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Page 18 of 44

`sam-coverage.py` now prints the min and max coverage per alignment too.

Not secure

Added indexing to `callHaplotypesBcftools` in `bowtie2.py`.

Not secure

Fixed errors from new version of flake8.

Added `--callHaplotypesBcftools` to `bowtie2.py`.

Not secure

Added `--noFilter` option to `sam-coverage.py` and `sam-coverage-depth.py`
to allow them to run faster when no special filtering is needed.

Added `--callHaplotypesGATK` to `bin-make-consensys.py`.

Has known vulnerabilities

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