winsfs has been updated to work from the banded SAF representation that angsd now outputs by default, in addition to the old format. The internal representation, however, is not banded. That is, the values that are implicitly zero in the banded SAF files are filled in by explicit zeros when reading. This is correct, but it is inefficient in terms of run-time and memory usage for very large sample sizes.
I'll be adding an internal, banded SAF representation at some point to deal with this, and I'm opening this issue to track this work.
winsfshas been updated to work from the banded SAF representation thatangsdnow outputs by default, in addition to the old format. The internal representation, however, is not banded. That is, the values that are implicitly zero in the banded SAF files are filled in by explicit zeros when reading. This is correct, but it is inefficient in terms of run-time and memory usage for very large sample sizes.I'll be adding an internal, banded SAF representation at some point to deal with this, and I'm opening this issue to track this work.