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blachlylab / dhtslib

D bindings and OOP wrappers for htslib
MIT License
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dhtslib.vcf.record poor test coverage #94

Closed jblachly closed 3 years ago

jblachly commented 3 years ago

When compiling nanoprof, a dhtslib compile error in dhtslib.vcf.record was noted:

../lib/source/nanoprof/lib/alignment.d(409,41): Deprecation: function dhtslib.sam.reader.SAMReader.targetId is deprecated - u
se these properties from SAMHeader
../../../dhtslib/source/dhtslib/vcf/record.d(599,10): Error: template instance isIntegral!T template isIntegral is not define
d
source/app.d(137,30):        while looking for match for add!("INFO", float[])

This is because std.traits was not in scope for this module, presumably because it was at one time but then record.d brought out into its own module and missed that. I fixed this in f853ff15fb743f1caff7e976ec726901ec2f999e

HOWEVER, this wasn't picked up in dhtslib CI testing, which means test coverage in vcf.record is poor or nonexistant. @charlesgregory please add a few tests for this module

jblachly commented 3 years ago

https://codecov.io/gh/blachlylab/dhtslib/src/f853ff15fb743f1caff7e976ec726901ec2f999e/source/dhtslib/vcf/record.d

Looks like it was add and addInfo specifically that were totally uncovered, rest of file looks OK