2.0 RC version. je markdupes does not deal with UMI from BAM TAG (still
expected in read names)
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- .project 23 additions, 0 deletions.project
- .settings/org.eclipse.core.resources.prefs 6 additions, 0 deletions.settings/org.eclipse.core.resources.prefs
- .settings/org.eclipse.jdt.core.prefs 8 additions, 0 deletions.settings/org.eclipse.jdt.core.prefs
- .settings/org.eclipse.jdt.ui.prefs 3 additions, 0 deletions.settings/org.eclipse.jdt.ui.prefs
- .settings/org.eclipse.m2e.core.prefs 4 additions, 0 deletions.settings/org.eclipse.m2e.core.prefs
- dist/README.md 9 additions, 0 deletionsdist/README.md
- dist/je 2 additions, 2 deletionsdist/je
- dist/je_2.0.RC.tar.gz 0 additions, 0 deletionsdist/je_2.0.RC.tar.gz
- dist/je_2.0.RC/je 18 additions, 0 deletionsdist/je_2.0.RC/je
- dist/je_2.0.RC/je_2.0.RC_bundle.jar 0 additions, 0 deletionsdist/je_2.0.RC/je_2.0.RC_bundle.jar
- dist/je_2.0.RC/log4j.xml 19 additions, 0 deletionsdist/je_2.0.RC/log4j.xml
- pom.xml 1 addition, 1 deletionpom.xml
- src/main/java/org/embl/gbcs/je/FastqWriterLayout.java 37 additions, 47 deletionssrc/main/java/org/embl/gbcs/je/FastqWriterLayout.java
- src/main/java/org/embl/gbcs/je/JeTry.java 3 additions, 3 deletionssrc/main/java/org/embl/gbcs/je/JeTry.java
- src/main/java/org/embl/gbcs/je/JeUtils.java 60 additions, 1 deletionsrc/main/java/org/embl/gbcs/je/JeUtils.java
- src/main/java/org/embl/gbcs/je/ReadLayoutConsumer.java 64 additions, 58 deletionssrc/main/java/org/embl/gbcs/je/ReadLayoutConsumer.java
- src/main/java/org/embl/gbcs/je/SampleMatch.java 3 additions, 0 deletionssrc/main/java/org/embl/gbcs/je/SampleMatch.java
- src/main/java/org/embl/gbcs/je/demultiplexer/DemultiplexCLI.java 45 additions, 39 deletions...n/java/org/embl/gbcs/je/demultiplexer/DemultiplexCLI.java
- src/main/java/org/embl/gbcs/je/demultiplexer/Demultiplexer.java 1 addition, 17 deletions...in/java/org/embl/gbcs/je/demultiplexer/Demultiplexer.java
- src/main/java/org/embl/gbcs/je/jeclipper/Jeclipper.java 29 additions, 2 deletionssrc/main/java/org/embl/gbcs/je/jeclipper/Jeclipper.java
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