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update of command line docu
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‎trident.md‎

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@@ -199,24 +199,25 @@ While reading the `.janno` file `trident` trims all leading and trailing whitesp
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```default
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Usage: trident init ((-p|--genoOne FILE) | --genoFile FILE --snpFile FILE
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--indFile FILE |
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--bedFile FILE --bimFile FILE --famFile FILE |
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--vcfFile FILE) [--snpSet SET] (-o|--outPackagePath DIR)
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--bedFile FILE --bimFile FILE --famFile FILE |
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--vcfFile FILE) [--snpSet SET] (-o|--outPackagePath DIR)
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[-n|--outPackageName STRING] [--minimal]
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Create a new Poseidon package from genotype data
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Available options:
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-h,--help Show this help text
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-p,--genoOne FILE One of the input genotype data files. Expects .bed,
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.bed.gz, .bim, .bim.gz or .fam for PLINK, or .geno,
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.geno.gz, .snp, .snp.gz or .ind for EIGENSTRAT. The
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other files must be in the same directory and must
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have the same base name. If a gzipped file is given,
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it is assumed that the file pairs (.geno.gz, .snp.gz)
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or (.bim.gz, .bed.gz) are both zipped, but not the
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.fam or .ind file. If a .ind or .fam file is given,
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it is assumed that none of the file triples is
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zipped. For VCF please see option --vcfFile
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.bed.gz, .bim, .bim.gz or .fam for PLINK, .geno,
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.geno.gz, .snp, .snp.gz or .ind for EIGENSTRAT,
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or.vcf or .vcf.gz for VCF. In case of EIGENSTRAT and
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PLINK, the two other files must be in the same
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directory and must have the same base name. If a
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gzipped file is given, it is assumed that the file
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pairs (.geno.gz, .snp.gz) or (.bim.gz, .bed.gz) are
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both zipped, but not the .fam or .ind file. If a .ind
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or .fam file is given, it is assumed that none of the
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file triples is zipped.
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--genoFile FILE Eigenstrat genotype matrix, optionally gzipped.
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Accepted file endings are .geno, .geno.gz
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--snpFile FILE Eigenstrat snp positions file, optionally gzipped.
@@ -358,7 +359,7 @@ Usage: trident forge ((-d|--baseDir DIR) |
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--vcfFile FILE) [--snpSet SET])
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[--forgeFile FILE | (-f|--forgeString DSL)]
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[--selectSnps FILE] [--intersect] [--outFormat FORMAT]
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[--onlyGeno | --minimal | --preservePyml]
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[--onlyGeno | --minimal | --preservePyml] [-z|--zip]
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(-o|--outPackagePath DIR) [-n|--outPackageName STRING]
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[--packagewise] [--outPlinkPopName MODE] [--ordered]
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@@ -369,15 +370,16 @@ Available options:
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-h,--help Show this help text
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-d,--baseDir DIR A base directory to search for Poseidon packages.
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-p,--genoOne FILE One of the input genotype data files. Expects .bed,
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.bed.gz, .bim, .bim.gz or .fam for PLINK, or .geno,
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.geno.gz, .snp, .snp.gz or .ind for EIGENSTRAT. The
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other files must be in the same directory and must
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have the same base name. If a gzipped file is given,
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it is assumed that the file pairs (.geno.gz, .snp.gz)
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or (.bim.gz, .bed.gz) are both zipped, but not the
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.fam or .ind file. If a .ind or .fam file is given,
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it is assumed that none of the file triples is
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zipped. For VCF please see option --vcfFile
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.bed.gz, .bim, .bim.gz or .fam for PLINK, .geno,
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.geno.gz, .snp, .snp.gz or .ind for EIGENSTRAT,
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or.vcf or .vcf.gz for VCF. In case of EIGENSTRAT and
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PLINK, the two other files must be in the same
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directory and must have the same base name. If a
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gzipped file is given, it is assumed that the file
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pairs (.geno.gz, .snp.gz) or (.bim.gz, .bed.gz) are
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both zipped, but not the .fam or .ind file. If a .ind
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or .fam file is given, it is assumed that none of the
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file triples is zipped.
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--genoFile FILE Eigenstrat genotype matrix, optionally gzipped.
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Accepted file endings are .geno, .geno.gz
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--snpFile FILE Eigenstrat snp positions file, optionally gzipped.
@@ -455,6 +457,8 @@ Available options:
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CHANGELOG file (if available) are copied to the
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output package. Only works for a singular source
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package.
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-z,--zip Should the resulting genotype- and snp-files be
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gzipped?
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-o,--outPackagePath DIR Path to the output package directory.
