CRAM Support

Added support for specifying reference FASTA to be used for reading CRAM files

Bugfix

Fixed bug in how mean-off-genotype-frequency is calculated in germline mode. Thanks @asp8200! 🍰

Less Confusion

Got rid of admittedly confusing default output for non-genotypable sites. Code could benefit from some refactoring (too much stuff is happening in client.py), but that will have to wait.

Details

Added details about major and minor alleles in output JSON file

Support BED files with more than three columns

Thanks to @asp8200 for spotting this issue and fixing it.

Typos

Fixed typos in summary section of output JSON file

Detailed Output

Added more details in JSON output file

Typo

Fixed typo in JSON output file

Base Quality Threshold

Implemented optional minimum_base_quality option. Only bases with at least this quality are counted.

Bugfix

There were some issues when installing snpahoy with pysam<0.15 using conda.