For non-coordinate sorts, picard SortSam does not output a BAM index, even if CREATE_INDEX is true. This puts an existence check around the rename of the BAI file and also makes the output bam_index an optional output. Fortunately, it appears that we are not using the generated index in any of our pipelines as something always consumes and transforms the BAM downstream, so it ends up reindexed.
For non-coordinate sorts,
picard SortSamdoes not output a BAM index, even ifCREATE_INDEXistrue. This puts an existence check around the rename of the BAI file and also makes the output bam_index an optional output. Fortunately, it appears that we are not using the generated index in any of our pipelines as something always consumes and transforms the BAM downstream, so it ends up reindexed.Resolves #155