Update Avro converters and move them to the hpg-bigdata-core package (currently, they are in the hpg-bigdata-app package). In addtion, current implementation converts the whole file from VCF/BAM/SAM to Avro. It would be nice if some specific classes for Variant and Alignment exist with basic filters using lambdas:
Update Avro converters and move them to the hpg-bigdata-core package (currently, they are in the hpg-bigdata-app package). In addtion, current implementation converts the whole file from VCF/BAM/SAM to Avro. It would be nice if some specific classes for Variant and Alignment exist with basic filters using lambdas:
VariantAvroSerializer avroSerializer = new VariantAvroSerializer(); avroSerializer.addRegionFilter(new Region("1", 1, 800000)) .addRegionFilter(new Region("1", 798801, 222800000)) .addFilter(v -> v.getStudies().get(0).getFiles().get(0).getAttributes().get("NS").equals("60")); avroSerializer.toAvro(inputFilename, outputFilename);