ChangqingW

On [line 88](https://github.com/LuyiTian/FLAMES/blob/18fb83c7f09baf8325efac1506ef5380de580661/python/count_tr.py#L88), read_dict[r][0] will be assigned with `(tr, rec.get_tag("AS"), tr_cov, float(rec.query_alignment_length)/rec.infer_read_length(), rec.mapping_quality)`, contradicting the comment on [line 106](https://github.com/LuyiTian/FLAMES/blob/18fb83c7f09baf8325efac1506ef5380de580661/python/count_tr.py#L106) `# transcript_id, pct_ref, pct_reads`. `hit[1] > 0.8` was used on [line...

[feature request] Show bullet threading on hover

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I was wondering if it is possible to show bullet threading when hovering the block / bullet, instead of only when the block is active.

Hi peng, I tried matching the dark theme in the PDF viewer. I never coded CSS before though so not sure how match the margin color without hard-coding hex values....

See [#208](https://github.com/ConesaLab/SQANTI3/issues/208)

When running `topologygsa` with kegg hsa, I got the following error: ``` kegg.gs

Warning message: Ignoring unknown parameters (group.selfish, label, utr.geom)

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When using `ggbio::autoplot` and `geom_alignment` on `CompressedGRangesList` and `GRanges`, ggplot throw warnings for unknown parameters. (`group.selfish ` for `CompressedGRangesList`, `label, utr.geom ` for `GRanges`) [isoform_gff.rds.zip](https://github.com/lawremi/ggbio/files/8947441/isoform_gff.rds.zip) ``` library(ggbio) isoform_gff

Unrecognized nucleotide 'B' error when sequence field in BAM file omitted

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**Describe the bug** When using `Rsamtools::pileup` and the bam file provided contains records where the sequence field is omitted (as `*`), this error message is shown: ``` Error in value[[3L]](cond)...

For sites with no counts, attribute("gene_count") always returns NaN, even when other sites of the same gene have non-zero counts ``` >>> sites_for_gene = result.gene_id() == 'ENSG00000001460.18' >>> result.counts().loc[sites_for_gene] 1...

As of pandas 2.0, append (previously deprecated) [was removed](https://pandas.pydata.org/docs/whatsnew/v2.0.0.html#removal-of-prior-version-deprecations-changes). https://github.com/mortazavilab/lapa/blob/eb16fee51637b9c4af1cfc2a1ed5a349b7ba858b/setup.py#L13 The install instructions should either change to `pandas

I have been using TxDb to parse GFF and obtain transcripts, but I have been getting these errors intermittently, which seem to be gc related and hard to reproduce: ```...