sambamba slice <finalContig> returns both the reads mapped to the final contig and all unmapped reads

[russHyde]

Hi,
Have been using sambamba for a couple of days. I split up a human genome bam file (header at the bottom of the note) using the code

sambamba_v0.4.6 slice
-o temp.chrY.bam
.bam
'chrY'

For all other contigs, comparable code gives all reads that are mapped to that contig, whereas for chrY, this returned a suspiciously large bam file (larger than the chrX file). I checked through temp.chrY.bam and all of the unmapped reads from my bam were present in this file, that is, every read that is sliced out using

sambamba_v0.4.6 slice
-o temp.unmapped.bam
.bam
'*'

is also present in the chrY file.

I was wondering whether this might be a bug related to chrY being the final contig in my bam file and can provide an example sam file if required

All the best, sambamba is a fine tool and I'm sure I can work around the problem.
Russ,
U. Liverpool

@hd VN:1.3 SO:queryname
@sq SN:chr1 LN:249250621
@sq SN:chr2 LN:243199373
@sq SN:chr3 LN:198022430
@sq SN:chr4 LN:191154276
@sq SN:chr5 LN:180915260
@sq SN:chr6 LN:171115067
@sq SN:chr7 LN:159138663
@sq SN:chr8 LN:146364022
@sq SN:chr9 LN:141213431
@sq SN:chr10 LN:135534747
@sq SN:chr11 LN:135006516
@sq SN:chr12 LN:133851895
@sq SN:chr13 LN:115169878
@sq SN:chr14 LN:107349540
@sq SN:chr15 LN:102531392
@sq SN:chr16 LN:90354753
@sq SN:chr17 LN:81195210
@sq SN:chr18 LN:78077248
@sq SN:chr19 LN:59128983
@sq SN:chr20 LN:63025520
@sq SN:chr21 LN:48129895
@sq SN:chr22 LN:51304566
@sq SN:chrX LN:155270560
@sq SN:chrY LN:59373566

[lomereiter]

Thanks for the detailed description, the bugfix was just a single line.