├── .github └── workflows │ └── tests.yml ├── .gradle ├── 7.5.1 │ ├── checksums │ │ └── checksums.lock │ ├── dependencies-accessors │ │ ├── dependencies-accessors.lock │ │ └── gc.properties │ ├── executionHistory │ │ ├── executionHistory.bin │ │ └── executionHistory.lock │ ├── fileChanges │ │ └── last-build.bin │ ├── fileHashes │ │ ├── fileHashes.bin │ │ ├── fileHashes.lock │ │ └── resourceHashesCache.bin │ └── gc.properties ├── buildOutputCleanup │ ├── buildOutputCleanup.lock │ ├── cache.properties │ └── outputFiles.bin ├── file-system.probe └── vcs-1 │ └── gc.properties ├── .idea ├── .gitignore ├── compiler.xml ├── gradle.xml ├── jarRepositories.xml ├── kotlinc.xml ├── misc.xml ├── uiDesigner.xml └── vcs.xml ├── LICENSE ├── README.md ├── build.gradle.kts ├── build ├── classes │ └── kotlin │ │ ├── main │ │ ├── META-INF │ │ │ └── bamscope.kotlin_module │ │ └── com │ │ │ └── jslfree080 │ │ │ ├── bamscope │ │ │ └── RunBAMScopeKt.class │ │ │ ├── cli │ │ │ ├── BAMScopeCommand$run$1.class │ │ │ └── BAMScopeCommand.class │ │ │ └── process │ │ │ ├── BlockAdjustment.class │ │ │ ├── CheckWidthAgain.class │ │ │ ├── CheckWidthFirst.class │ │ │ ├── ExtractReference$special$$inlined$sortedBy$1.class │ │ │ ├── ExtractReference.class │ │ │ ├── ParseRead.class │ │ │ ├── PlotAlignment$letsPlot$p$1.class │ │ │ ├── PlotAlignment$letsPlot$p$2.class │ │ │ ├── PlotAlignment$letsPlot$p$3.class │ │ │ ├── PlotAlignment$letsPlot$p$4.class │ │ │ ├── PlotAlignment.class │ │ │ ├── ReadSamtools.class │ │ │ ├── RunSamtools.class │ │ │ └── cigars │ │ │ ├── CigarDeletion.class │ │ │ ├── CigarInsertion.class │ │ │ ├── CigarMatch.class │ │ │ ├── CigarPadding.class │ │ │ ├── CigarSkippedRegion.class │ │ │ ├── CigarSoftClip.class │ │ │ └── ParameterMID.class │ │ └── test │ │ ├── META-INF │ │ └── bamscope.kotlin_module │ │ └── com │ │ └── jslfree080 │ │ └── process │ │ ├── CheckWidthAgainTest.class │ │ └── CheckWidthFirstTest.class ├── distributions │ ├── bamscope-1.1.0.tar │ └── bamscope-1.1.0.zip ├── kotlin │ ├── bamscopejar-classes.txt │ ├── compileKotlin │ │ ├── cacheable │ │ │ ├── caches-jvm │ │ │ │ ├── inputs │ │ │ │ │ ├── source-to-output.tab │ │ │ │ │ ├── source-to-output.tab.keystream │ │ │ │ │ ├── source-to-output.tab.keystream.len │ │ │ │ │ ├── source-to-output.tab.len │ │ │ │ │ ├── source-to-output.tab.values.at │ │ │ │ │ ├── source-to-output.tab_i │ │ │ │ │ └── source-to-output.tab_i.len │ │ │ │ ├── jvm │ │ │ │ │ └── kotlin │ │ │ │ │ │ ├── class-attributes.tab │ │ │ │ │ │ ├── class-attributes.tab.keystream │ │ │ │ │ │ ├── class-attributes.tab.keystream.len │ │ │ │ │ │ ├── class-attributes.tab.len │ │ │ │ │ │ ├── class-attributes.tab.values.at │ │ │ │ │ │ ├── class-attributes.tab_i │ │ │ │ │ │ ├── class-attributes.tab_i.len │ │ │ │ │ │ ├── class-fq-name-to-source.tab │ │ │ │ │ │ ├── class-fq-name-to-source.tab.keystream │ │ │ │ │ │ ├── class-fq-name-to-source.tab.keystream.len │ │ │ │ │ │ ├── class-fq-name-to-source.tab.len │ │ │ │ │ │ ├── class-fq-name-to-source.tab.values.at │ │ │ │ │ │ ├── class-fq-name-to-source.tab_i │ │ │ │ │ │ ├── class-fq-name-to-source.tab_i.len │ │ │ │ │ │ ├── internal-name-to-source.tab │ │ │ │ │ │ ├── internal-name-to-source.tab.keystream │ │ │ │ │ │ ├── internal-name-to-source.tab.keystream.len │ │ │ │ │ │ ├── internal-name-to-source.tab.len │ │ │ │ │ │ ├── internal-name-to-source.tab.values.at │ │ │ │ │ │ ├── internal-name-to-source.tab_i │ │ │ │ │ │ ├── internal-name-to-source.tab_i.len │ │ │ │ │ │ ├── package-parts.tab │ │ │ │ │ │ ├── package-parts.tab.keystream │ │ │ │ │ │ ├── package-parts.tab.keystream.len │ │ │ │ │ │ ├── package-parts.tab.len │ │ │ │ │ │ ├── package-parts.tab.values.at │ │ │ │ │ │ ├── package-parts.tab_i │ │ │ │ │ │ ├── package-parts.tab_i.len │ │ │ │ │ │ ├── proto.tab │ │ │ │ │ │ ├── proto.tab.keystream │ │ │ │ │ │ ├── proto.tab.keystream.len │ │ │ │ │ │ ├── proto.tab.len │ │ │ │ │ │ ├── proto.tab.values.at │ │ │ │ │ │ ├── proto.tab_i │ │ │ │ │ │ ├── proto.tab_i.len │ │ │ │ │ │ ├── source-to-classes.tab │ │ │ │ │ │ ├── source-to-classes.tab.keystream │ │ │ │ │ │ ├── source-to-classes.tab.keystream.len │ │ │ │ │ │ ├── source-to-classes.tab.len │ │ │ │ │ │ ├── source-to-classes.tab.values.at │ │ │ │ │ │ ├── source-to-classes.tab_i │ │ │ │ │ │ ├── source-to-classes.tab_i.len │ │ │ │ │ │ ├── subtypes.tab │ │ │ │ │ │ ├── subtypes.tab.keystream │ │ │ │ │ │ ├── subtypes.tab.keystream.len │ │ │ │ │ │ ├── subtypes.tab.len │ │ │ │ │ │ ├── subtypes.tab.values.at │ │ │ │ │ │ ├── subtypes.tab_i │ │ │ │ │ │ ├── subtypes.tab_i.len │ │ │ │ │ │ ├── supertypes.tab │ │ │ │ │ │ ├── supertypes.tab.keystream │ │ │ │ │ │ ├── supertypes.tab.keystream.len │ │ │ │ │ │ ├── supertypes.tab.len │ │ │ │ │ │ ├── supertypes.tab.values.at │ │ │ │ │ │ ├── supertypes.tab_i │ │ │ │ │ │ └── supertypes.tab_i.len │ │ │ │ └── lookups │ │ │ │ │ ├── counters.tab │ │ │ │ │ ├── file-to-id.tab │ │ │ │ │ ├── file-to-id.tab.keystream │ │ │ │ │ ├── file-to-id.tab.keystream.len │ │ │ │ │ ├── file-to-id.tab.len │ │ │ │ │ ├── file-to-id.tab.values.at │ │ │ │ │ ├── file-to-id.tab_i │ │ │ │ │ ├── file-to-id.tab_i.len │ │ │ │ │ ├── id-to-file.tab │ │ │ │ │ ├── id-to-file.tab.keystream │ │ │ │ │ ├── id-to-file.tab.keystream.len │ │ │ │ │ ├── id-to-file.tab.len │ │ │ │ │ ├── id-to-file.tab.values.at │ │ │ │ │ ├── id-to-file.tab_i │ │ │ │ │ ├── id-to-file.tab_i.len │ │ │ │ │ ├── lookups.tab │ │ │ │ │ ├── lookups.tab.keystream │ │ │ │ │ ├── lookups.tab.keystream.len │ │ │ │ │ ├── lookups.tab.len │ │ │ │ │ ├── lookups.tab.values.at │ │ │ │ │ ├── lookups.tab_i │ │ │ │ │ └── lookups.tab_i.len │ │ │ └── last-build.bin │ │ └── local-state │ │ │ └── build-history.bin │ ├── compileTestKotlin │ │ ├── cacheable │ │ │ ├── caches-jvm │ │ │ │ ├── inputs │ │ │ │ │ ├── source-to-output.tab │ │ │ │ │ ├── source-to-output.tab.keystream │ │ │ │ │ ├── source-to-output.tab.keystream.len │ │ │ │ │ ├── source-to-output.tab.len │ │ │ │ │ ├── source-to-output.tab.values.at │ │ │ │ │ ├── source-to-output.tab_i │ │ │ │ │ └── source-to-output.tab_i.len │ │ │ │ ├── jvm │ │ │ │ │ └── kotlin │ │ │ │ │ │ ├── class-attributes.tab │ │ │ │ │ │ ├── class-attributes.tab.keystream │ │ │ │ │ │ ├── class-attributes.tab.keystream.len │ │ │ │ │ │ ├── class-attributes.tab.len │ │ │ │ │ │ ├── class-attributes.tab.values.at │ │ │ │ │ │ ├── class-attributes.tab_i │ │ │ │ │ │ ├── class-attributes.tab_i.len │ │ │ │ │ │ ├── class-fq-name-to-source.tab │ │ │ │ │ │ ├── class-fq-name-to-source.tab.keystream │ │ │ │ │ │ ├── class-fq-name-to-source.tab.keystream.len │ │ │ │ │ │ ├── class-fq-name-to-source.tab.len │ │ │ │ │ │ ├── class-fq-name-to-source.tab.values.at │ │ │ │ │ │ ├── class-fq-name-to-source.tab_i │ │ │ │ │ │ ├── class-fq-name-to-source.tab_i.len │ │ │ │ │ │ ├── internal-name-to-source.tab │ │ │ │ │ │ ├── internal-name-to-source.tab.keystream │ │ │ │ │ │ ├── internal-name-to-source.tab.keystream.len │ │ │ │ │ │ ├── internal-name-to-source.tab.len │ │ │ │ │ │ ├── internal-name-to-source.tab.values.at │ │ │ │ │ │ ├── internal-name-to-source.tab_i │ │ │ │ │ │ ├── internal-name-to-source.tab_i.len │ │ │ │ │ │ ├── proto.tab │ │ │ │ │ │ ├── proto.tab.keystream │ │ │ │ │ │ ├── proto.tab.keystream.len │ │ │ │ │ │ ├── proto.tab.len │ │ │ │ │ │ ├── proto.tab.values.at │ │ │ │ │ │ ├── proto.tab_i │ │ │ │ │ │ ├── proto.tab_i.len │ │ │ │ │ │ ├── source-to-classes.tab │ │ │ │ │ │ ├── source-to-classes.tab.keystream │ │ │ │ │ │ ├── source-to-classes.tab.keystream.len │ │ │ │ │ │ ├── source-to-classes.tab.len │ │ │ │ │ │ ├── source-to-classes.tab.values.at │ │ │ │ │ │ ├── source-to-classes.tab_i │ │ │ │ │ │ └── source-to-classes.tab_i.len │ │ │ │ └── lookups │ │ │ │ │ ├── counters.tab │ │ │ │ │ ├── file-to-id.tab │ │ │ │ │ ├── file-to-id.tab.keystream │ │ │ │ │ ├── file-to-id.tab.keystream.len │ │ │ │ │ ├── file-to-id.tab.len │ │ │ │ │ ├── file-to-id.tab.values.at │ │ │ │ │ ├── file-to-id.tab_i │ │ │ │ │ ├── file-to-id.tab_i.len │ │ │ │ │ ├── id-to-file.tab │ │ │ │ │ ├── id-to-file.tab.keystream │ │ │ │ │ ├── id-to-file.tab.keystream.len │ │ │ │ │ ├── id-to-file.tab.len │ │ │ │ │ ├── id-to-file.tab.values.at │ │ │ │ │ ├── id-to-file.tab_i │ │ │ │ │ ├── id-to-file.tab_i.len │ │ │ │ │ ├── lookups.tab │ │ │ │ │ ├── lookups.tab.keystream │ │ │ │ │ ├── lookups.tab.keystream.len │ │ │ │ │ ├── lookups.tab.len │ │ │ │ │ ├── lookups.tab.values.at │ │ │ │ │ ├── lookups.tab_i │ │ │ │ │ └── lookups.tab_i.len │ │ │ └── last-build.bin │ │ └── local-state │ │ │ └── build-history.bin │ ├── kaptGenerateStubsKotlin │ │ ├── cacheable │ │ │ ├── caches-jvm │ │ │ │ ├── inputs │ │ │ │ │ ├── source-to-output.tab │ │ │ │ │ ├── source-to-output.tab.keystream │ │ │ │ │ ├── source-to-output.tab.keystream.len │ │ │ │ │ ├── source-to-output.tab.len │ │ │ │ │ ├── source-to-output.tab.values.at │ │ │ │ │ ├── source-to-output.tab_i │ │ │ │ │ └── source-to-output.tab_i.len │ │ │ │ ├── jvm │ │ │ │ │ └── kotlin │ │ │ │ │ │ ├── class-attributes.tab │ │ │ │ │ │ ├── class-attributes.tab.keystream │ │ │ │ │ │ ├── class-attributes.tab.keystream.len │ │ │ │ │ │ ├── class-attributes.tab.len │ │ │ │ │ │ ├── class-attributes.tab.values.at │ │ │ │ │ │ ├── class-attributes.tab_i │ │ │ │ │ │ ├── class-attributes.tab_i.len │ │ │ │ │ │ ├── class-fq-name-to-source.tab │ │ │ │ │ │ ├── class-fq-name-to-source.tab.keystream │ │ │ │ │ │ ├── class-fq-name-to-source.tab.keystream.len │ │ │ │ │ │ ├── class-fq-name-to-source.tab.len │ │ │ │ │ │ ├── class-fq-name-to-source.tab.values.at │ │ │ │ │ │ ├── class-fq-name-to-source.tab_i │ │ │ │ │ │ ├── class-fq-name-to-source.tab_i.len │ │ │ │ │ │ ├── internal-name-to-source.tab │ │ │ │ │ │ ├── internal-name-to-source.tab.keystream │ │ │ │ │ │ ├── internal-name-to-source.tab.keystream.len │ │ │ │ │ │ ├── internal-name-to-source.tab.len │ │ │ │ │ │ ├── internal-name-to-source.tab.values.at │ │ │ │ │ │ ├── internal-name-to-source.tab_i │ │ │ │ │ │ ├── internal-name-to-source.tab_i.len │ │ │ │ │ │ ├── package-parts.tab │ │ │ │ │ │ ├── package-parts.tab.keystream │ │ │ │ │ │ ├── package-parts.tab.keystream.len │ │ │ │ │ │ ├── package-parts.tab.len │ │ │ │ │ │ ├── package-parts.tab.values.at │ │ │ │ │ │ ├── package-parts.tab_i │ │ │ │ │ │ ├── package-parts.tab_i.len │ │ │ │ │ │ ├── proto.tab │ │ │ │ │ │ ├── proto.tab.keystream │ │ │ │ │ │ ├── proto.tab.keystream.len │ │ │ │ │ │ ├── proto.tab.len │ │ │ │ │ │ ├── proto.tab.values.at │ │ │ │ │ │ ├── proto.tab_i │ │ │ │ │ │ ├── proto.tab_i.len │ │ │ │ │ │ ├── source-to-classes.tab │ │ │ │ │ │ ├── source-to-classes.tab.keystream │ │ │ │ │ │ ├── source-to-classes.tab.keystream.len │ │ │ │ │ │ ├── source-to-classes.tab.len │ │ │ │ │ │ ├── source-to-classes.tab.values.at │ │ │ │ │ │ ├── source-to-classes.tab_i │ │ │ │ │ │ ├── source-to-classes.tab_i.len │ │ │ │ │ │ ├── subtypes.tab │ │ │ │ │ │ ├── subtypes.tab.keystream │ │ │ │ │ │ ├── subtypes.tab.keystream.len │ │ │ │ │ │ ├── subtypes.tab.len │ │ │ │ │ │ ├── subtypes.tab.values.at │ │ │ │ │ │ ├── subtypes.tab_i │ │ │ │ │ │ ├── subtypes.tab_i.len │ │ │ │ │ │ ├── supertypes.tab │ │ │ │ │ │ ├── supertypes.tab.keystream │ │ │ │ │ │ ├── supertypes.tab.keystream.len │ │ │ │ │ │ ├── supertypes.tab.len │ │ │ │ │ │ ├── supertypes.tab.values.at │ │ │ │ │ │ ├── supertypes.tab_i │ │ │ │ │ │ └── supertypes.tab_i.len │ │ │ │ └── lookups │ │ │ │ │ ├── counters.tab │ │ │ │ │ ├── file-to-id.tab │ │ │ │ │ ├── file-to-id.tab.keystream │ │ │ │ │ ├── file-to-id.tab.keystream.len │ │ │ │ │ ├── file-to-id.tab.len │ │ │ │ │ ├── file-to-id.tab.values.at │ │ │ │ │ ├── file-to-id.tab_i │ │ │ │ │ ├── file-to-id.tab_i.len │ │ │ │ │ ├── id-to-file.tab │ │ │ │ │ ├── id-to-file.tab.keystream │ │ │ │ │ ├── id-to-file.tab.keystream.len │ │ │ │ │ ├── id-to-file.tab.len │ │ │ │ │ ├── id-to-file.tab.values.at │ │ │ │ │ ├── id-to-file.tab_i │ │ │ │ │ ├── id-to-file.tab_i.len │ │ │ │ │ ├── lookups.tab │ │ │ │ │ ├── lookups.tab.keystream │ │ │ │ │ ├── lookups.tab.keystream.len │ │ │ │ │ ├── lookups.tab.len │ │ │ │ │ ├── lookups.tab.values.at │ │ │ │ │ ├── lookups.tab_i │ │ │ │ │ └── lookups.tab_i.len │ │ │ └── last-build.bin │ │ └── local-state │ │ │ └── build-history.bin │ └── kaptGenerateStubsTestKotlin │ │ ├── cacheable │ │ └── last-build.bin │ │ └── local-state │ │ └── build-history.bin ├── libs │ └── bamscope.jar ├── reports │ └── tests │ │ └── test │ │ ├── classes │ │ ├── com.jslfree080.process.CheckWidthAgainTest.html │ │ └── com.jslfree080.process.CheckWidthFirstTest.html │ │ ├── css │ │ ├── base-style.css │ │ └── style.css │ │ ├── index.html │ │ ├── js │ │ └── report.js │ │ └── packages │ │ └── com.jslfree080.process.html ├── scripts │ ├── bamscope │ └── bamscope.bat ├── test-results │ └── test │ │ ├── TEST-com.jslfree080.process.CheckWidthAgainTest.xml │ │ ├── TEST-com.jslfree080.process.CheckWidthFirstTest.xml │ │ └── binary │ │ ├── output.bin │ │ ├── output.bin.idx │ │ └── results.bin └── tmp │ ├── jar │ └── MANIFEST.MF │ └── kapt3 │ ├── classes │ └── main │ │ └── META-INF │ │ └── native-image │ │ └── picocli-generated │ │ └── com.jslfree080 │ │ └── bamscope │ │ ├── proxy-config.json │ │ ├── reflect-config.json │ │ └── resource-config.json │ ├── incApCache │ ├── main │ │ ├── ap-classpath-entries.bin │ │ ├── apt-cache.bin │ │ ├── classpath-entries.bin │ │ ├── classpath-structure.bin │ │ └── java-cache.bin │ └── test │ │ ├── ap-classpath-entries.bin │ │ ├── classpath-entries.bin │ │ └── classpath-structure.bin │ ├── incrementalData │ └── main │ │ ├── META-INF │ │ └── bamscope.kotlin_module │ │ └── com │ │ └── jslfree080 │ │ ├── bamscope │ │ └── RunBAMScopeKt.class │ │ ├── cli │ │ └── BAMScopeCommand.class │ │ └── process │ │ ├── BlockAdjustment.class │ │ ├── CheckWidthAgain.class │ │ ├── CheckWidthFirst.class │ │ ├── ExtractReference.class │ │ ├── ParseRead.class │ │ ├── PlotAlignment.class │ │ ├── ReadSamtools.class │ │ ├── RunSamtools.class │ │ └── cigars │ │ ├── CigarDeletion.class │ │ ├── CigarInsertion.class │ │ ├── CigarMatch.class │ │ ├── CigarPadding.class │ │ ├── CigarSkippedRegion.class │ │ ├── CigarSoftClip.class │ │ └── ParameterMID.class │ └── stubs │ └── main │ ├── com │ └── jslfree080 │ │ ├── bamscope │ │ ├── RunBAMScopeKt.java │ │ └── RunBAMScopeKt.kapt_metadata │ │ ├── cli │ │ ├── BAMScopeCommand.java │ │ └── BAMScopeCommand.kapt_metadata │ │ └── process │ │ ├── BlockAdjustment.java │ │ ├── BlockAdjustment.kapt_metadata │ │ ├── CheckWidthAgain.java │ │ ├── CheckWidthAgain.kapt_metadata │ │ ├── CheckWidthFirst.java │ │ ├── CheckWidthFirst.kapt_metadata │ │ ├── ExtractReference.java │ │ ├── ExtractReference.kapt_metadata │ │ ├── ParseRead.java │ │ ├── ParseRead.kapt_metadata │ │ ├── PlotAlignment.java │ │ ├── PlotAlignment.kapt_metadata │ │ ├── ReadSamtools.java │ │ ├── ReadSamtools.kapt_metadata │ │ ├── RunSamtools.java │ │ ├── RunSamtools.kapt_metadata │ │ └── cigars │ │ ├── CigarDeletion.java │ │ ├── CigarDeletion.kapt_metadata │ │ ├── CigarInsertion.java │ │ ├── CigarInsertion.kapt_metadata │ │ ├── CigarMatch.java │ │ ├── CigarMatch.kapt_metadata │ │ ├── CigarPadding.java │ │ ├── CigarPadding.kapt_metadata │ │ ├── CigarSkippedRegion.java │ │ ├── CigarSkippedRegion.kapt_metadata │ │ ├── CigarSoftClip.java │ │ ├── CigarSoftClip.kapt_metadata │ │ ├── ParameterMID.java │ │ └── ParameterMID.kapt_metadata │ └── error │ └── NonExistentClass.java ├── gradle.properties ├── gradle └── wrapper │ ├── gradle-wrapper.jar │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat ├── settings.gradle.kts └── src ├── main └── kotlin │ └── com │ └── jslfree080 │ ├── bamscope │ └── RunBAMScope.kt │ ├── cli │ └── CommandLine.kt │ └── process │ ├── BlockAdjustment.kt │ ├── CheckWidthAgain.kt │ ├── CheckWidthFirst.kt │ ├── ExtractReference.kt │ ├── ParseRead.kt │ ├── PlotAlignment.kt │ ├── ReadSamtools.kt │ ├── RunSamtools.kt │ └── cigars │ ├── CigarDeletion.kt │ ├── CigarInsertion.kt │ ├── CigarMatch.kt │ ├── CigarPadding.kt │ ├── CigarSkippedRegion.kt │ ├── CigarSoftClip.kt │ └── ParameterMID.kt └── test └── kotlin └── com └── jslfree080 └── process ├── CheckWidthAgainTest.kt └── CheckWidthFirstTest.kt /.github/workflows/tests.yml: -------------------------------------------------------------------------------- 1 | name: Test 2 | 3 | on: 4 | push: 5 | branches: 6 | - main 7 | 8 | jobs: 9 | test: 10 | runs-on: ${{ matrix.os }}-latest 11 | strategy: 12 | matrix: 13 | java: [ 11 ] 14 | os: [ 'ubuntu', 'macos' ] 15 | steps: 16 | - uses: actions/checkout@v3 17 | - uses: actions/setup-java@v3 18 | with: 19 | java-version: ${{ matrix.Java }} 20 | distribution: 'adopt' 21 | cache: gradle 22 | - name: Grant execute permission for gradlew 23 | run: chmod +x gradlew 24 | - name: Test with Gradle 25 | run: ./gradlew --info test 26 | - name: Build the jar and run a commandline 27 | run: java -jar build/libs/bamscope.jar -h 28 | -------------------------------------------------------------------------------- /.gradle/7.5.1/checksums/checksums.lock: 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10 | 14 | 15 | 19 | 20 | -------------------------------------------------------------------------------- /.idea/kotlinc.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 6 | -------------------------------------------------------------------------------- /.idea/misc.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /.idea/vcs.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2023 Jungsoo Lee 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # bamscope 2 | ![Build Status](https://github.com/jslfree080/bamscope/actions/workflows/tests.yml/badge.svg?branch=main) 3 | [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/jslfree080/bamscope/blob/main/LICENSE) 4 | 5 | A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. 6 | 7 | demonstration 8 | demonstration 9 | 10 | ## Interpretation of Output Image 11 | 12 | The images produced display the alignment of the bases using colored blocks. The opacity of each block reflects the quality score of the base, with blocks valued near 1 displayed for high-quality scores near 40 and those valued near 0 for low-quality scores close to 0. The strandedness of each read's alignment is indicated in both the leftmost and rightmost columns, where '→' indicates a forward strand alignment and '←' indicates a reverse strand alignment. 13 | 14 | ## Prerequisites 15 | 16 | Bamscope requires **Java 11** or later versions to build and run. 17 | 18 | Also, [samtools](https://github.com/samtools/samtools) should be pre-installed to support accessing file formats such as BAM and FASTA. 19 | 20 | ## Building 21 | 22 | * Clone the repo: 23 | ``` 24 | git clone https://github.com/jslfree080/bamscope.git 25 | cd bamscope/ 26 | ``` 27 | 28 | * Build an executable Bamscope jar with all dependencies packaged: 29 | ``` 30 | ./gradlew build 31 | ``` 32 | 33 | ## Usage 34 | 35 | ### Command line 36 | 37 | The resulting jar will be in `build/libs`. 38 | 39 | ``` 40 | Usage: java -jar build/libs/bamscope.jar [options] 41 | 42 | Parameters: 43 | Input chromosomal position ex) (chr)N:XXXXXXXX 44 | or path to a VCF file. or path/to/x.vcf 45 | Path to an indexed BAM file. ex) path/to/x.bam 46 | 47 | Options: 48 | -f, --format= File format of an output image. default) png 49 | -h, --help Show this help message and exit. 50 | -o, --outPath= Path to an output image. default) . 51 | -r, --refPath= Path to a reference FASTA. ex) path/to/x.fasta(.fa) 52 | -s, --sPath= Path to the samtools. ex) /usr/local/bin/samtools 53 | -w, --width= Width of start to interest position. default) 50 54 | ``` 55 | 56 | * Example usage for a specific position: 57 | ``` 58 | java -jar build/libs/bamscope.jar 18:53254446 ~/Downloads/x.bam -r ~/Downloads/x.fasta -o ~/Desktop/ 59 | ``` 60 | 61 | * Example usage with VCF file (⚠️ This option may be computationally intensive): 62 | ``` 63 | java -jar build/libs/bamscope.jar ~/Desktop/x.vcf ~/Downloads/x.bam -r ~/Downloads/x.fasta -o ~/Desktop/ 64 | ``` 65 | 66 | ## License 67 | 68 | Code and documentation released under the [MIT license](https://github.com/jslfree080/bamscope/blob/master/LICENSE). 69 | -------------------------------------------------------------------------------- /build.gradle.kts: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | import org.jetbrains.kotlin.gradle.tasks.KotlinCompile 26 | 27 | plugins { 28 | kotlin("jvm") version "1.8.0" 29 | application 30 | kotlin("kapt") version "1.8.0" // kotlin.kapt 31 | } 32 | 33 | group = "com.jslfree080" 34 | version = "1.1.0" 35 | 36 | repositories { 37 | mavenCentral() 38 | } 39 | 40 | dependencies { 41 | testImplementation(kotlin("test")) 42 | 43 | implementation("info.picocli:picocli:4.7.0") // picocli library 44 | kapt("info.picocli:picocli-codegen:4.7.0") // picocli-codegen as kapt 45 | 46 | implementation("org.jetbrains.lets-plot:lets-plot-batik:3.0.0") 47 | implementation("org.jetbrains.lets-plot:lets-plot-jfx:3.0.0") 48 | implementation("org.jetbrains.lets-plot:lets-plot-common:3.0.0") 49 | implementation("org.jetbrains.lets-plot:lets-plot-kotlin-jvm:4.2.0") 50 | implementation("org.jetbrains.lets-plot:lets-plot-image-export:3.0.0") 51 | implementation("org.slf4j:slf4j-simple:2.0.6") // dependencies for lets-plot library 52 | } 53 | 54 | tasks.test { 55 | useJUnitPlatform() 56 | } 57 | 58 | tasks.withType { 59 | kotlinOptions.jvmTarget = "11" // version of jvmTarget 60 | } 61 | 62 | kapt { // kapt block with the argument project 63 | arguments { 64 | arg("project", "${project.group}/${project.name}") 65 | } 66 | } 67 | 68 | application { 69 | mainClass.set("RunBAMScopeKt") 70 | } 71 | 72 | tasks.withType { 73 | // Otherwise you'll get a "No main manifest attribute" error 74 | manifest { 75 | attributes["Main-Class"] = "com.jslfree080.bamscope.RunBAMScopeKt" 76 | archiveFileName.set("bamscope.jar") 77 | } 78 | 79 | // To avoid the duplicate handling strategy error 80 | duplicatesStrategy = 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13 |

