Bs kvg improve model #41
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bshifaw
commented
Nov 7, 2024
bshifaw
commented
- Adding option to search all short reads, not only the reads that fall within regions of the reference the long reads have aligned to.
- Breaking detect_relavent_loci function into subfunctions
- Fix: Handling short read sample records that might have a missing chrom info
…the tree each time. The final merging pass iterates over loci and tries to merge overlapping intervals within each contig. However, the code inserts current_interval directly into new_tree only if there are no overlaps. If there are overlaps, it calculates min_start and max_end to create a merged_interval. If two or more intervals overlap, the code will keep overwriting new_tree in each iteration, potentially losing previously calculated merged intervals from earlier iterations.
…s that may not have a name
bshifaw
commented
Nov 7, 2024
| found_items | ||
| .load(Ordering::Relaxed) | ||
| .to_formatted_string(&Locale::en), | ||
| tid_to_chrom.get(&read.tid()).unwrap(), |
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The code was panicking when working a particular sample that may have records missing chromosome info so a default unknown name was added for these situation.
Searching for similar reads (2,479 found, most recent at chrUn_JTFH01001822v1_decoy:470) ... [00:33:20] 737,000,000
thread '<unnamed>' panicked at src/hidive/src/rescue.rs:107:55:
called `Option::unwrap()` on a `None` value
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
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Yeah, I saw that too. I just put in an "unwrap_or" and supply a contig name of "unknown" if we don't have anything in the tid_to_chrom map.
added 5 commits
November 14, 2024 15:23
…r reads into its own function and helper functions
…and-interval, unmapped
added 2 commits
December 2, 2024 15:36
# Conflicts: # src/hidive/src/main.rs # src/hidive/src/rescue.rs # src/skydive/src/stage.rs # train.sh
kvg
added a commit
that referenced
this pull request
Dec 3, 2024
* Auto-detect where to search in a genome to rescue reads * Accumulate the merged intervals continuously rather than overwriting the tree each time. The final merging pass iterates over loci and tries to merge overlapping intervals within each contig. However, the code inserts current_interval directly into new_tree only if there are no overlaps. If there are overlaps, it calculates min_start and max_end to create a merged_interval. If two or more intervals overlap, the code will keep overwriting new_tree in each iteration, potentially losing previously calculated merged intervals from earlier iterations. * added fetches option to rescue.rs, option search all, contig, contig-and-interval, unmapped --------- Co-authored-by: Kiran Garimella <[email protected]> Co-authored-by: bshifaw <[email protected]>
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