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hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly
Apache License 2.0
83 stars 21 forks source link

fold AffineGapPenaltyAlignment into ReadAlignment #600

Closed ryan-williams closed 7 years ago

ryan-williams commented 7 years ago

AffineGapPenaltyAlignment was a standalone object with one public method (in spirit; scoreAlignmentPaths was public but shouldn't/needn't have been. I made it package-private here so that tests can access it) that was the main way of creating a ReadAlignment; arguably that makes it just a ReadAlignment constructor, so I've folded it into ReadAlignment accordingly.

I also package-privated the direct ReadAlignment constructor and moved AlignmentState to its own file.

coveralls commented 7 years ago

Coverage Status

Coverage remained the same at 78.704% when pulling 7aef3fc62369d3951f3e1892783315e1dfa74fe5 on ryan-williams:agp into be6074747e1ae2f628d1d53be18e5eb091b611dd on hammerlab:master.

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.2%) to 78.847% when pulling 478899e49cedc1a3b4be23447efd14d9ca83eff4 on ryan-williams:agp into dfdfea6c9bda4040a7dd67decb862d9988b9c33c on hammerlab:master.

ryan-williams commented 7 years ago

merging this in sans review