CheckWidthAgainTest

14 |
15 | all > 16 | com.jslfree080.process > CheckWidthAgainTest
17 |
18 | 19 | 20 | 52 | 58 | 59 |
21 |
22 | 23 | 24 | 30 | 36 | 42 | 48 | 49 |
25 |
26 |
1
27 |

tests

28 |
29 | 		31 |
32 |
0
33 |

failures

34 |
35 | 		37 |
38 |
0
39 |

ignored

40 |
41 | 		43 |
44 |
0.030s
45 |

duration

46 |
47 |
50 |
51 | 		53 |
54 |
100%
55 |

successful

56 |
57 |
60 |
61 |
62 |
    63 |
  • 64 | Tests 65 |
    • 66 |
67 |
68 |

Tests

69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 |
TestDurationResult
testExpDecayResult()0.030spassed
83 |
84 |
85 | 94 |
95 | 96 | 97 | -------------------------------------------------------------------------------- /build/reports/tests/test/classes/com.jslfree080.process.CheckWidthFirstTest.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | Test results - CheckWidthFirstTest 7 | 8 | 9 | 10 | 11 | 12 |
13 |

CheckWidthFirstTest

14 |
15 | all > 16 | com.jslfree080.process > CheckWidthFirstTest
17 |
18 | 19 | 20 | 52 | 58 | 59 |
21 |
22 | 23 | 24 | 30 | 36 | 42 | 48 | 49 |
25 |
26 |
1
27 |

tests

28 |
29 | 		31 |
32 |
0
33 |

failures

34 |
35 | 		37 |
38 |
0
39 |

ignored

40 |
41 | 		43 |
44 |
0.002s
45 |

duration

46 |
47 |
50 |
51 | 		53 |
54 |
100%
55 |

successful

56 |
57 |
60 |
61 |
62 |
    63 |
  • 64 | Tests 65 |
    • 66 |
67 |
68 |

Tests

69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 |
TestDurationResult
testFixedResult()0.002spassed
83 |
84 |
85 | 94 |
95 | 96 | 97 | -------------------------------------------------------------------------------- /build/reports/tests/test/css/base-style.css: -------------------------------------------------------------------------------- 1 | 2 | body { 3 | margin: 0; 4 | padding: 0; 5 | font-family: sans-serif; 6 | font-size: 12pt; 7 | } 8 | 9 | body, a, a:visited { 10 | color: #303030; 11 | } 12 | 13 | #content { 14 | padding-left: 50px; 15 | padding-right: 50px; 16 | padding-top: 30px; 17 | padding-bottom: 30px; 18 | } 19 | 20 | #content h1 { 21 | font-size: 160%; 22 | margin-bottom: 10px; 23 | } 24 | 25 | #footer { 26 | margin-top: 100px; 27 | font-size: 80%; 28 | white-space: nowrap; 29 | } 30 | 31 | #footer, #footer a { 32 | color: #a0a0a0; 33 | } 34 | 35 | #line-wrapping-toggle { 36 | vertical-align: middle; 37 | } 38 | 39 | #label-for-line-wrapping-toggle { 40 | vertical-align: middle; 41 | } 42 | 43 | ul { 44 | margin-left: 0; 45 | } 46 | 47 | h1, h2, h3 { 48 | white-space: nowrap; 49 | } 50 | 51 | h2 { 52 | font-size: 120%; 53 | } 54 | 55 | ul.tabLinks { 56 | padding-left: 0; 57 | padding-top: 10px; 58 | padding-bottom: 10px; 59 | overflow: auto; 60 | min-width: 800px; 61 | width: auto !important; 62 | width: 800px; 63 | } 64 | 65 | ul.tabLinks li { 66 | float: left; 67 | height: 100%; 68 | list-style: none; 69 | padding-left: 10px; 70 | padding-right: 10px; 71 | padding-top: 5px; 72 | padding-bottom: 5px; 73 | margin-bottom: 0; 74 | -moz-border-radius: 7px; 75 | border-radius: 7px; 76 | margin-right: 25px; 77 | border: solid 1px #d4d4d4; 78 | background-color: #f0f0f0; 79 | } 80 | 81 | ul.tabLinks li:hover { 82 | background-color: #fafafa; 83 | } 84 | 85 | ul.tabLinks li.selected { 86 | background-color: #c5f0f5; 87 | border-color: #c5f0f5; 88 | } 89 | 90 | ul.tabLinks a { 91 | font-size: 120%; 92 | display: block; 93 | outline: none; 94 | text-decoration: none; 95 | margin: 0; 96 | padding: 0; 97 | } 98 | 99 | ul.tabLinks li h2 { 100 | margin: 0; 101 | padding: 0; 102 | } 103 | 104 | div.tab { 105 | } 106 | 107 | div.selected { 108 | display: block; 109 | } 110 | 111 | div.deselected { 112 | display: none; 113 | } 114 | 115 | div.tab table { 116 | min-width: 350px; 117 | width: auto !important; 118 | width: 350px; 119 | border-collapse: collapse; 120 | } 121 | 122 | div.tab th, div.tab table { 123 | border-bottom: solid #d0d0d0 1px; 124 | } 125 | 126 | div.tab th { 127 | text-align: left; 128 | white-space: nowrap; 129 | padding-left: 6em; 130 | } 131 | 132 | div.tab th:first-child { 133 | padding-left: 0; 134 | } 135 | 136 | div.tab td { 137 | white-space: nowrap; 138 | padding-left: 6em; 139 | padding-top: 5px; 140 | padding-bottom: 5px; 141 | } 142 | 143 | div.tab td:first-child { 144 | padding-left: 0; 145 | } 146 | 147 | div.tab td.numeric, div.tab th.numeric { 148 | text-align: right; 149 | } 150 | 151 | span.code { 152 | display: inline-block; 153 | margin-top: 0em; 154 | margin-bottom: 1em; 155 | } 156 | 157 | span.code pre { 158 | font-size: 11pt; 159 | padding-top: 10px; 160 | padding-bottom: 10px; 161 | padding-left: 10px; 162 | padding-right: 10px; 163 | margin: 0; 164 | background-color: #f7f7f7; 165 | border: solid 1px #d0d0d0; 166 | min-width: 700px; 167 | width: auto !important; 168 | width: 700px; 169 | } 170 | 171 | span.wrapped pre { 172 | word-wrap: break-word; 173 | white-space: pre-wrap; 174 | word-break: break-all; 175 | } 176 | 177 | label.hidden { 178 | display: none; 179 | } -------------------------------------------------------------------------------- /build/reports/tests/test/css/style.css: -------------------------------------------------------------------------------- 1 | 2 | #summary { 3 | margin-top: 30px; 4 | margin-bottom: 40px; 5 | } 6 | 7 | #summary table { 8 | border-collapse: collapse; 9 | } 10 | 11 | #summary td { 12 | vertical-align: top; 13 | } 14 | 15 | .breadcrumbs, .breadcrumbs a { 16 | color: #606060; 17 | } 18 | 19 | .infoBox { 20 | width: 110px; 21 | padding-top: 15px; 22 | padding-bottom: 15px; 23 | text-align: center; 24 | } 25 | 26 | .infoBox p { 27 | margin: 0; 28 | } 29 | 30 | .counter, .percent { 31 | font-size: 120%; 32 | font-weight: bold; 33 | margin-bottom: 8px; 34 | } 35 | 36 | #duration { 37 | width: 125px; 38 | } 39 | 40 | #successRate, .summaryGroup { 41 | border: solid 2px #d0d0d0; 42 | -moz-border-radius: 10px; 43 | border-radius: 10px; 44 | } 45 | 46 | #successRate { 47 | width: 140px; 48 | margin-left: 35px; 49 | } 50 | 51 | #successRate .percent { 52 | font-size: 180%; 53 | } 54 | 55 | .success, .success a { 56 | color: #008000; 57 | } 58 | 59 | div.success, #successRate.success { 60 | background-color: #bbd9bb; 61 | border-color: #008000; 62 | } 63 | 64 | .failures, .failures a { 65 | color: #b60808; 66 | } 67 | 68 | .skipped, .skipped a { 69 | color: #c09853; 70 | } 71 | 72 | div.failures, #successRate.failures { 73 | background-color: #ecdada; 74 | border-color: #b60808; 75 | } 76 | 77 | ul.linkList { 78 | padding-left: 0; 79 | } 80 | 81 | ul.linkList li { 82 | list-style: none; 83 | margin-bottom: 5px; 84 | } 85 | -------------------------------------------------------------------------------- /build/reports/tests/test/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | Test results - Test Summary 7 | 8 | 9 | 10 | 11 | 12 |
13 |

Test Summary

14 |
15 | 16 | 17 | 49 | 55 | 56 |
18 |
19 | 20 | 21 | 27 | 33 | 39 | 45 | 46 |
22 |
23 |
2
24 |

tests

25 |
26 | 		28 |
29 |
0
30 |

failures

31 |
32 | 		34 |
35 |
0
36 |

ignored

37 |
38 | 		40 |
41 |
0.032s
42 |

duration

43 |
44 |
47 |
48 | 		50 |
51 |
100%
52 |

successful

53 |
54 |
57 |
58 |
59 | 67 |
68 |

Packages

69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 |
PackageTestsFailuresIgnoredDurationSuccess rate
83 | com.jslfree080.process 84 | 2000.032s100%
93 |
94 |
95 |

Classes

96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 122 | 123 | 124 | 125 | 126 | 127 | 128 | 129 |
ClassTestsFailuresIgnoredDurationSuccess rate
110 | com.jslfree080.process.CheckWidthAgainTest 111 | 1000.030s100%
120 | com.jslfree080.process.CheckWidthFirstTest 121 | 1000.002s100%
130 |
131 |
132 | 141 |
142 | 143 | 144 | -------------------------------------------------------------------------------- /build/reports/tests/test/packages/com.jslfree080.process.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | Test results - Package com.jslfree080.process 7 | 8 | 9 | 10 | 11 | 12 |
13 |

