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vgteam / sv-genotyping-paper

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Reorganize to prepare for adding yeast and other methods parts #3

Closed jmonlong closed 5 years ago

jmonlong commented 5 years ago

I renamed and reorganized a bit the files so that it's easier for David and I to add our parts, and to navigate the scripts. Let me know if you disagree.

Basically I made a human/yeast split at the beginning and moved the markdown files for each dataset (e.g. HGSVC.md) to the README of relevant dataset folder, where I'll add the other methods commands. Now it looks like this:

├── human
│   ├── chmpd
│   │   ├── add-genotypes.py
│   │   ├── data.txt
│   │   ├── make-explicit.py
│   │   └── README.md
│   ├── giab
│   │   ├── bayestyper
│   │   │   └── README.md
│   │   ├── delly
│   │   │   └── README.md
│   │   ├── README.md
│   │   └── svtyper
│   │       └── README.md
│   ├── hgsvc
│   │   ├── bayestyper
│   │   │   └── README.md
│   │   ├── delly
│   │   │   └── README.md
│   │   ├── hap-merge.py
│   │   ├── HG00514.hap0.vcf.gz
│   │   ├── HG00514.hap1.vcf.gz
│   │   ├── HG00733.hap0.vcf.gz
│   │   ├── HG00733.hap1.vcf.gz
│   │   ├── make-vcf.sh
│   │   ├── NA19240.hap0.vcf.gz
│   │   ├── NA19240.hap1.vcf.gz
│   │   ├── README.md
│   │   └── svtyper
│   │       └── README.md
│   ├── README.md
│   ├── svpop
│   │   ├── download.sh
│   │   ├── README.md
│   │   └── vcf-add-bed-seqs.py
│   └── toil-scripts
│       ├── call.sh
│       ├── construct.sh
│       ├── eval.sh
│       ├── map.sh
│       ├── mce.sh
│       ├── README.md
│       └── simulate.sh
├── README.md
└── yeast

I'll add the commands for Delly, SVTyper and maybe BayesTyper. Then the evaluation commands and the simulation experiment.

eldariont commented 5 years ago

I like the new structure and hope it is okay if I merge this now in order to be able to add the yeast scripts.

glennhickey commented 5 years ago

Looks great!