Thank you Pierre Lindenbaum :)
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converting SAMRecord to JSON or String format
I want to develop RESTful web service which will provide bam reads in JSON format. I used SamFileReader (htsjdk.samtools.SAMFileReader) for reading bam file and then using SAMRecordIterator to get SAMRecord. But when I try to convert it into String/ JSON it throws following error :
Method not implemented for: class htsjdk.samtools.SAMSequenceRecord (through reference chain: htsjdk.samtools.BAMRecord["header"]->htsjdk.samtools.SAMFileHeader["sequenceDictionary"]->htsjdk.samtools.SAMSequenceDictionary["sequences"]->java.util.UnmodifiableRandomAccessList[0]->htsjdk.samtools.SAMSequenceRecord["id"])
I tried following ways to create JSON for SamRecord :
- Used com.fasterxml.jackson.databind.ObjectMapper and ObjectWriter with "writeValueAsString()" API.
- Used directly Response Body annotation for request URL method.
- Tried to use JSONSerializer from "net.sf.json" and same error occured.
Is there any other way to convert SamRecord to JSON/String ?
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Biostar
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dsvispute91 •
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dsvispute91 •
1 answer
SAMRecord is not treated as a POJO: when jackson tries to serialize a samrecord, it finds that a samrecord is linked to a header. and jacksons tries to serialize everything
https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html#getHeader--
which contains a whole sequence dictionary
which contains a list of https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMSequenceRecord.html
which contains a getter "getId" with the following implementation: https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java#L87
public String getId() {
throw new UnsupportedOperationException("Method not implemented for: " + this.getClass());
}
the best way is to create your very own serializer.
FYI, I wrote a SAMTojson : https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/util/samtools/SamJsonWriterFactory.java
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