Bug report : Cannot find sample.realign.sort.bam for long read typing

[lidd77]

HIello, for long read hla typing , specHLA will call annoHLA.pl . I have read the whole long_read_typing.py, but cannot find any code to create $sample.realign.sort.bam .

for the below code in annoHLA.py , maybe it need some correction for long read typing ?

if($allele =~ /DRB1\*14:01/){ 
     system("samtools  mpileup -r HLA_DRB1:9519-9519 -t DP -t SP -uvf $db/hla.ref.extend.fa **$dir/$sample.realign.sort.bam** --output $workdir/snp.vcf"); } 

 

use $dir/DRB1.bam , not $sample.realign.sort.bam , is it right ?

Expecting your reply !