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new I/O for the crop-unmapped module

Thomas Krannich requested to merge fix-crop-unmapped-io into main

According to the popins4snake roadmap there have been three properties missing from the crop-unmapped module:

  1. 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.

  2. 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.

  3. The humanSeqs are needed as option. According to the I/O parser, this is implemented already. TBDiscussed

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