I am getting 'ArrayIndexOutOfBoundsException: 1 error with miraligner.
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- Dominant language
- Java
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Description
I am getting 'ArrayIndexOutOfBoundsException: 1 error with miraligner. Also sometimes it is "Javalangerror" too.
Can someone help me with that.
detail of the error is-
Format is not fasta, guessing tabular
species found
Go to mapping...
Mismatches: 1
Trimming: 3
Addition: 3
Species: hsa
Tue May 29 23:12:13 EDT 2018
Reading reads
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1
at miraligner.tools.getseq(tools.java:98)
at miraligner.map.readseq(map.java:87)
at miraligner.Main.main(Main.java:85)
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the stack trace at miraligner/tools.java:98, then follow its callers in miraligner/map.java:87 and miraligner/Main.java:85. Reproduce the failure using the reported input and inspect the expected format around the read-loading step; done means identifying and fixing the cause of the ArrayIndexOutOfBoundsException and confirming the mapping proceeds.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100