kallisto pseudobam producing bin files... not bam... how to fix?

Question

[jocelyn.petitto]

I posted about this issue in the git for kallisto ( https://github.com/pachterlab/kallisto/issues/286 ) but I am trying to determine what to do in the meantime. Why would I be getting an output with a *.bin instead of a *.bam ?

Ultimately, I need the read counts re: what fragment is being ascribed to what via the kallisto algorithm as I have non-canonical mitochondrial ncRNA that have sequence similarity with another gene and must figure out a statistical method for properly ascribing reads to transcripts.

[GenoMax]

Is that an unfortunate spelling error on programmer's part? Have you tried to rename .bin to .bam and checking with samtools to see if it is indeed a BAM file?