PrepareHetero:Sort order warning and lazy parsing genotype fields triggers vague error

[mmterpstra]

Tabix indexing triggers sorting error

Tabix indexing on the line below assumes vcf-sort(vcftools package) natural sort order(1,10,11, etc) instead of picard tools sort by chromosome size/dictionary order (1,2,3, etc).

MADSEQ/R/PreProcessingShow.R

Line 367 in 4a71380

try(indexTabix(vcffile,"vcf"))

This triggers the following warning:

[E::hts_idx_push] Unsorted positions on sequence #1: 865534 followed by 865482
Error in value[[3L]](cond) : index build failed
``


# Lazy parsing
Lazy parsing assuming GATK ordering on:
https://github.com/ykong2/MADSEQ/blob/4a71380b53853cdfec26fd366b4fdd0031fea3ff/R/PreProcessingShow.R#L390

This assumes the genotype fields are formatted starting GT:AD:DP just like gatk does by default (freebayes has different ordering). 

All variants processed
processing vcf file
Error in S4Vectors:::normarg_names(value, class(x), length(x)) :
attempt to set too many names (2) on IRanges object of length 0
Calls: prepareHetero ... names<- -> setNames -> names<- -> names<- ->
Execution halted

Fix since this github is inactive

(for i in *.vcf.gz; do zcat $i | perl -wnae 'BEGIN{use Data::Dumper;}; if(not(m/^#/)){my @vals=split(":",$F[9]); my @keys = split(":",$F[8]); my %gt_parsed;for my $key ( @keys){$gt_parsed{$key}=shift(@vals);};$F[8] = "GT:AD:DP";$F[9]=join(":",@gt_parsed{"GT","AD","DP"})}; print join("\t",@f)."\n"' | vcf-sort | bgzip -c > $(basename $i .vcf.gz).vcftoolssort.vcf.gz; done)&