Package com.jslfree080.process

14 |
15 | all > com.jslfree080.process
16 |
17 | 18 | 19 | 51 | 57 | 58 |
20 |
21 | 22 | 23 | 29 | 35 | 41 | 47 | 48 |
24 |
25 |
2
26 |

tests

27 |
28 | 		30 |
31 |
0
32 |

failures

33 |
34 | 		36 |
37 |
0
38 |

ignored

39 |
40 | 		42 |
43 |
0.032s
44 |

duration

45 |
46 |
49 |
50 | 		52 |
53 |
100%
54 |

successful

55 |
56 |
59 |
60 |
61 | 66 |
67 |

Classes

68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 93 | 94 | 95 | 96 | 97 | 98 | 99 |
ClassTestsFailuresIgnoredDurationSuccess rate
81 | CheckWidthAgainTest 82 | 1000.030s100%
91 | CheckWidthFirstTest 92 | 1000.002s100%
100 |
101 |
102 | 111 |
112 | 113 | 114 | -------------------------------------------------------------------------------- /build/test-results/test/TEST-com.jslfree080.process.CheckWidthAgainTest.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | -------------------------------------------------------------------------------- /build/test-results/test/TEST-com.jslfree080.process.CheckWidthFirstTest.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | -------------------------------------------------------------------------------- /build/test-results/test/binary/output.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/test-results/test/binary/output.bin -------------------------------------------------------------------------------- /build/test-results/test/binary/output.bin.idx: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /build/test-results/test/binary/results.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/test-results/test/binary/results.bin -------------------------------------------------------------------------------- /build/tmp/jar/MANIFEST.MF: -------------------------------------------------------------------------------- 1 | Manifest-Version: 1.0 2 | Main-Class: com.jslfree080.bamscope.RunBAMScopeKt 3 | 4 | -------------------------------------------------------------------------------- /build/tmp/kapt3/classes/main/META-INF/native-image/picocli-generated/com.jslfree080/bamscope/proxy-config.json: -------------------------------------------------------------------------------- 1 | [ 2 | ] 3 | -------------------------------------------------------------------------------- /build/tmp/kapt3/classes/main/META-INF/native-image/picocli-generated/com.jslfree080/bamscope/reflect-config.json: -------------------------------------------------------------------------------- 1 | [ 2 | { 3 | "name" : "com.jslfree080.cli.BAMScopeCommand", 4 | "allDeclaredConstructors" : true, 5 | "allPublicConstructors" : true, 6 | "allDeclaredMethods" : true, 7 | "allPublicMethods" : true, 8 | "fields" : [ 9 | { "name" : "bamPath" }, 10 | { "name" : "chrPos" }, 11 | { "name" : "format" }, 12 | { "name" : "help" }, 13 | { "name" : "outPath" }, 14 | { "name" : "refPath" }, 15 | { "name" : "sPath" }, 16 | { "name" : "width" } 17 | ] 18 | } 19 | ] 20 | -------------------------------------------------------------------------------- /build/tmp/kapt3/classes/main/META-INF/native-image/picocli-generated/com.jslfree080/bamscope/resource-config.json: -------------------------------------------------------------------------------- 1 | { 2 | "bundles" : [ 3 | ], 4 | "resources" : [ 5 | ] 6 | } 7 | -------------------------------------------------------------------------------- /build/tmp/kapt3/incApCache/main/ap-classpath-entries.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/incApCache/main/ap-classpath-entries.bin -------------------------------------------------------------------------------- /build/tmp/kapt3/incApCache/main/apt-cache.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/incApCache/main/apt-cache.bin 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{"\u0000\u0014\n\u0000\n\u0002\u0010\u0002\n\u0000\n\u0002\u0010\u0011\n\u0002\u0010\u000e\n\u0002\b\u0002\u001a\u0019\u0010\u0000\u001a\u00020\u00012\f\u0010\u0002\u001a\b\u0012\u0004\u0012\u00020\u00040\u0003\u00a2\u0006\u0002\u0010\u0005\u00a8\u0006\u0006"}, d2 = {"main", "", "args", "", "", "([Ljava/lang/String;)V", "bamscope"}) 6 | public final class RunBAMScopeKt { 7 | 8 | public static final void main(@org.jetbrains.annotations.NotNull() 9 | java.lang.String[] args) { 10 | } 11 | } -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/bamscope/RunBAMScopeKt.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/bamscope/RunBAMScopeKt.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/cli/BAMScopeCommand.java: -------------------------------------------------------------------------------- 1 | package com.jslfree080.cli; 2 | 3 | import java.lang.System; 4 | 5 | @kotlin.Metadata(mv = {1, 8, 0}, k = 1, d1 = {"\u0000(\n\u0002\u0018\u0002\n\u0002\u0018\u0002\n\u0002\b\u0002\n\u0002\u0010\u000e\n\u0002\b\u0003\n\u0002\u0010\u000b\n\u0002\b\u0004\n\u0002\u0010\b\n\u0000\n\u0002\u0010\u0002\n\u0000\b\u0007\u0018\u00002\u00020\u0001B\u0005\u00a2\u0006\u0002\u0010\u0002J\b\u0010\u000e\u001a\u00020\u000fH\u0016R\u0012\u0010\u0003\u001a\u00020\u00048\u0002@\u0002X\u0083.\u00a2\u0006\u0002\n\u0000R\u0012\u0010\u0005\u001a\u00020\u00048\u0002@\u0002X\u0083.\u00a2\u0006\u0002\n\u0000R\u0012\u0010\u0006\u001a\u00020\u00048\u0002@\u0002X\u0083\u000e\u00a2\u0006\u0002\n\u0000R\u0012\u0010\u0007\u001a\u00020\b8\u0002@\u0002X\u0083\u000e\u00a2\u0006\u0002\n\u0000R\u0012\u0010\t\u001a\u00020\u00048\u0002@\u0002X\u0083\u000e\u00a2\u0006\u0002\n\u0000R\u0012\u0010\n\u001a\u00020\u00048\u0002@\u0002X\u0083\u000e\u00a2\u0006\u0002\n\u0000R\u0012\u0010\u000b\u001a\u00020\u00048\u0002@\u0002X\u0083\u000e\u00a2\u0006\u0002\n\u0000R\u0012\u0010\f\u001a\u00020\r8\u0002@\u0002X\u0083\u000e\u00a2\u0006\u0002\n\u0000\u00a8\u0006\u0010"}, d2 = {"Lcom/jslfree080/cli/BAMScopeCommand;", "Ljava/lang/Runnable;", "()V", "bamPath", "", "chrPos", "format", "help", "", "outPath", "refPath", "sPath", "width", "", "run", "", "bamscope"}) 6 | @picocli.CommandLine.Command(name = "bamscope", version = {"bamscope 1.1.0"}, description = {"A command line tool (in Kotlin/JVM) for visualizing BAM alignments."}) 7 | public final class BAMScopeCommand implements java.lang.Runnable { 8 | @picocli.CommandLine.Parameters(index = "0", description = {"Input chromosomal position ex) (chr)N:XXXXXXXX\n or path to a VCF file. or path/to/x.vcf"}) 9 | private java.lang.String chrPos; 10 | @picocli.CommandLine.Parameters(index = "1", description = {"Path to an indexed BAM file. ex) path/to/x.bam"}) 11 | private java.lang.String bamPath; 12 | @picocli.CommandLine.Option(names = {"-f", "--format"}, description = {"File format of an output image. default) png"}) 13 | private java.lang.String format = "png"; 14 | @picocli.CommandLine.Option(names = {"-h", "--help"}, usageHelp = true, description = {"Show this help message and exit."}) 15 | private boolean help = false; 16 | @picocli.CommandLine.Option(names = {"-o", "--outPath"}, description = {"Path to an output image. default) ."}) 17 | private java.lang.String outPath = "."; 18 | @picocli.CommandLine.Option(names = {"-r", "--refPath"}, description = {"Path to a reference FASTA. ex) path/to/x.fasta(.fa)"}) 19 | private java.lang.String refPath = "noReferencePath"; 20 | @picocli.CommandLine.Option(names = {"-s", "--sPath"}, description = {"Path to the samtools. ex) /usr/local/bin/samtools"}) 21 | private java.lang.String sPath = "samtools"; 22 | @picocli.CommandLine.Option(names = {"-w", "--width"}, description = {"Width of start to interest position. default) 50"}) 23 | private int width = 50; 24 | 25 | public BAMScopeCommand() { 26 | super(); 27 | } 28 | 29 | @java.lang.Override() 30 | public void run() { 31 | } 32 | } -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/cli/BAMScopeCommand.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/cli/BAMScopeCommand.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/BlockAdjustment.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/BlockAdjustment.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/CheckWidthAgain.java: -------------------------------------------------------------------------------- 1 | package com.jslfree080.process; 2 | 3 | import java.lang.System; 4 | 5 | @kotlin.Metadata(mv = {1, 8, 0}, k = 1, d1 = {"\u0000\u001e\n\u0002\u0018\u0002\n\u0002\u0010\u0000\n\u0000\n\u0002\u0010\b\n\u0000\n\u0002\u0010!\n\u0002\b\u0004\n\u0002\u0010\u000b\n\u0000\u0018\u00002\u00020\u0001B\u001b\u0012\u0006\u0010\u0002\u001a\u00020\u0003\u0012\f\u0010\u0004\u001a\b\u0012\u0004\u0012\u00020\u00030\u0005\u00a2\u0006\u0002\u0010\u0006J\u0006\u0010\t\u001a\u00020\nR\u000e\u0010\u0007\u001a\u00020\u0003X\u0082\u0004\u00a2\u0006\u0002\n\u0000R\u000e\u0010\b\u001a\u00020\u0003X\u0082\u0004\u00a2\u0006\u0002\n\u0000R\u000e\u0010\u0002\u001a\u00020\u0003X\u0082\u0004\u00a2\u0006\u0002\n\u0000R\u0014\u0010\u0004\u001a\b\u0012\u0004\u0012\u00020\u00030\u0005X\u0082\u0004\u00a2\u0006\u0002\n\u0000\u00a8\u0006\u000b"}, d2 = {"Lcom/jslfree080/process/CheckWidthAgain;", "", "width", "", "yCoordinates", "", "(ILjava/util/List;)V", "higherLimit", "lowerLimit", "expDecayResult", "", "bamscope"}) 6 | public final class CheckWidthAgain { 7 | private final int width = 0; 8 | private final java.util.List yCoordinates = null; 9 | private final int lowerLimit = 0; 10 | private final int higherLimit = 0; 11 | 12 | public CheckWidthAgain(int width, @org.jetbrains.annotations.NotNull() 13 | java.util.List yCoordinates) { 14 | super(); 15 | } 16 | 17 | public final boolean expDecayResult() { 18 | return false; 19 | } 20 | } -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/CheckWidthAgain.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/CheckWidthAgain.