Updating hal genomes is documented here, but it remains a finicky process. Some pipeline scripting could go a long way to help. But something as simple as error messages in the event of unexpected input is needed too.
So if halAddToBranch expects alignments of a certain form (ie with some input sequences compatible across them), it should take a second to check the names and sizes before starting and return a useful error if something's wrong.
Updating hal genomes is documented here, but it remains a finicky process. Some pipeline scripting could go a long way to help. But something as simple as error messages in the event of unexpected input is needed too.
So if
halAddToBranchexpects alignments of a certain form (ie with some input sequences compatible across them), it should take a second to check the names and sizes before starting and return a useful error if something's wrong.