-writePhase is useful to be able to run ChromoPainter on pre-existing PBWT files. Also, -readPhase was not quite correct for v2 files. This should make both of these work properly.
The writeTransposedHaplotypes is implemented naively, but this should be OK as any Phase file that can be used, can also be written and read. Multiple passes appear to be necessary to transpose without creating the whole L by N data matrix in memory.
-writePhase is useful to be able to run ChromoPainter on pre-existing PBWT files. Also, -readPhase was not quite correct for v2 files. This should make both of these work properly.
The writeTransposedHaplotypes is implemented naively, but this should be OK as any Phase file that can be used, can also be written and read. Multiple passes appear to be necessary to transpose without creating the whole L by N data matrix in memory.