brass fails when input bai file does not having the expected naming convention

[anoronh4]

brass fails when the bam file names are like this:

sample.bam
sample.bai

as opposed to this:

sample.bam
sample.bam.bai

because the bai files are supposedly not found. i think we can fix this in one of the following ways:

1. recreate the index when the bai name is expected to cause issues.
2. have the pipeline exit with error or emit a warning when the input bai file does not match expected naming convention.