poonchilam

@kishwarshafin sure - * a small subset of my bam: https://drive.google.com/file/d/1UbeoCf4iZHyWDeQPDpxJcaz4i2OBOZg-/view?usp=sharing * reference fasta `mm10_2020_A.fa.gz`: https://drive.google.com/file/d/1M6_MOUgRlnzhh6rFcmTuzjXvLas10kb4/view?usp=sharing

Also it'd be better to make the chromosome id be consistent between vcf and bam.., now it's like `1` in vcf but it's actually `chr1` in bam

Oh nevermind if I set --chrom chr1 then in vcf it'll also be chr1, sorry I was just being dumb

> Remora is not currently designed to work with spliced RNA alignments. This is not currently on the roadmap, but is certainly possible. The fix would be to [this function...

Got it, thanks @marcus1487. The differences come from map_ref_to_signal() ``` def map_ref_to_signal(*, query_to_signal, ref_to_query_knots): return np.floor( np.interp( ref_to_query_knots, np.arange(query_to_signal.size), query_to_signal, ) ).astype(int) ``` if stick to it, the `ref_to_signal` array...

@marcus1487 I found out I don't need another interpolation in `map_ref_to_signal()` at all 🤦‍♀️ the spliced read's ref_to_signal is now like where the last 73 bases are soft clippings. I...