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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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sam2tsv #159

Closed mohammedmsk closed 4 years ago

mohammedmsk commented 4 years ago

Hello,

I was using an old version of sam2tsv on an alignment sam file generated by a tool called paladin (https://github.com/ToniWestbrook/paladin).

Error

With the most updated version of this tool it does not work giving an error like: Ignoring SAM validation error due to lenient parsing: Error parsing text SAM file. Invalid character in read bases; File some.sam; Line 1525

I believe this is most likely because now the new tool is checking for standard bases A T G C to be present and is failing because sequences are actually amino acids.

Is it possible to have a version of the tool where read base checking is not done.

Thanks.

lindenb commented 4 years ago

sorry no, this is checked via the htsjdk library (not on my side). https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/samtools/SAMLineParser.java#L378

mohammedmsk commented 4 years ago

Thanks for the reply.

While running the tool like above it actually does produce the output but with error complaints on every line. Which is fine. So it serves the purpose for now. Closing the issue.