bamtofastq outputs empty reads at beginning of fastqs for specific bam file

[mebbert]

Hello, Related to #866, we have a specific sample where bamtofastq outputs empty reads at the beginning of fq1 and fq2 before printing out the rest of the reads. I inspected the .bam file and it appears normal and also passes samtools quickcheck. I also verified the issue remains in current master (v2.30.0-56-gbb64808f).

Could you take a look?

Here are the first two reads of each file:

FQ1

@/1

+

@HWI-ST466:144429521:C3K1DACXX:5:1101:2805:66731/1
TCTTTTCCATTCCCTACAATCAATTTCAAATCAGAGATTAAAACATTATTTAGAAAAAGTATAATTTCAATTCAAAAGTGTATAATCAAAATAATCTAAC
+
???????????I????I???I?????I????I?I?I???????I????????I?????I????????I?????????I?I????????????????????

FQ2

@/2

+

@HWI-ST466:144429521:C3K1DACXX:5:1101:2805:66731/2
TGTTAATTTCATGGTACATGAGTGGCTATCATACTGGCTATTATATGGTAAGTAATCACTCAGCATCTTTTCCTGACAATTTTTTTGTAGTTATGTGACT
+
?????????I??II??I??I?I?III???I???I?III????????II???I????I?I?I?II??I????I??I?I?????????I??I????I?I???

Command

Here is our command: bedtools2/bin/bedtools bamtofastq -i minimal_example.bam -fq my_fq1.fq -fq2 my_fq2.fq 2> /dev/null

Minimal example file

I don't feel comfortable posting this specific sample on GitHub since it cannot be deleted, but I can email you a secure link to download it.