
+<div class="counter">0.031s</div>
 <p>duration</p>
 </div>
 </td>
@@ -83,7 +83,7 @@ <h2>Classes</h2>
 <td>1</td>
 <td>0</td>
 <td>0</td>
-<td>0.025s</td>
+<td>0.029s</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>0.001s</td>
+<td>0.002s</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. 5. 오후 2:38:40</p>
+<a href="http://www.gradle.org">Gradle 7.5.1</a> at 2023. 2. 6. 오후 7:13:54</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=$APP_HOME/lib/bamscope-0.6.0.jar:$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-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
 
 
 # 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-0.6.0.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-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
 
 
 @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="2023-02-05T05:38:40" hostname="jungsoo080ui-MacBookPro.local" time="0.025">
+<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">
   <properties/>
-  <testcase name="testExpDecayResult()" classname="com.jslfree080.process.CheckWidthAgainTest" time="0.025"/>
+  <testcase name="testExpDecayResult()" classname="com.jslfree080.process.CheckWidthAgainTest" time="0.029"/>
   <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="2023-02-05T05:38:40" hostname="jungsoo080ui-MacBookPro.local" time="0.001">
+<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">
   <properties/>
-  <testcase name="testFixedResult()" classname="com.jslfree080.process.CheckWidthFirstTest" time="0.001"/>
+  <testcase name="testFixedResult()" classname="com.jslfree080.process.CheckWidthFirstTest" time="0.002"/>
   <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/incrementalData/main/com/jslfree080/process/ParseRead.class b/build/tmp/kapt3/incrementalData/main/com/jslfree080/process/ParseRead.class
diff --git a/build/tmp/kapt3/incrementalData/main/com/jslfree080/process/PlotAlignment.class b/build/tmp/kapt3/incrementalData/main/com/jslfree080/process/PlotAlignment.class
diff --git a/build/tmp/kapt3/stubs/main/com/jslfree080/bamscope/RunBAMScopeKt.kapt_metadata b/build/tmp/kapt3/stubs/main/com/jslfree080/bamscope/RunBAMScopeKt.kapt_metadata