'missing SAM header' when opening SAM files
Created by: AlexanderDilthey
Hi,
There seems to be an issue with iterating over alignments in a SAM file. I get the errors
[E::sam_parse1] missing SAM header
[W::sam_read1] parse error at line 4
although there are headers.
Code for reproducing the problem:
use Bio::DB::HTS;
my $sam = Bio::DB::HTS->new(-bam => 'test.sam');
my $alignment_iterator = $sam->features(-iterator => 1);
$alignment_iterator->next_seq;
and test.sam:
@HD VN:1.5 SO:coordinate
@SQ SN:ref LN:100
r001 99 ref 1 30 1M3D2M = 37 3 TAT *
r002 99 ref 1 30 1M2D2M = 37 3 TAT *
samtools can view the SAM without problems.