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/CheckWidthFirst.java: -------------------------------------------------------------------------------- 1 | package com.jslfree080.process; 2 | 3 | import java.lang.System; 4 | 5 | @kotlin.Metadata(mv = {1, 8, 0}, k = 1, d1 = {"\u0000\u0018\n\u0002\u0018\u0002\n\u0002\u0010\u0000\n\u0000\n\u0002\u0010\b\n\u0002\b\u0002\n\u0002\u0010\u000b\n\u0000\u0018\u00002\u00020\u0001B\r\u0012\u0006\u0010\u0002\u001a\u00020\u0003\u00a2\u0006\u0002\u0010\u0004J\u0006\u0010\u0005\u001a\u00020\u0006R\u000e\u0010\u0002\u001a\u00020\u0003X\u0082\u0004\u00a2\u0006\u0002\n\u0000\u00a8\u0006\u0007"}, d2 = {"Lcom/jslfree080/process/CheckWidthFirst;", "", "width", "", "(I)V", "fixedResult", "", "bamscope"}) 6 | public final class CheckWidthFirst { 7 | private final int width = 0; 8 | 9 | public CheckWidthFirst(int width) { 10 | super(); 11 | } 12 | 13 | public final boolean fixedResult() { 14 | return false; 15 | } 16 | } -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/CheckWidthFirst.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/CheckWidthFirst.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/ExtractReference.java: -------------------------------------------------------------------------------- 1 | package com.jslfree080.process; 2 | 3 | import java.lang.System; 4 | 5 | @kotlin.Metadata(mv = {1, 8, 0}, k = 1, d1 = {"\u0000 \n\u0002\u0018\u0002\n\u0002\u0010\u0000\n\u0000\n\u0002\u0010 \n\u0002\u0018\u0002\n\u0002\u0010\b\n\u0000\n\u0002\u0010\u000e\n\u0002\b\f\u0018\u00002\u00020\u0001B9\u0012\u0018\u0010\u0002\u001a\u0014\u0012\u0010\u0012\u000e\u0012\u0004\u0012\u00020\u0005\u0012\u0004\u0012\u00020\u00050\u00040\u0003\u0012\u0018\u0010\u0006\u001a\u0014\u0012\u0010\u0012\u000e\u0012\u0004\u0012\u00020\u0005\u0012\u0004\u0012\u00020\u00070\u00040\u0003\u00a2\u0006\u0002\u0010\bJ\f\u0010\u0012\u001a\b\u0012\u0004\u0012\u00020\u00070\u0003R\u000e\u0010\t\u001a\u00020\u0005X\u0082\u000e\u00a2\u0006\u0002\n\u0000R\u000e\u0010\n\u001a\u00020\u0005X\u0082\u000e\u00a2\u0006\u0002\n\u0000R,\u0010\u000b\u001a\u0014\u0012\u0010\u0012\u000e\u0012\u0004\u0012\u00020\u0005\u0012\u0004\u0012\u00020\u00070\u00040\u0003X\u0086\u000e\u00a2\u0006\u000e\n\u0000\u001a\u0004\b\f\u0010\r\"\u0004\b\u000e\u0010\u000fR \u0010\u0010\u001a\u0014\u0012\u0010\u0012\u000e\u0012\u0004\u0012\u00020\u0005\u0012\u0004\u0012\u00020\u00050\u00040\u0003X\u0082\u0004\u00a2\u0006\u0002\n\u0000R\u000e\u0010\u0011\u001a\u00020\u0005X\u0082\u000e\u00a2\u0006\u0002\n\u0000R \u0010\u0006\u001a\u0014\u0012\u0010\u0012\u000e\u0012\u0004\u0012\u00020\u0005\u0012\u0004\u0012\u00020\u00070\u00040\u0003X\u0082\u0004\u00a2\u0006\u0002\n\u0000\u00a8\u0006\u0013"}, d2 = {"Lcom/jslfree080/process/ExtractReference;", "", "pairForShift", "", "Lkotlin/Pair;", "", "samtoolsFaidxPair", "", "(Ljava/util/List;Ljava/util/List;)V", "adder", "incrementer", "newSamtoolsMap", "getNewSamtoolsMap", "()Ljava/util/List;", "setNewSamtoolsMap", "(Ljava/util/List;)V", "pairForShiftSorted", "refReader", "returnBasesRef", "bamscope"}) 6 | public final class ExtractReference { 7 | private final java.util.List> samtoolsFaidxPair = null; 8 | private final java.util.List> pairForShiftSorted = null; 9 | @org.jetbrains.annotations.NotNull() 10 | private java.util.List> newSamtoolsMap; 11 | private int refReader = 0; 12 | private int adder = 0; 13 | private int incrementer = 0; 14 | 15 | public ExtractReference(@org.jetbrains.annotations.NotNull() 16 | java.util.List> pairForShift, @org.jetbrains.annotations.NotNull() 17 | java.util.List> samtoolsFaidxPair) { 18 | super(); 19 | } 20 | 21 | @org.jetbrains.annotations.NotNull() 22 | public final java.util.List> getNewSamtoolsMap() { 23 | return null; 24 | } 25 | 26 | public final void setNewSamtoolsMap(@org.jetbrains.annotations.NotNull() 27 | java.util.List> p0) { 28 | } 29 | 30 | @org.jetbrains.annotations.NotNull() 31 | public final java.util.List returnBasesRef() { 32 | return null; 33 | } 34 | } -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/ExtractReference.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/ExtractReference.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/ParseRead.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/ParseRead.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/PlotAlignment.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/PlotAlignment.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/ReadSamtools.java: -------------------------------------------------------------------------------- 1 | package com.jslfree080.process; 2 | 3 | import java.lang.System; 4 | 5 | @kotlin.Metadata(mv = {1, 8, 0}, k = 1, d1 = {"\u0000\u001a\n\u0002\u0018\u0002\n\u0002\u0010\u0010\n\u0000\n\u0002\u0010\u000e\n\u0002\b\u0002\n\u0002\u0010 \n\u0002\b\b\b\u0086\u0001\u0018\u00002\b\u0012\u0004\u0012\u00020\u00000\u0001B\u000f\b\u0002\u0012\u0006\u0010\u0002\u001a\u00020\u0003\u00a2\u0006\u0002\u0010\u0004J4\u0010\u0005\u001a\b\u0012\u0004\u0012\u00020\u00030\u00062\u0006\u0010\u0007\u001a\u00020\u00032\u0006\u0010\b\u001a\u00020\u00032\u0006\u0010\t\u001a\u00020\u00032\u0006\u0010\n\u001a\u00020\u00032\u0006\u0010\u000b\u001a\u00020\u0003R\u000e\u0010\u0002\u001a\u00020\u0003X\u0082\u0004\u00a2\u0006\u0002\n\u0000j\u0002\b\fj\u0002\b\r\u00a8\u0006\u000e"}, d2 = {"Lcom/jslfree080/process/ReadSamtools;", "", "samtoolsCommand", "", "(Ljava/lang/String;ILjava/lang/String;)V", "processToLines", "", "path1", "path2", "chr", "pos1", "pos2", "VIEW", "FAIDX", "bamscope"}) 6 | public enum ReadSamtools { 7 | /*public static final*/ VIEW /* = new VIEW(null) */, 8 | /*public static final*/ FAIDX /* = new FAIDX(null) */; 9 | private final java.lang.String samtoolsCommand = null; 10 | 11 | ReadSamtools(java.lang.String samtoolsCommand) { 12 | } 13 | 14 | @org.jetbrains.annotations.NotNull() 15 | public final java.util.List processToLines(@org.jetbrains.annotations.NotNull() 16 | java.lang.String path1, @org.jetbrains.annotations.NotNull() 17 | java.lang.String path2, @org.jetbrains.annotations.NotNull() 18 | java.lang.String chr, @org.jetbrains.annotations.NotNull() 19 | java.lang.String pos1, @org.jetbrains.annotations.NotNull() 20 | java.lang.String pos2) { 21 | return null; 22 | } 23 | } -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/ReadSamtools.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/ReadSamtools.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/RunSamtools.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/RunSamtools.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarDeletion.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarDeletion.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarInsertion.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarInsertion.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarMatch.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarMatch.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarPadding.java: -------------------------------------------------------------------------------- 1 | package com.jslfree080.process.cigars; 2 | 3 | import java.lang.System; 4 | 5 | @kotlin.Metadata(mv = {1, 8, 0}, k = 1, d1 = {"\u0000\u0012\n\u0002\u0018\u0002\n\u0002\u0010\u0000\n\u0000\n\u0002\u0010\b\n\u0002\b\t\u0018\u00002\u00020\u0001B\r\u0012\u0006\u0010\u0002\u001a\u00020\u0003\u00a2\u0006\u0002\u0010\u0004J\u0006\u0010\u000b\u001a\u00020\u0003R\u001a\u0010\u0005\u001a\u00020\u0003X\u0086\u000e\u00a2\u0006\u000e\n\u0000\u001a\u0004\b\u0006\u0010\u0007\"\u0004\b\b\u0010\u0004R\u001a\u0010\u0002\u001a\u00020\u0003X\u0086\u000e\u00a2\u0006\u000e\n\u0000\u001a\u0004\b\t\u0010\u0007\"\u0004\b\n\u0010\u0004\u00a8\u0006\f"}, d2 = {"Lcom/jslfree080/process/cigars/CigarPadding;", "", "refPos", "", "(I)V", "count", "getCount", "()I", "setCount", "getRefPos", "setRefPos", "returnShiftedRefPos", "bamscope"}) 6 | public final class CigarPadding { 7 | private int refPos; 8 | private int count = 0; 9 | 10 | public CigarPadding(int refPos) { 11 | super(); 12 | } 13 | 14 | public final int getRefPos() { 15 | return 0; 16 | } 17 | 18 | public final void setRefPos(int p0) { 19 | } 20 | 21 | public final int getCount() { 22 | return 0; 23 | } 24 | 25 | public final void setCount(int p0) { 26 | } 27 | 28 | public final int returnShiftedRefPos() { 29 | return 0; 30 | } 31 | } -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarPadding.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarPadding.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarSkippedRegion.java: -------------------------------------------------------------------------------- 1 | package com.jslfree080.process.cigars; 2 | 3 | import java.lang.System; 4 | 5 | @kotlin.Metadata(mv = {1, 8, 0}, k = 1, d1 = {"\u0000\u0012\n\u0002\u0018\u0002\n\u0002\u0010\u0000\n\u0000\n\u0002\u0010\b\n\u0002\b\t\u0018\u00002\u00020\u0001B\r\u0012\u0006\u0010\u0002\u001a\u00020\u0003\u00a2\u0006\u0002\u0010\u0004J\u0006\u0010\u000b\u001a\u00020\u0003R\u001a\u0010\u0005\u001a\u00020\u0003X\u0086\u000e\u00a2\u0006\u000e\n\u0000\u001a\u0004\b\u0006\u0010\u0007\"\u0004\b\b\u0010\u0004R\u001a\u0010\u0002\u001a\u00020\u0003X\u0086\u000e\u00a2\u0006\u000e\n\u0000\u001a\u0004\b\t\u0010\u0007\"\u0004\b\n\u0010\u0004\u00a8\u0006\f"}, d2 = {"Lcom/jslfree080/process/cigars/CigarSkippedRegion;", "", "refPos", "", "(I)V", "count", "getCount", "()I", "setCount", "getRefPos", "setRefPos", "returnShiftedRefPos", "bamscope"}) 6 | public final class CigarSkippedRegion { 7 | private int refPos; 8 | private int count = 0; 9 | 10 | public CigarSkippedRegion(int refPos) { 11 | super(); 12 | } 13 | 14 | public final int getRefPos() { 15 | return 0; 16 | } 17 | 18 | public final void setRefPos(int p0) { 19 | } 20 | 21 | public final int getCount() { 22 | return 0; 23 | } 24 | 25 | public final void setCount(int p0) { 26 | } 27 | 28 | public final int returnShiftedRefPos() { 29 | return 0; 30 | } 31 | } -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarSkippedRegion.