Trancriptome alignment and alignment liftover

[Daniel-Liu-c0deb0t]

• [x] Read GTF/GFF annotations file
• [x] Use cellranger's transcriptome crate (note: custom wrapper structs for transcripts/genes/exons/etc. are used to only track necessary info and for serde)
• [x] Interval data structure to map exons -> transcripts
• [x] Align reads to all intersecting transcripts (sorted by seed hit count)
• [x] Update tests

Note that the transcript sequences and genes are also saved in the index.

[Daniel-Liu-c0deb0t]

Oh we will need to update the CI to access cellranger.

[sjackman]

Oh we will need to update the CI to access cellranger.

@emreerhan Could you please set up credentials to access 10xDev/cellranger from Thermite GitHub Actions CI? You can crib from here:

https://github.com/10XDev/cellranger/blob/4bc3c109df3036db5f898767867cd403c8bbfdf2/.github/workflows/test.yml#L122-L127

[Daniel-Liu-c0deb0t]

Next up is adding some handwritten tests with fake GTF files to check what edge cases I might have missed.

[Daniel-Liu-c0deb0t]

Last step: adding a few difficult spliced alignment tests.

[github-actions[bot]]

file1 identical alignment to ref fraction: 0.932334 file2 identical alignment to ref fraction: 0.975536 file1 and file2 identical alignments fraction: 1e-05

[github-actions[bot]]

file1 identical alignment to ref fraction: 0.932334 file2 identical alignment to ref fraction: 0.975536 file1 and file2 identical alignments fraction: 1e-05

[Daniel-Liu-c0deb0t]

I addressed all the comments and cleaned up the code.

[github-actions[bot]]

file1 identical alignment to ref fraction: 0.932334 file2 identical alignment to ref fraction: 0.975736 file1 and file2 identical alignments fraction: 8e-06

[github-actions[bot]]

file1 identical alignment to ref fraction: 0.932334 file2 identical alignment to ref fraction: 0.975736 file1 and file2 identical alignments fraction: 8e-06