A issue with miraligner
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- Dominant language
- Java
- Stars
- 14
- Forks
- 3
- PR merge metrics
- No merged PRs in 30d
Description
Hi
detail of the issue is
$ java -jar miraligner.jar -sub 1 -trim 3 -add 3 -s hsa -i test/test.fa -db DB -o a
Format is not tabular,guessing fasta
species found
Go to mapping...
Mismatches: 1
Trimming: 3
Addition: 3
Species: hsa
...
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1
at miraligner.tools.getFreq(tools.java:122)
at miraligner.map.readseq(map.java:296)
at miraligner.Main.main(Main.java:99)
The test.fa is downloaded from https://github.com/lpantano/seqbuster/tree/miraligner/miraligner/test
and,my java version is:
openjdk version "1.8.0_151"
OpenJDK Runtime Environment (build 1.8.0_151-b12)
OpenJDK 64-Bit Server VM (build 25.151-b12, mixed mode)
Thank you !
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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
Reproduce the command with miraligner.jar and test/test.fa, then inspect miraligner/tools.java:122 and the callers at miraligner/map.java:296 and miraligner/Main.java:99. Compare the input format and parsed fields at the failing point; done means the reported command completes without ArrayIndexOutOfBoundsException or the failure is reported clearly for invalid input.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100