[Samtools-help] Help with adding alignments via SAMFileWriter

[David He <Dav...@oi...>]

Hi all,

I'm writing a small Java program to take a few records from a bam sorted by queryname (samtools sort -n) and put them into a new bam file. I use SAMRecord.addalignment, but I keep getting a java.lang.IllegalArgumenException, saying the alignments are added out of order.

Here is the message:

Alignments added out of order in SAMFileWriterImpl.addAlignment for XXXXXXXX_sorted_by_name_1.bam. Sort order is queryname. Offending records are at 
[61P47_I280_100512:4:1:1050:7407#0] and [61P47_I280_100512:4:1:1050:11051#0].

I guess it's comparing these two querynames as strings in which case I can see why they would be out of order. But why does 'samtools sort' put 7407 before 11051? Is there a way around this short of setting the sortOrder to unsorted? If anyone can point me in the right direction, that would be much appreciated. Thank you.

Regards,
David