Is your feature request related to a problem? Please describe.
There are several classes annotated as "Deprecated", it seems some of them are old and no longer used but some of them are opposite.
Describe alternatives you've considered
we try to delete the below classes, it seems they are no longer used.
SignatureCompareRelated,
SignatureCompareRelatedSimple,
SignatureCompareRelatedSimpleGenotype.java
SignatureFindRelated.java
SignatureFindRelatedMulti.java
SignatureWTFExomes.java
we may remove the "Deprecated" annotation from the below classes:
CompareGenotypeBespoke used inside qsignatureCompare.wdl
SignatureGenerator used inside qsignatureGenerator.wdl (have to remove deprecated)
QSigCompare seems well maintained with completed unit test
QSigCompareDistance seems well maintained with completed unit test
There are other executable classes inside qsignature, they seem functional and well tested, and widely used.
Compare.java has a unit test
SignatureGeneratorBespoke.java has a unit test
SignatureCompareRelatedSimpleGenotypeMT.java used inside qsig_compare.wdl
We are not sure below four classes should be deprecated or not, they don't have related unit tests and seems not used.
Is your feature request related to a problem? Please describe. There are several classes annotated as "Deprecated", it seems some of them are old and no longer used but some of them are opposite.
Describe alternatives you've considered
we try to delete the below classes, it seems they are no longer used.
we may remove the "Deprecated" annotation from the below classes:
There are other executable classes inside qsignature, they seem functional and well tested, and widely used.
We are not sure below four classes should be deprecated or not, they don't have related unit tests and seems not used.