Disable normal_bam and cancer_bam options?

[chris....@gmail.com]

The normal_bam and cancer_bam options don't seem to be fully implemented (when they are set, generate_quadtree is not called leading to an immediate segfault in generate_breakpoints).

Two points:

1. You should check if generate_quadtree did in fact populate control_blocks and tumor_blocks as expected (assert(control_blocks.size() >= 100))

2. To avoid confusing users, until the BAM support is complete you should quit with an informative error.

Chris

[skill...@gmail.com]

Is it still the case that the bam options are not fully implemented? I'm getting a seg fault trying to use bam files but not on the example.

[SMufin]

Dear Chris,

You are right, the normal_bam and cancer_bam options are not fully implemented on the current version of the code. It is true that the application should print an informative message about this issue. Sorry for the confusion.

We are preparing an updated version of Smufin that will allows the users to use bam files as inputs. In the next days this version will be available for all the user.

Kind regards,

Smufin team.