Commit ce8607fc authored by Charles Girardot's avatar Charles Girardot

minor doc

parent 726a49b2
......@@ -9,8 +9,8 @@
<licenses>
<license>
<name>GPLv3</name>
<url><![CDATA[http://www.gnu.org/copyleft/gpl.html]]></url>
<name>MIT</name>
<url><![CDATA[https://opensource.org/licenses/MIT]]></url>
</license>
</licenses>
......@@ -27,7 +27,10 @@
by maven, this is performed by the src/shell/install-picard-deps-in-mvn-repos_from-git.sh
(you need to adapt path in there first !) The script also takes care of replacing
the jars in Je/lib to make sure we always distribute with the right custom
picard jars You can now build Je ! -->
picard jars You can now build Je !
TODO : Good news, my changes have been merged in picard so you should be able to switch to normal picard at next picard release
-->
......@@ -76,10 +79,12 @@
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<!-- Bind to packaging phase: the package phase will now produce 2 jars
: - the 'usual' one - one with all dependencies bundled -->
<!--
Bind to packaging phase: the package phase will now produce 2 jars:
- the 'usual' one
- one with all dependencies bundled
-->
<executions>
<execution>
<phase>package</phase>
......@@ -89,7 +94,7 @@
</execution>
</executions>
</plugin>
</plugins>
</plugins>
</build>
......
......@@ -137,7 +137,8 @@ public class MarkDuplicatesWithMolecularCode extends AbstractMarkDuplicatesComma
+ "\t to indicate that the three barcodes are molecular codes, use \n"
+ "\t\tSLOTS=-1 SLOTS=-2 SLOTS=-3\n"
+ "\t if only the 2 last ones should be considered (the third one being a sample encoding barcode), use \n"
+ "\t\tSLOTS=-1 SLOTS=-2\n"
+ "\t\tSLOTS=-1 SLOTS=-2"
+ "\t N.B.: UMI usage can be deactivate by explicitely setting SLOTS=null in the command line\n"
)
public List<Integer> SLOTS = null;
......
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