Hi
I am trying to sort the bam file by using the sort command:
samtools sort -n aln.bam aln.qsort
[W::sam_hdr_read] bgzf_check_EOF: Value too large for defined data type
[bam_sort_core] truncated file. Continue anyway.
I am not sure if "continue anyway" means it continues to sort or just aborts.
I checked the file size.
$ du -hs *
113G aln.bam
8.4M aln.bam.bai
28K aln.qsort.bam
So it does not seem like file is sorted. I have checked one previous thread
about this bug but could not find any solution. Anyone comments ? Suggestion
for any other tool ?
Thanks
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