pan

Process haplotype intermediate results for pie (https://github.com/JMencius/pie)

Installation

1. Local installation First navigate to the folder containing setup.py.

conda create -n pan python=3.8 -y;
conda activate pan
pip install .;

Usage

Usage: pan [OPTIONS]

Options:
  -i, --inlmdb TEXT      Path to the LMDB directory
  -r, --region TEXT      User defined region, e.g. chr1:10000-20000
  -c, --category TEXT    Sequencing platform or basecalling configuration to
                         summarize, option: pacbio, R9.HAC, R9.SUP, R10.HAC,
                         R10.SUP
  -t, --threads INTEGER  Parallel threads [default: 6]
  -m, --maxlen INTEGER   Max length to form pairs for variants [default:
                         2,473,538 gene level of Rbfox1]
  --max-span INTEGER     Maximum length for --region
  --verbose              Verbose mode
  --version              Show the version and exit.
  --help                 Show this message and exit.

Example

pan -i ./test -r chr6:28510120-33480577 -c R10.SUP