This small PR includes a bugfix for an issue raised by Adriano this week (adding handling for an input file for matUtils extract which includes empty lines midfile, previously causing a segfault).
I have also cut and paste all code related to Taxonium output and translation from convert.cpp to translation.cpp (and hpp respectively). This reduces the amount of cross inclusions of headers and eases inclusion of parts of the source code into other projects. This is refactor only and does not in any way change command line behavior.
This small PR includes a bugfix for an issue raised by Adriano this week (adding handling for an input file for matUtils extract which includes empty lines midfile, previously causing a segfault).
I have also cut and paste all code related to Taxonium output and translation from convert.cpp to translation.cpp (and hpp respectively). This reduces the amount of cross inclusions of headers and eases inclusion of parts of the source code into other projects. This is refactor only and does not in any way change command line behavior.