miraligner fails

[greatfireball]

Error calling command: java -jarmiraligner.jar -sub 1 -trim 3 -add 3 -s tca -freq -i [...] -db [...] -o [...]

STDERR: Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 10
        at miraligner.map.align3end(map.java:445)
        at miraligner.map.align2(map.java:422)
        at miraligner.map.readseq(map.java:198)
        at miraligner.Main.main(Main.java:85)

[greatfireball]

@DanielAmsel found similar issues on github:

• miraligner Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1 lpantano/seqcluster#18
• Small RNAseq pipeline (miraligner) bcbio/bcbio-nextgen#1357

The problem seems to be caused by the installed jre. Currently we are using 1.8, but should downgrade to 1.7, due to no available miraligner.jar solves that issue.

[greatfireball]

Nevertheless, we @DanielAmsel pointed onto another issue which might cause trouble #98

[greatfireball]

This issue need to be solved in the basecontainer