# AUTOGENERATED BY NBDEV! DO NOT EDIT!

__all__ = ["index", "modules", "custom_doc_links", "git_url"]

index = {"Args": "00_Main.ipynb",
         "checkParams": "00_Main.ipynb",
         "main": "00_Main.ipynb",
         "RData": "01_Core.ipynb",
         "RegionExtractor": "01_Core.ipynb",
         "MarkerMaker": "01_Core.ipynb",
         "get_family_with_var": "01_Core.ipynb",
         "phasing_haps": "01_Core.ipynb",
         "haplotyper": "01_Core.ipynb",
         "LinkageWriter": "01_Core.ipynb",
         "EncoderWorker": "01_Core.ipynb",
         "run_each_region": "01_Core.ipynb",
         "base": "02_Linkage.ipynb",
         "paramlink2": "02_Linkage.ipynb",
         "pedprobr": "02_Linkage.ipynb",
         "pedtools": "02_Linkage.ipynb",
         "update_haps_ped": "02_Linkage.ipynb",
         "hap2chp": "02_Linkage.ipynb",
         "generate_marker": "02_Linkage.ipynb",
         "recombination_pos": "02_Linkage.ipynb",
         "recombination_region": "02_Linkage.ipynb",
         "get_allele": "02_Linkage.ipynb",
         "name_haps": "02_Linkage.ipynb",
         "get_fam_hap": "02_Linkage.ipynb",
         "get_fam_geno": "02_Linkage.ipynb",
         "format_haps_bunch": "02_Linkage.ipynb",
         "hlod_fun": "04_Runner.ipynb",
         "calculate_ped_lod": "02_Linkage.ipynb",
         "parallel_lods": "02_Linkage.ipynb",
         "linkage_analysis": "02_Linkage.ipynb",
         "format_fam_lods": "02_Linkage.ipynb",
         "rows2one": "02_Linkage.ipynb",
         "get_lods_batch": "02_Linkage.ipynb",
         "get_lods_chrom": "02_Linkage.ipynb",
         "get_hlod_chrom": "02_Linkage.ipynb",
         "summarize_lods": "02_Linkage.ipynb",
         "mkpath": "03_Utils.ipynb",
         "Environment": "03_Utils.ipynb",
         "StdoutCapturer": "03_Utils.ipynb",
         "stdoutRedirect": "03_Utils.ipynb",
         "cd": "03_Utils.ipynb",
         "runCommand": "03_Utils.ipynb",
         "CMDWorker": "03_Utils.ipynb",
         "runCommands": "03_Utils.ipynb",
         "parmap": "03_Utils.ipynb",
         "downloadURL": "03_Utils.ipynb",
         "calculateFileMD5": "03_Utils.ipynb",
         "zipdir": "03_Utils.ipynb",
         "removeFiles": "03_Utils.ipynb",
         "removeEmptyDir": "03_Utils.ipynb",
         "copyFiles": "03_Utils.ipynb",
         "downloadResources": "03_Utils.ipynb",
         "getColumn": "03_Utils.ipynb",
         "wordCount": "03_Utils.ipynb",
         "fileLinesCount": "03_Utils.ipynb",
         "connected_components": "03_Utils.ipynb",
         "listit": "03_Utils.ipynb",
         "parseVCFline": "03_Utils.ipynb",
         "indexVCF": "03_Utils.ipynb",
         "extractSamplenames": "03_Utils.ipynb",
         "checkVCFBundle": "03_Utils.ipynb",
         "rewriteFamfile": "03_Utils.ipynb",
         "checkSamples": "03_Utils.ipynb",
         "NoCache": "03_Utils.ipynb",
         "Cache": "03_Utils.ipynb",
         "PseudoAutoRegion": "03_Utils.ipynb",
         "TFAMParser": "03_Utils.ipynb",
         "VERSION": "03_Utils.ipynb",
         "env": "03_Utils.ipynb",
         "isnotebook": "03_Utils.ipynb",
         "format": "04_Runner.ipynb",
         "format_plink": "04_Runner.ipynb",
         "format_mega2": "04_Runner.ipynb",
         "format_merlin": "04_Runner.ipynb",
         "format_linkage": "04_Runner.ipynb",
         "parse_tfam": "04_Runner.ipynb",
         "Pedigree": "04_Runner.ipynb",
         "run_linkage": "04_Runner.ipynb",
         "linkage_worker": "04_Runner.ipynb",
         "hinton": "04_Runner.ipynb",
         "heatmap": "04_Runner.ipynb",
         "html": "04_Runner.ipynb",
         "html_img": "04_Runner.ipynb",
         "html_table": "04_Runner.ipynb"}

modules = ["Main.py",
           "Core.py",
           "Linkage.py",
           "Utils.py",
           "Runner.py"]

doc_url = "https://changebio.github.io/SEQLinkage/"

git_url = "https://github.com/changebio/SEQLinkage/tree/master/"

def custom_doc_links(name): return None
