Themisto's command line interface and index output format will change with the v2.0.0 release (see Themisto 87ad71f8). This pull request adds the following changes for compatibility with both the new and the old versions:
Added the -i argument for inputting the mSWEEP group indicators file to mGEMS so that the number of the reference sequences in the pseudoalignment can be determined.
If mGEMS can't find the Themisto <=v1.2.0 files in the --themisto-index directory and the -i argument is not supplied, the program will throw an error instructing the user to supply the -i argument.
If the files are found, the -i argument is ignored and the program functions as it did previously.
Updated documentation with usage instructions for both Themisto <=v1.2..0 and >=v2.0.0.
Please wait until the release of Themisto v2.0.0 before merging this pull request.
Themisto's command line interface and index output format will change with the v2.0.0 release (see Themisto 87ad71f8). This pull request adds the following changes for compatibility with both the new and the old versions:
-iargument for inputting the mSWEEP group indicators file to mGEMS so that the number of the reference sequences in the pseudoalignment can be determined.--themisto-indexdirectory and the-iargument is not supplied, the program will throw an error instructing the user to supply the-iargument.-iargument is ignored and the program functions as it did previously.Please wait until the release of Themisto v2.0.0 before merging this pull request.