<commit_before>package Sanger::CGP::Vcf::VcfUtil;

##########LICENCE##########
# Copyright (c) 2014 Genome Research Ltd. 
#  
# Author: <NAME> <<EMAIL>> 
#  
# This file is part of cgpVcf. 
#  
# cgpVcf is free software: you can redistribute it and/or modify it under 
# the terms of the GNU Affero General Public License as published by the Free 
# Software Foundation; either version 3 of the License, or (at your option) any 
# later version. 
#  
# This program is distributed in the hope that it will be useful, but WITHOUT 
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 
# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more 
# details. 
#  
# You should have received a copy of the GNU Affero General Public License 
# along with this program. If not, see <http://www.gnu.org/licenses/>.
##########LICENCE##########


use Sanger::CGP::Vcf;
our $VERSION = Sanger::CGP::Vcf->VERSION;

use strict;
use warnings FATAL => 'all';
use Carp;
use Vcf;

1;

=head gen_tn_vcf_header

A string generator for generating a uniform header section for NORMAL/TUMOUR comparisons. Useful if you do not want to include the VcfTools lib.

@param1 wt_sample      - a Sanger::CGP::Pindel::OutputGen::Sample object representing the wild type sample.

@param2 mt_sample      - a Sanger::CGP::Pindel::OutputGen::Sample object representing the mutant type sample.

@param3 contigs        - an array-ref of Sanger::CGP::Pindel::OutputGen::Contig object.

@param4 process_logs   - an array-ref of Sanger::CGP::Vcf::VcfProcessLog objects.

@param5 reference_name - a String containing the name of the reference used in the VCF.

@param6 input_source   - a String containing the name and version of the application or source of the VCF data.

@param7 info           - an array-ref of hash-refs containing VCF formatted INFO data.

@param8 format         - an array-ref of hash-refs containing VCF formatted FORMAT data.

@param9 other          - an array-ref of hash-refs containing VCF formatted header data.

@returns               - String containing a fully formatted VCF header.<commit_msg>fixing documentation bugs<commit_after>package Sanger::CGP::Vcf::VcfUtil;

##########LICENCE##########
# Copyright (c) 2014 Genome Research Ltd. 
#  
# Author: <NAME> <<EMAIL>> 
#  
# This file is part of cgpVcf. 
#  
# cgpVcf is free software: you can redistribute it and/or modify it under 
# the terms of the GNU Affero General Public License as published by the Free 
# Software Foundation; either version 3 of the License, or (at your option) any 
# later version. 
#  
# This program is distributed in the hope that it will be useful, but WITHOUT 
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 
# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more 
# details. 
#  
# You should have received a copy of the GNU Affero General Public License 
# along with this program. If not, see <http://www.gnu.org/licenses/>.
##########LICENCE##########


use Sanger::CGP::Vcf;
our $VERSION = Sanger::CGP::Vcf->VERSION;

use strict;
use warnings FATAL => 'all';
use Carp;
use Vcf;

1;

=head gen_tn_vcf_header

A string generator for generating a uniform header section for NORMAL/TUMOUR comparisons. Useful if you do not want to include the VcfTools lib.

@param1 wt_sample      - a Sanger::CGP::Vcf::Sample object representing the wild type sample.

@param2 mt_sample      - a Sanger::CGP::Vcf::Sample object representing the mutant type sample.

@param3 contigs        - an array-ref of Sanger::CGP::Vcf::Contig object.

@param4 process_logs   - an array-ref of Sanger::CGP::Vcf::VcfProcessLog objects.

@param5 reference_name - a String containing the name of the reference used in the VCF.

@param6 input_source   - a String containing the name and version of the application or source of the VCF data.

@param7 info           - an array-ref of hash-refs containing VCF formatted INFO data.

@param8 format         - an array-ref of hash-refs containing VCF formatted FORMAT data.

@param9 other          - an array-ref of hash-refs containing VCF formatted header data.

@returns               - String containing a fully formatted VCF header.
{'fraction_non_alphanumeric': 0.09168241965973535, 'fraction_numerical': 0.007088846880907372, 'mean_word_length': 3.750841750841751, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 15, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1756990', 'n_tokens_mistral': 1257, 'n_tokens_neox': 1220, 'n_words': 537}