postalt.js MAPQ 0 on both chr17 and Alternate Contigs

[DarioS]

I have been examining some strange copy number results for the gene KANSL, which is on chr17, chr17_KI270908v1_alt and chr17_GL000258v2_alt. It turns out that almost all of the reads mapping to exons of the gene have MAPQ of 0 on both the primary chromosome, as well as the alternate contig(s). 100% sequence match to all three contigs. Bug?

[DarioS]

Related question: Does anyone use bwa-postalt.js in a production environment? We have been using it for cancer genomics with the aim of reporting results to cancer patients' doctors and running into issues with downstream analyses.