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarSkippedRegion.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarSoftClip.java: -------------------------------------------------------------------------------- 1 | package com.jslfree080.process.cigars; 2 | 3 | import java.lang.System; 4 | 5 | @kotlin.Metadata(mv = {1, 8, 0}, k = 1, d1 = {"\u0000\u0012\n\u0002\u0018\u0002\n\u0002\u0010\u0000\n\u0000\n\u0002\u0010\b\n\u0002\b\t\u0018\u00002\u00020\u0001B\r\u0012\u0006\u0010\u0002\u001a\u00020\u0003\u00a2\u0006\u0002\u0010\u0004J\u0006\u0010\u000b\u001a\u00020\u0003R\u001a\u0010\u0005\u001a\u00020\u0003X\u0086\u000e\u00a2\u0006\u000e\n\u0000\u001a\u0004\b\u0006\u0010\u0007\"\u0004\b\b\u0010\u0004R\u001a\u0010\u0002\u001a\u00020\u0003X\u0086\u000e\u00a2\u0006\u000e\n\u0000\u001a\u0004\b\t\u0010\u0007\"\u0004\b\n\u0010\u0004\u00a8\u0006\f"}, d2 = {"Lcom/jslfree080/process/cigars/CigarSoftClip;", "", "seqPos", "", "(I)V", "count", "getCount", "()I", "setCount", "getSeqPos", "setSeqPos", "returnShiftedSeqPos", "bamscope"}) 6 | public final class CigarSoftClip { 7 | private int seqPos; 8 | private int count = 0; 9 | 10 | public CigarSoftClip(int seqPos) { 11 | super(); 12 | } 13 | 14 | public final int getSeqPos() { 15 | return 0; 16 | } 17 | 18 | public final void setSeqPos(int p0) { 19 | } 20 | 21 | public final int getCount() { 22 | return 0; 23 | } 24 | 25 | public final void setCount(int p0) { 26 | } 27 | 28 | public final int returnShiftedSeqPos() { 29 | return 0; 30 | } 31 | } -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarSoftClip.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/CigarSoftClip.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/ParameterMID.kapt_metadata: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/build/tmp/kapt3/stubs/main/com/jslfree080/process/cigars/ParameterMID.kapt_metadata -------------------------------------------------------------------------------- /build/tmp/kapt3/stubs/main/error/NonExistentClass.java: -------------------------------------------------------------------------------- 1 | package error; 2 | 3 | public final class NonExistentClass { 4 | } -------------------------------------------------------------------------------- /gradle.properties: -------------------------------------------------------------------------------- 1 | kotlin.code.style=official 2 | -------------------------------------------------------------------------------- /gradle/wrapper/gradle-wrapper.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jslfree080/bamscope/56d216caf46e9afca50472c0ba3e32f45d77bc4b/gradle/wrapper/gradle-wrapper.jar -------------------------------------------------------------------------------- /gradle/wrapper/gradle-wrapper.properties: -------------------------------------------------------------------------------- 1 | distributionBase=GRADLE_USER_HOME 2 | distributionPath=wrapper/dists 3 | distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip 4 | zipStoreBase=GRADLE_USER_HOME 5 | zipStorePath=wrapper/dists -------------------------------------------------------------------------------- /gradlew.bat: -------------------------------------------------------------------------------- 1 | @rem 2 | @rem Copyright 2015 the original author or authors. 3 | @rem 4 | @rem Licensed under the Apache License, Version 2.0 (the "License"); 5 | @rem you may not use this file except in compliance with the License. 6 | @rem You may obtain a copy of the License at 7 | @rem 8 | @rem https://www.apache.org/licenses/LICENSE-2.0 9 | @rem 10 | @rem Unless required by applicable law or agreed to in writing, software 11 | @rem distributed under the License is distributed on an "AS IS" BASIS, 12 | @rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | @rem See the License for the specific language governing permissions and 14 | @rem limitations under the License. 15 | @rem 16 | 17 | @if "%DEBUG%" == "" @echo off 18 | @rem ########################################################################## 19 | @rem 20 | @rem Gradle startup script for Windows 21 | @rem 22 | @rem ########################################################################## 23 | 24 | @rem Set local scope for the variables with windows NT shell 25 | if "%OS%"=="Windows_NT" setlocal 26 | 27 | set DIRNAME=%~dp0 28 | if "%DIRNAME%" == "" set DIRNAME=. 29 | set APP_BASE_NAME=%~n0 30 | set APP_HOME=%DIRNAME% 31 | 32 | @rem Resolve any "." and ".." in APP_HOME to make it shorter. 33 | for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi 34 | 35 | @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. 36 | set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m" 37 | 38 | @rem Find java.exe 39 | if defined JAVA_HOME goto findJavaFromJavaHome 40 | 41 | set JAVA_EXE=java.exe 42 | %JAVA_EXE% -version >NUL 2>&1 43 | if "%ERRORLEVEL%" == "0" goto execute 44 | 45 | echo. 46 | echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 47 | echo. 48 | echo Please set the JAVA_HOME variable in your environment to match the 49 | echo location of your Java installation. 50 | 51 | goto fail 52 | 53 | :findJavaFromJavaHome 54 | set JAVA_HOME=%JAVA_HOME:"=% 55 | set JAVA_EXE=%JAVA_HOME%/bin/java.exe 56 | 57 | if exist "%JAVA_EXE%" goto execute 58 | 59 | echo. 60 | echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 61 | echo. 62 | echo Please set the JAVA_HOME variable in your environment to match the 63 | echo location of your Java installation. 64 | 65 | goto fail 66 | 67 | :execute 68 | @rem Setup the command line 69 | 70 | set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar 71 | 72 | 73 | @rem Execute Gradle 74 | "%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %* 75 | 76 | :end 77 | @rem End local scope for the variables with windows NT shell 78 | if "%ERRORLEVEL%"=="0" goto mainEnd 79 | 80 | :fail 81 | rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of 82 | rem the _cmd.exe /c_ return code! 83 | if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 84 | exit /b 1 85 | 86 | :mainEnd 87 | if "%OS%"=="Windows_NT" endlocal 88 | 89 | :omega 90 | -------------------------------------------------------------------------------- /settings.gradle.kts: -------------------------------------------------------------------------------- 1 | 2 | rootProject.name = "bamscope" 3 | 4 | -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/bamscope/RunBAMScope.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.bamscope 26 | 27 | import picocli.CommandLine 28 | import com.jslfree080.cli.BAMScopeCommand 29 | 30 | fun main(args: Array) { 31 | CommandLine(BAMScopeCommand()).execute(*args) 32 | } -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/process/CheckWidthAgain.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process 26 | 27 | import kotlin.math.* 28 | 29 | class CheckWidthAgain(private val width: Int, private val yCoordinates: MutableList) { 30 | private val lowerLimit = ceil(40 * exp(-0.0015 * (yCoordinates.max() + 2))).toInt() 31 | private val higherLimit = floor(51 * exp(0.0055 * (yCoordinates.max() + 2))).toInt() 32 | 33 | fun expDecayResult(): Boolean { 34 | return if (width !in lowerLimit..higherLimit) { 35 | System.err.println( 36 | "Try setting width (current: $width) between $lowerLimit to $higherLimit for this read depth!" 37 | ) 38 | false 39 | } else { 40 | true 41 | } 42 | } 43 | } -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/process/CheckWidthFirst.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process 26 | 27 | class CheckWidthFirst(private val width: Int) { 28 | fun fixedResult(): Boolean { 29 | return if (width !in 1..400) { 30 | System.err.println( 31 | "Width (current: $width) should be always positive value no more than 400!" 32 | ) 33 | false 34 | } else { 35 | true 36 | } 37 | } 38 | } -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/process/ExtractReference.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process 26 | 27 | class ExtractReference(pairForShift: List>, 28 | private val samtoolsFaidxPair: List>) { 29 | private val pairForShiftSorted = pairForShift.sortedBy { it.first } 30 | var newSamtoolsMap = emptyList>() 31 | private var refReader = 0 32 | private var adder = 0 33 | private var incrementer = 0 34 | 35 | fun returnBasesRef(): List { 36 | (pairForShiftSorted.indices).forEach { 37 | while (samtoolsFaidxPair 38 | .map { (list1, _) -> list1 }[refReader] 39 | < 40 | pairForShiftSorted 41 | .map { (list1, _) -> list1 }[it]) { 42 | newSamtoolsMap = newSamtoolsMap + 43 | samtoolsFaidxPair 44 | .filter { (list1, _) -> list1 == samtoolsFaidxPair.map { (list1, _) -> list1 }[refReader] } 45 | .map { (list1, list2) -> list1 + adder to list2 } 46 | refReader += 1 47 | if (samtoolsFaidxPair.map { (list1, _) -> list1 }[refReader] == 48 | pairForShiftSorted.map { (list1, _) -> list1 }[it]) { break } 49 | } 50 | for (idx in 0 until pairForShiftSorted.map { (_, list2) -> list2 }[it]) { 51 | incrementer = adder 52 | newSamtoolsMap = newSamtoolsMap + 53 | listOf(pairForShiftSorted.map { (list1, _) -> list1 }[it] + incrementer).zip(listOf("gap")) 54 | adder += 1 55 | } 56 | } 57 | while (true) { 58 | try { 59 | newSamtoolsMap = newSamtoolsMap + 60 | samtoolsFaidxPair 61 | .filter { (list1, _) -> list1 == samtoolsFaidxPair.map { (list1, _) -> list1 }[refReader] } 62 | .map { (list1, list2) -> list1 + adder to list2 } 63 | refReader += 1 64 | } catch (_: IndexOutOfBoundsException) { break } 65 | } 66 | return newSamtoolsMap.map { (_, list2) -> list2 } 67 | } 68 | } -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/process/ReadSamtools.