According to the popins4snake roadmap there have been three properties missing from the crop-unmapped module:
The output should not automatically overwrite the "mates.bam". This is addressed by introducing a new -o option to the crop-unmapped module. The default output remains "mates.bam" but a different output filename can be specified s.t. an existing file named "mates.bam" is not overwritten.
No POPINS_SAMPLE_INFO should be written. This is addressed by a new --printSampleInfo flag for the crop-unmapped module. Unless the program flag is set, there is no POPINS_SAMPLE_INFO written.
The humanSeqs are needed as option. According to the I/O parser, this is implemented already. TBDiscussed