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-n,--outPackageName STRING
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The output package name. This is optional: If no name
@@ -716,25 +720,26 @@ Usage: trident genoconvert ((-d|--baseDir DIR) |
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--snpFile FILE --indFile FILE |
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--bedFile FILE --bimFile FILE --famFile FILE |
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--vcfFile FILE) [--snpSet SET])
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--outFormat FORMAT [--onlyGeno]
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[-o|--outPackagePath DIR] [--removeOld]
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[--outPlinkPopName MODE] [--onlyLatest]
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--outFormat FORMAT [-o|--outPackagePath DIR]
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[--removeOld] [--outPlinkPopName MODE] [--onlyLatest]
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[-z|--zip]
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Convert the genotype data in a Poseidon package to a different file format
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Available options:
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-h,--help Show this help text
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-d,--baseDir DIR A base directory to search for Poseidon packages.
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-p,--genoOne FILE One of the input genotype data files. Expects .bed,
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.bed.gz, .bim, .bim.gz or .fam for PLINK, or .geno,
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.geno.gz, .snp, .snp.gz or .ind for EIGENSTRAT. The
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other files must be in the same directory and must
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have the same base name. If a gzipped file is given,
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it is assumed that the file pairs (.geno.gz, .snp.gz)
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or (.bim.gz, .bed.gz) are both zipped, but not the
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.fam or .ind file. If a .ind or .fam file is given,
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it is assumed that none of the file triples is
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zipped. For VCF please see option --vcfFile
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.bed.gz, .bim, .bim.gz or .fam for PLINK, .geno,
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.geno.gz, .snp, .snp.gz or .ind for EIGENSTRAT,
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or.vcf or .vcf.gz for VCF. In case of EIGENSTRAT and
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PLINK, the two other files must be in the same
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directory and must have the same base name. If a
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gzipped file is given, it is assumed that the file
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pairs (.geno.gz, .snp.gz) or (.bim.gz, .bed.gz) are
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both zipped, but not the .fam or .ind file. If a .ind
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or .fam file is given, it is assumed that none of the
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file triples is zipped.
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--genoFile FILE Eigenstrat genotype matrix, optionally gzipped.
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Accepted file endings are .geno, .geno.gz
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--snpFile FILE Eigenstrat snp positions file, optionally gzipped.
@@ -756,12 +761,13 @@ Available options:
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(default: Other)
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--outFormat FORMAT the format of the output genotype data: EIGENSTRAT or
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PLINK.
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--onlyGeno Should only the resulting genotype data be returned?
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This means the output will not be a Poseidon package.
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-o,--outPackagePath DIR Path to the output package directory. This is
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optional: If no path is provided, then the output is
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written to the directories where the input genotype
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data file (.bed/.geno) is stored. (default: Nothing)
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-o,--outPackagePath DIR Path for the converted genotype files to be written
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to. If a path is provided, only the converted
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genotype files are written out, with no change of the
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original package. If no path is provided, genotype
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files will be converted in-place, including a change
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in the POSEIDON.yml file to yield an updated valid
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package (default: Nothing)
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--removeOld Remove the old genotype files when creating the new
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ones.
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--outPlinkPopName MODE Where to write the population/group name into the FAM
@@ -771,6 +777,8 @@ Available options:
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--onlyLatest Consider only the latest versions of packages, or the
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groups and individuals within the latest versions of
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packages, respectively.
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-z,--zip Should the resulting genotype- and snp-files be
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gzipped?
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```
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</details>
@@ -1104,15 +1112,16 @@ Available options:
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compatible with trident.
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--pyml FILE Path to a POSEIDON.yml file.
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-p,--genoOne FILE One of the input genotype data files. Expects .bed,
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.bed.gz, .bim, .bim.gz or .fam for PLINK, or .geno,
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.geno.gz, .snp, .snp.gz or .ind for EIGENSTRAT. The
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other files must be in the same directory and must
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have the same base name. If a gzipped file is given,
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it is assumed that the file pairs (.geno.gz, .snp.gz)
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or (.bim.gz, .bed.gz) are both zipped, but not the
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.fam or .ind file. If a .ind or .fam file is given,
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it is assumed that none of the file triples is
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zipped. For VCF please see option --vcfFile
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.bed.gz, .bim, .bim.gz or .fam for PLINK, .geno,
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.geno.gz, .snp, .snp.gz or .ind for EIGENSTRAT,
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or.vcf or .vcf.gz for VCF. In case of EIGENSTRAT and
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PLINK, the two other files must be in the same
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directory and must have the same base name. If a
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gzipped file is given, it is assumed that the file
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pairs (.geno.gz, .snp.gz) or (.bim.gz, .bed.gz) are
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both zipped, but not the .fam or .ind file. If a .ind
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or .fam file is given, it is assumed that none of the
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file triples is zipped.
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--genoFile FILE Eigenstrat genotype matrix, optionally gzipped.
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Accepted file endings are .geno, .geno.gz
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--snpFile FILE Eigenstrat snp positions file, optionally gzipped.

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