Hi developers,

I encountered a mysterious issue when using Pheniqs for barcode correction.

Basically, when performing the correction, I first prepare a CRAM file containing barcodes to be corrected and a json file according to the tutorial, then run Pheniqs. However, the resulting BAM files is one record less than the CRAM, and the missing one seems to be always the last record in the CRAM.

This happens only occasionally. For example, I run the same code for 6 times and capture one (bam3):

$ samtools view -c pbmc_500_10p_2_aa.corrected.bam
450000
$ samtools view -c pbmc_500_10p_2_aa.corrected.bam1
450000
$ samtools view -c pbmc_500_10p_2_aa.corrected.bam2
450000
$ samtools view -c pbmc_500_10p_2_aa.corrected.bam3
449999
$ samtools view -c pbmc_500_10p_2_aa.corrected.bam4
450000
$ samtools view -c pbmc_500_10p_2_aa.corrected.bam5
450000

Not a big matter, but still annoying, I can provide more info if you would like to look into it.

Thanks,

--Kai