Version 0.7.9 Bug fixes, most importantly to work around a regression in pysam. installation: - Require pysam version earlier than buggy 0.9 (#86) fix, reference: - If the majority of target bins have no or very low coverage, warn the user about this, skip bias corrections, and mask out the low-coverage target bins during centering to ensure the output is still vaguely usable and sane. This issue could occur because the wrong target BED was used initially, or maybe hybridization failed in library prep. reference: - Ensure the output table's columns are ordered correctly. In some cases it was possible for the output tables columns to be ordered differently, which still works in CNVkit, but is weird. call, rescale, export: - Check specified gender more sensibly; on failure, default to female. Specifically, use case-insensitive string comparison to test whether the given argument means "male". Treating chrX as having neutral ploidy is probably a less surprising fallback, especially if the "-y" flag is forgotten elsewhere in the pipeline.