updated readme

Author: andand

README.md

@@ -15,42 +15,42 @@ Download the latest POGENOM distribution from https://github.com/EnvGen/POGENOM/
 
 Either:
 
-`perl pogenom.pl --vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --genome_size GENOME_SIZE [-h]`
+`perl pogenom.pl --vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --genome_size GENOME_SIZE [--help]`
 
 Or:
 
-`perl pogenom.pl -vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --gff_file GFF_FILE [-h]`
+`perl pogenom.pl -vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --gff_file GFF_FILE [--help]`
 
 
 
 ### Required arguments
 
-`--vcf_file VCF_FILE`            Specify vcf file with data from a single or multiple samples.
+`--vcf_file VCF_FILE`                   Specify vcf file with data from a single or multiple samples.
 
-`--out OUTPUT_FILES_PREFIX`        Specify the prefix of the output file name(s) (overwrites existing files with same names).
+`--out OUTPUT_FILES_PREFIX`             Specify the prefix of the output file name(s) (overwrites existing files with same names).
 
-`--genome_size GENOME_SIZE`      Specify genome size (in bp; integer). Not required if `--gff_file` is given.
+`--genome_size GENOME_SIZE`             Specify genome size (in bp; integer). Not required if `--gff_file` is given.
 
 
 
 ### Optional arguments
 
-`--gff_file GFF_FILE`            Specify gff file. Either this or `--genome_size` must be given.
+`--gff_file GFF_FILE`                   Specify gff file. Either this or `--genome_size` must be given.
 
 `--genetic_code_file GENETIC_CODE_FILE` Specify genetic code file. E.g. `standard_genetic_code.txt` in the POGENOM distribution.
 
-`--loci_file LOCI_FILE`          Specify file with ids for loci to include.
+`--loci_file LOCI_FILE`                 Specify file with ids for loci to include.
 
-`--min_count MIN_COUNT`          Specify minimum coverage for a locus to be included for the sample.
+`--min_count MIN_COUNT`                 Specify minimum coverage for a locus to be included for the sample.
 
-`--min_found MIN_FOUND_IN`       Specify minimum number samples that a locus need to be present in to be included.
+`--min_found MIN_FOUND_IN`              Specify minimum number samples that a locus need to be present in to be included.
 
-`--subsample SUBSAMPLE`          Specify coverage level at which to subsample.
+`--subsample SUBSAMPLE`                 Specify coverage level at which to subsample.
 
-`--keep_haplotypes`              If this is used, POGENOM will not split haplotypes into single-nucleotide variants, which is otherwise the default behaviour.
-`--vcf_version`                  Specify VCF file format version. Can be set to 4.2 or 4.1 (default).
+`--keep_haplotypes`                     If this is used, POGENOM will not split haplotypes into single-nucleotide variants, which is otherwise the default behaviour.
+`--vcf_version`                         Specify VCF file format version. Can be set to 4.2 or 4.1 (default).
 
-`-h`							To print help message on screen.
+`--help`                                To print help message on screen.
 
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