Gene fusions and arbitrary cDNA entry

[andrewrech]

To enable:

1. Neoepitope predictions from gene fusions
   • JAFFA: de novo assembly of raw RNA reads aligned to a reference transcriptome -> cDNA with identified breakpoint
2. Other manual sequence entry without a transcript ID

---

• [ ] accept JAFFA cDNA, breakpoint output to predict over novel sequence portion
• [x] add entry to garnish_neoepitopes with coding (cDNA), MHC only to predict over whole entered cDNA

[andrewrech]

24 Peptide entry added

[andrewrech]

Write function to send three rows to garnish_predictions:

1. 30-mer pep_mut window over gene fusion breakpoint
2. 15-mer pep_wtover gene A, NA pep_mut
3. 15-mer pep_wt over gene B, NA pep_mut

Overlaps with wt are filtered prior predictions.

[andrewrech]

37

[andrewrech]

54a5bdc16e513b44a096d50d831633cdf1542c07

[andrewrech]

84d9f7415a05f211630fcd0dba4c30c5de43cf48