<commit_before>#!/packages/perl/5.14.2/bin/perl
##!/usr/bin/perl
##
##  This script incorporates BAF information for each segment in copy number data if available.
##  It calculates the median(MEDIANBAF), median minor allele frequency (min(alt,ref)) for both 
##  control (MEDIANCONTROLMAF) and affected/tumor (MEDIANMAF), median abs(0.5-BAF) (MEDIANBAFDEV), and number
##  of BAFs (NBAF) across a segment. In addition, a Wilcoxon Rank Sum Test (RANKSUMVALUE) and a test of two 
##  proportions (ZSTAT and ZPVALUE) are performed between the control and affected/tumor alternate allele 
##  frequencies. This additional information can be used to support a shift from diploidy in copy number.
##
##  ARGUMENTS:
##	ARGV[0] is SAMPLE.cna.seg.vcf from annotSeg.pl
##	ARGV[1] is baf.txt from parseMergeVCF.pl<commit_msg>Update header with Statistics::R requirement<commit_after>#!/packages/perl/5.14.2/bin/perl
##!/usr/bin/perl
##
##  This script incorporates BAF information for each segment in copy number data if available.
##  It calculates the median(MEDIANBAF), median minor allele frequency (min(alt,ref)) for both 
##  control (MEDIANCONTROLMAF) and affected/tumor (MEDIANMAF), median abs(0.5-BAF) (MEDIANBAFDEV), and number
##  of BAFs (NBAF) across a segment. In addition, a Wilcoxon Rank Sum Test (RANKSUMVALUE) and a test of two 
##  proportions (ZSTAT and ZPVALUE) are performed between the control and affected/tumor alternate allele 
##  frequencies. This additional information can be used to support a shift from diploidy in copy number. 
##  This script requires Statistics::R http://search.cpan.org/~gmpassos/Statistics-R-0.02/lib/Statistics/R.pm.
##
##  ARGUMENTS:
##	ARGV[0] is SAMPLE.cna.seg.vcf from annotSeg.pl
##	ARGV[1] is baf.txt from parseMergeVCF.pl
{'fraction_non_alphanumeric': 0.10716300056401579, 'fraction_numerical': 0.01071630005640158, 'mean_word_length': 4.778501628664495, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, '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': '1329028', 'n_tokens_mistral': 603, 'n_tokens_neox': 568, 'n_words': 200}