Removed deprecated VariantContextWriterFactory

[magicDGS]

Description

Removed ancient factory for create VariantContextWriter. Found in #707.

Checklist

• Code compiles correctly
• New tests covering changes and new functionality
• All tests passing
• Extended the README / documentation, if necessary
• Is not backward compatible (breaks binary or source compatibility)

[coveralls]

Coverage increased (+0.1%) to 70.145% when pulling fbb4439 on magicDGS:dgs_remove_VariantContextWriterFactory into de27f18 on samtools:master.

[ronlevine]

Does sortOnTheFly need to be added to VariantContextWriterBuilder ?

[magicDGS]

I can add these two static method, but they are just syntactic sugar for the SortingVariantContextWriter constructors. This only requires two change appearances of the following lines of code:

final VariantContextWriter sortingWriter = VariantContextWriterFactory.sortOnTheFly(writer, 1000);
...
final VariantContextWriter sortingWriter = VariantContextWriterFactory.sortOnTheFly(writer, 1000, true);

for these:

final VariantContextWriter sortingWriter = new SortingVariantContextWriter(writer, 1000);
...
final VariantContextWriter sortingWriter = new SortingVariantContextWriter(writer, 1000, true);

I don't think that it is necessary, because code that is using these methods should be refactored anyway. But of course, I could include it.

[ronlevine]

@magicDGS I agree with you, no need to add it. The builder pattern should not have any static methods plus it the a VERY thin wrapper around SortingVariantContextWriter.

[yfarjoun]

PR in picard ready for this broadinstitute/picard#710 (tests pass)

[yfarjoun]

👍