bamtobed -bedpe bug results in additional entry in BED

[k1sauce]

bamtobed adds an additional entry that does not exists in the BAM file. This seems to occur when the last read is unpaired and the previous read is paired in a name sorted BAM containing paired-end data.

Here is a simple name sorted test SAM (with 2 paired reads and 1 orphan read) to reproduce the error

@HD	VN:1.6	SO:queryname
@SQ	SN:chr1	LN:248956422
A00000:000:H00AAAAAA:1:2488:32949:32283	83	chr1	153875873	60	75M	=	153875807	-141	GACCCTCACCCCTCCACACCATCACCCCTCACCCACTTATAGTTTTCTCAGCTTCTTCATCCATCCCCTTCCTGN	,FFFFFFFF:FFFFFFFF,F,F:FFF:FFFFF:F,FF,FF:FFFFFFF:FFFFF,FF:FFF:,F:FF:FFF:FF#
A00000:000:H00AAAAAA:1:2488:32949:32283	163	chr1	153875807	60	73M	=	153875873	141	AGTCATAGACGNATCCCNCTCCGNCGGGAAGANCATTCCCGCTATACAACTTCAAAGTAACGAGACAACTNAG	FFFFF##FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFF#FFFFFFFFFFFFFFFFF:FFFFFFFFF#
A00000:000:H00AAAAAA:1:2488:32949:32440	81	chr1	2376163	60	74M	=	2375914	-323	TACGAATCACTACGACCGCTCCTAGGCCNAGCTGCCGCAGCTTATCTCACAATCGGCATGCTCTACTTTGACTC	FFFFFFFFFFFFFFF,FFF,F,FFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF:FFFFFFFFFFF#

I convert to BAM and run bedtools bamtobed like:

samtools view -hb test.sam > test.small.bam
bedtools bamtobed -bedpe -I test.small.bam > test.small.bed

which gives the following output:

cat test.small.bed
chr1	153875806	153875879	chr1	153875872	153875947	A00000:000:H00AAAAAA:1:2488:32949:32283	60	+	-
chr1	153875806	153875879	chr1	153875806	153875879	A00000:000:H00AAAAAA:1:2488:32949:32283	60	+	+

The expected output is, of course, only the paired read:

chr1	153875806	153875879	chr1	153875872	153875947	A00000:000:H00AAAAAA:1:2488:32949:32283	60	+	-

Hence bamtobed give the message:

*****WARNING: Query A00000:000:H00AAAAAA:1:2488:32949:32440 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.

As you can see, there is an additional entry in the BED.

bedtools --version bedtools v2.30.0