Clarify --assembly in documentation

[famosab]

location of the GRIDSS assembly BAM. This file will be created by GRIDSS. The default filename adds a .assembly.bam suffix to the output file.

To me it is not clear, what the prerequisites are that this assembly "works". If I understand the paper correctly, the assembly is a sort of preprocessing step to the structural variant calling and thus always conducted. But I always got empty bam files so far. I tried using one bam file as input and two bam files as input as well as using the index yielded from bwa index. However I only tried with test data which could simply lack structural variants.

Any clarification would be welcome on the following questions:

1. How many input bam files are needed for an assembly?

File to write breakend assemblies to. It is strongly recommended that the assembly filename corresponds to the OUTPUT filename.

2. What excatly needs to be handed to the --assembly flag: Is it a filename, is it a path?