Integrate legacy function into create_fragment_file

We have a branch with a function to convert a bam to a fragments file that was never merged (branch: bam-fragments). Meanwhile, we implemented and merged this functionality (sctoolbox.tools.create_fragment_file). The task is to compare both functions and port missing features from the legacy function into the current one. Especially, look at these parameters in the legacy function: fragments, cells, tmpdir, min_distance, and max_distance.