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process 26 | 27 | enum class ReadSamtools(private val samtoolsCommand: String) { 28 | VIEW("view"), FAIDX("faidx"); 29 | 30 | fun processToLines(path1: String, path2: String, chr: String, pos1: String, pos2: String): List { 31 | val samtoolsProcess: Process = ProcessBuilder(path1, samtoolsCommand, path2, "$chr:$pos1-$pos2") 32 | .redirectOutput(ProcessBuilder.Redirect.PIPE) 33 | .start() 34 | val samtoolsOutput = samtoolsProcess.inputStream.bufferedReader().use { it.readText() } 35 | return samtoolsOutput.split("\n") 36 | } 37 | } -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/process/RunSamtools.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process 26 | 27 | class RunSamtools(chrPos: String, bamPath: String, width: Int, refPath: String, sPath: String) { 28 | val chr = chrPos.split(":")[0] 29 | val intPos = chrPos.split(":")[1] 30 | val startPos = (intPos.toInt() - width).toString() 31 | val endPos = (intPos.toInt() + width).toString() 32 | // Run samtools to extract the reads within the specified region 33 | val samtoolsViewLines = ReadSamtools.VIEW.processToLines(sPath, bamPath, chr, startPos, endPos) 34 | // Run samtools to extract the reference sequence 35 | private val extraPos = (2 * endPos.toInt() - startPos.toInt()).toString() 36 | private val samtoolsFaidxLines = if (refPath == "noReferencePath") listOf("noReference", "") 37 | else ReadSamtools.FAIDX.processToLines(sPath, refPath, chr, startPos, extraPos) 38 | private val samtoolsFaidxString = samtoolsFaidxLines.drop(1).joinToString("") 39 | val samtoolsFaidxPair = (startPos.toInt() until extraPos.toInt()).zip(samtoolsFaidxString.toList()) 40 | .map { (list1, list2) -> list1 to list2.toString() } 41 | } -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/process/cigars/CigarDeletion.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process.cigars 26 | 27 | import java.lang.StringBuilder 28 | 29 | class CigarDeletion(private val sb: StringBuilder, 30 | var parameterMID: ParameterMID, 31 | var seqPos: Int, 32 | var refPos: Int) { 33 | var count = 0 34 | var partialIncrement = 0 35 | 36 | fun commonAppend() { 37 | for (c in 0 until count) { 38 | parameterMID.yCoordinates.add(parameterMID.yCoordinate) 39 | 40 | parameterMID.positions.add(refPos + c) 41 | 42 | sb.append(if ((parameterMID.flag and 0x10) == 0x10) "-" else "+") 43 | parameterMID.directions.add(sb.toString()) 44 | sb.setLength(0) 45 | } 46 | } 47 | 48 | fun pseudoReferenceForLegendAppend() { 49 | for (c in 0 until count) { 50 | sb.append(parameterMID.seq[seqPos]) 51 | parameterMID.pseudoReferenceForLegend.add(sb.toString()) 52 | sb.setLength(0) 53 | } 54 | } 55 | 56 | fun basesAppend() { 57 | for (c in 0 until count) { 58 | sb.append("del") 59 | parameterMID.bases.add(sb.toString()) 60 | sb.setLength(0) 61 | } 62 | } 63 | 64 | fun qualitiesAppend() { 65 | for (c in 0 until count) { 66 | parameterMID.qualities.add(0) 67 | } 68 | } 69 | 70 | fun blockNumbersAppend() { 71 | for (c in 0 until count) { 72 | parameterMID.blockNumbers.add(parameterMID.blockNumber) 73 | } 74 | } 75 | 76 | fun partialIncrementsWithZeroAppend() { 77 | for (c in 0 until count) { 78 | parameterMID.partialIncrementsWithZero.add(partialIncrement) 79 | } 80 | } 81 | 82 | fun returnShiftedParameterMID(): ParameterMID { 83 | return ParameterMID( 84 | parameterMID.yCoordinate, 85 | parameterMID.yCoordinates, 86 | parameterMID.positions, 87 | parameterMID.flag, 88 | parameterMID.directions, 89 | parameterMID.seq, 90 | parameterMID.pseudoReferenceForLegend, 91 | parameterMID.bases, 92 | parameterMID.qualities, 93 | parameterMID.blockNumber, 94 | parameterMID.blockNumbers, 95 | parameterMID.partialIncrementsWithZero) 96 | } 97 | 98 | fun returnShiftedRefPos(): Int { 99 | refPos += count 100 | return refPos 101 | } 102 | } -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/process/cigars/CigarMatch.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process.cigars 26 | 27 | import java.lang.StringBuilder 28 | 29 | class CigarMatch(private val sb: StringBuilder, 30 | var parameterMID: ParameterMID, 31 | var seqPos: Int, 32 | var refPos: Int, 33 | var qual: String) { 34 | var count = 0 35 | var partialIncrement = 0 36 | 37 | fun commonAppend() { 38 | for (c in 0 until count) { 39 | parameterMID.yCoordinates.add(parameterMID.yCoordinate) 40 | 41 | parameterMID.positions.add(refPos + c) 42 | 43 | sb.append(if ((parameterMID.flag and 0x10) == 0x10) "-" else "+") 44 | parameterMID.directions.add(sb.toString()) 45 | sb.setLength(0) 46 | } 47 | } 48 | 49 | fun pseudoReferenceForLegendAppend() { 50 | for (c in 0 until count) { 51 | sb.append(parameterMID.seq[seqPos + c]) 52 | parameterMID.pseudoReferenceForLegend.add(sb.toString()) 53 | sb.setLength(0) 54 | } 55 | } 56 | 57 | fun basesAppend() { 58 | for (c in 0 until count) { 59 | sb.append(parameterMID.seq[seqPos + c]) 60 | parameterMID.bases.add(sb.toString()) 61 | sb.setLength(0) 62 | } 63 | } 64 | 65 | fun qualitiesAppend() { 66 | for (c in 0 until count) { 67 | parameterMID.qualities.add(qual[seqPos + c].code - 33) 68 | } 69 | } 70 | 71 | fun blockNumbersAppend() { 72 | for (c in 0 until count) { 73 | parameterMID.blockNumbers.add(parameterMID.blockNumber) 74 | } 75 | } 76 | 77 | fun partialIncrementsWithZeroAppend() { 78 | for (c in 0 until count) { 79 | parameterMID.partialIncrementsWithZero.add(partialIncrement) 80 | } 81 | } 82 | 83 | fun returnShiftedParameterMID(): ParameterMID { 84 | return ParameterMID( 85 | parameterMID.yCoordinate, 86 | parameterMID.yCoordinates, 87 | parameterMID.positions, 88 | parameterMID.flag, 89 | parameterMID.directions, 90 | parameterMID.seq, 91 | parameterMID.pseudoReferenceForLegend, 92 | parameterMID.bases, 93 | parameterMID.qualities, 94 | parameterMID.blockNumber, 95 | parameterMID.blockNumbers, 96 | parameterMID.partialIncrementsWithZero) 97 | } 98 | 99 | fun returnShiftedSeqPos(): Int { 100 | seqPos += count 101 | return seqPos 102 | } 103 | 104 | fun returnShiftedRefPos(): Int { 105 | refPos += count 106 | return refPos 107 | } 108 | } -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/process/cigars/CigarPadding.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process.cigars 26 | 27 | class CigarPadding(var refPos: Int) { 28 | var count = 0 29 | 30 | fun returnShiftedRefPos(): Int { 31 | refPos += count 32 | return refPos 33 | } 34 | } -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/process/cigars/CigarSkippedRegion.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process.cigars 26 | 27 | class CigarSkippedRegion(var refPos: Int) { 28 | var count = 0 29 | 30 | fun returnShiftedRefPos(): Int { 31 | refPos += count 32 | return refPos 33 | } 34 | } -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/process/cigars/CigarSoftClip.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process.cigars 26 | 27 | class CigarSoftClip(var seqPos: Int) { 28 | var count = 0 29 | 30 | fun returnShiftedSeqPos(): Int { 31 | seqPos += count 32 | return seqPos 33 | } 34 | } -------------------------------------------------------------------------------- /src/main/kotlin/com/jslfree080/process/cigars/ParameterMID.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process.cigars 26 | 27 | class ParameterMID(val yCoordinate: Int, 28 | val yCoordinates: MutableList, 29 | val positions: MutableList, 30 | val flag: Int, 31 | val directions: MutableList, 32 | val seq: String, 33 | val pseudoReferenceForLegend: MutableList, 34 | val bases: MutableList, 35 | val qualities: MutableList, 36 | var blockNumber: Int, 37 | val blockNumbers: MutableList, 38 | val partialIncrementsWithZero: MutableList) -------------------------------------------------------------------------------- /src/test/kotlin/com/jslfree080/process/CheckWidthAgainTest.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process 26 | 27 | import org.junit.jupiter.api.Assertions.* 28 | import org.junit.jupiter.api.Test 29 | 30 | internal class CheckWidthAgainTest { 31 | @Test 32 | fun testExpDecayResult() { 33 | val checkWidthAgain = CheckWidthAgain(50, mutableListOf(1)) 34 | val result = checkWidthAgain.expDecayResult() 35 | assertTrue(result) 36 | } 37 | } -------------------------------------------------------------------------------- /src/test/kotlin/com/jslfree080/process/CheckWidthFirstTest.kt: -------------------------------------------------------------------------------- 1 | /* 2 | * MIT License 3 | * 4 | * Copyright (c) 2023 Jungsoo Lee 5 | * 6 | * Permission is hereby granted, free of charge, to any person obtaining a copy 7 | * of this software and associated documentation files (the "Software"), to deal 8 | * in the Software without restriction, including without limitation the rights 9 | * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | * copies of the Software, and to permit persons to whom the Software is 11 | * furnished to do so, subject to the following conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be included in all 14 | * copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | * SOFTWARE. 23 | */ 24 | 25 | package com.jslfree080.process 26 | 27 | import org.junit.jupiter.api.Assertions.* 28 | import org.junit.jupiter.api.Test 29 | 30 | internal class CheckWidthFirstTest { 31 | @Test 32 | fun testFixedResult() { 33 | val checkWidthFirst = CheckWidthFirst(50) 34 | val result = checkWidthFirst.fixedResult() 35 | assertTrue(result) 36 | } 37 | } --------------------------------------------------------------------------------