Segmentation fault with samtools rmdup

[Azazel]

I am running into a Seg fault when using samtools rmdup.

I have paired-end alignments from bwa and filter them so that I retain only those pairs which are actually pairs, which have both fragments properly aligned, with no fragment unmapped, and with no next fragment unmapped:

~/samtools-0.1.12a/samtools view -h -b -F 0xC -f 0x3 input.bam -o ~/foobar.bam

Now I want to remove duplicates...

~/samtools-0.1.12a/samtools rmdup ~/foobar.bam ~/rmdupped.bam

...and get this:

[bam_rmdup_core] processing reference chr2...
[...] (long output omitted, here it goes through the chromosomes)
[bam_rmdup_core] processing reference chr2...
[bam_rmdup_core] 1 unmatched pairs
[bam_rmdup_core] processing reference chrX...
Segmentation fault

My questions are:

What can I do about the Segmentation fault?

Why does it report "1 unmatched pairs", I thought that through the previous filtering (see above) there can not be any unmatched pairs anymore? How can I identify the unmatched pair, if there really is one (I tried samtools view -f 0x4, that doesn't find anything though)?

I am using samtools version Version: 0.1.12a (r862).

Any help would be much appreciated. Thanks.

[deyler]

perhaps sort first?

Have you tried sorting first?

The samtools man page says:

samtools rmdup [-sS] <input.srt.bam> <out.bam>

Which implies that the input should be sorted.